Starting phenix.real_space_refine on Tue Aug 26 18:05:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fc8_28976/08_2025/8fc8_28976_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fc8_28976/08_2025/8fc8_28976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fc8_28976/08_2025/8fc8_28976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fc8_28976/08_2025/8fc8_28976.map" model { file = "/net/cci-nas-00/data/ceres_data/8fc8_28976/08_2025/8fc8_28976_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fc8_28976/08_2025/8fc8_28976_trim.cif" } resolution = 3.47 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= 0.010 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 112 5.16 5 Cl 8 4.86 5 C 12936 2.51 5 N 3236 2.21 5 O 3476 1.98 5 H 19384 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39152 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 9711 Classifications: {'peptide': 617} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 593} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'XQ3': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'XQ3': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'XQ3': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'XQ3': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 13.41, per 1000 atoms: 0.34 Number of scatterers: 39152 At special positions: 0 Unit cell: (158.76, 158.76, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 8 17.00 S 112 16.00 O 3476 8.00 N 3236 7.00 C 12936 6.00 H 19384 1.00 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: 4.07 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4656 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 68.9% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 222 through 228 removed outlier: 3.595A pdb=" N ASN A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.549A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.596A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 335 through 357 removed outlier: 3.744A pdb=" N LYS A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.810A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'A' and resid 445 through 451 removed outlier: 3.523A pdb=" N ALA A 451 " --> pdb=" O HIS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 removed outlier: 3.905A pdb=" N GLU A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 491 removed outlier: 3.536A pdb=" N TYR A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 535 removed outlier: 3.794A pdb=" N TYR A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 512 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 514 " --> pdb=" O ARG A 510 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 532 " --> pdb=" O ASN A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 removed outlier: 3.591A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 569 removed outlier: 3.944A pdb=" N LEU A 551 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 588 removed outlier: 4.274A pdb=" N VAL A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 595 removed outlier: 3.801A pdb=" N THR A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY A 595 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 636 removed outlier: 4.099A pdb=" N SER A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 611 " --> pdb=" O GLN A 607 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE A 615 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 679 removed outlier: 3.587A pdb=" N GLY A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 688 Processing helix chain 'A' and resid 691 through 709 Processing helix chain 'A' and resid 709 through 728 removed outlier: 4.507A pdb=" N ILE A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 716 " --> pdb=" O ASN A 712 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 747 removed outlier: 3.559A pdb=" N SER A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 222 through 228 removed outlier: 3.595A pdb=" N ASN B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.549A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.597A pdb=" N VAL B 254 " --> pdb=" O CYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 335 through 357 removed outlier: 3.744A pdb=" N LYS B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.811A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 445 through 451 removed outlier: 3.522A pdb=" N ALA B 451 " --> pdb=" O HIS B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 removed outlier: 3.905A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 491 removed outlier: 3.537A pdb=" N TYR B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 535 removed outlier: 3.794A pdb=" N TYR B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 509 " --> pdb=" O THR B 505 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 512 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 514 " --> pdb=" O ARG B 510 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 532 " --> pdb=" O ASN B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.592A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 569 removed outlier: 3.944A pdb=" N LEU B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 588 removed outlier: 4.273A pdb=" N VAL B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.801A pdb=" N THR B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY B 595 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 636 removed outlier: 4.099A pdb=" N SER B 603 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 611 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE B 615 " --> pdb=" O PHE B 611 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL B 620 " --> pdb=" O ARG B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 679 removed outlier: 3.587A pdb=" N GLY B 679 " --> pdb=" O LYS B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 688 Processing helix chain 'B' and resid 691 through 709 Processing helix chain 'B' and resid 709 through 728 removed outlier: 4.507A pdb=" N ILE B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 716 " --> pdb=" O ASN B 712 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 747 removed outlier: 3.559A pdb=" N SER B 747 " --> pdb=" O ASP B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 756 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 168 through 177 Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 222 through 228 removed outlier: 3.595A pdb=" N ASN C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 removed outlier: 3.549A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.596A pdb=" N VAL C 254 " --> pdb=" O CYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 335 through 357 removed outlier: 3.744A pdb=" N LYS C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.810A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'C' and resid 445 through 451 removed outlier: 3.524A pdb=" N ALA C 451 " --> pdb=" O HIS C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 466 removed outlier: 3.905A pdb=" N GLU C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 491 removed outlier: 3.536A pdb=" N TYR C 472 " --> pdb=" O ALA C 468 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 535 removed outlier: 3.794A pdb=" N TYR C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU C 509 " --> pdb=" O THR C 505 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 512 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY C 513 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 514 " --> pdb=" O ARG C 510 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 532 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 544 removed outlier: 3.591A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 569 removed outlier: 3.944A pdb=" N LEU C 551 " --> pdb=" O GLY C 547 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 564 " --> pdb=" O VAL C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 588 removed outlier: 4.274A pdb=" N VAL C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 595 removed outlier: 3.800A pdb=" N THR C 593 " --> pdb=" O ALA C 589 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY C 595 " --> pdb=" O TYR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 636 removed outlier: 4.099A pdb=" N SER C 603 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE C 611 " --> pdb=" O GLN C 607 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE C 615 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C 620 " --> pdb=" O ARG C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 679 removed outlier: 3.587A pdb=" N GLY C 679 " --> pdb=" O LYS C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 688 Processing helix chain 'C' and resid 691 through 709 Processing helix chain 'C' and resid 709 through 728 removed outlier: 4.507A pdb=" N ILE C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA C 716 " --> pdb=" O ASN C 712 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU C 717 " --> pdb=" O MET C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 747 removed outlier: 3.559A pdb=" N SER C 747 " --> pdb=" O ASP C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 756 Processing helix chain 'D' and resid 151 through 161 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 222 through 228 removed outlier: 3.595A pdb=" N ASN D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 removed outlier: 3.550A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.596A pdb=" N VAL D 254 " --> pdb=" O CYS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 323 through 331 Processing helix chain 'D' and resid 335 through 357 removed outlier: 3.744A pdb=" N LYS D 340 " --> pdb=" O ARG D 336 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 391 removed outlier: 3.811A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 440 Processing helix chain 'D' and resid 445 through 451 removed outlier: 3.523A pdb=" N ALA D 451 " --> pdb=" O HIS D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 466 removed outlier: 3.905A pdb=" N GLU D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 491 removed outlier: 3.537A pdb=" N TYR D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 535 removed outlier: 3.793A pdb=" N TYR D 508 " --> pdb=" O THR D 504 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU D 509 " --> pdb=" O THR D 505 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 512 " --> pdb=" O TYR D 508 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU D 514 " --> pdb=" O ARG D 510 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 532 " --> pdb=" O ASN D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 544 removed outlier: 3.592A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 569 removed outlier: 3.944A pdb=" N LEU D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 564 " --> pdb=" O VAL D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 588 removed outlier: 4.273A pdb=" N VAL D 577 " --> pdb=" O ALA D 573 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 595 removed outlier: 3.801A pdb=" N THR D 593 " --> pdb=" O ALA D 589 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY D 595 " --> pdb=" O TYR D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 636 removed outlier: 4.098A pdb=" N SER D 603 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE D 611 " --> pdb=" O GLN D 607 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE D 615 " --> pdb=" O PHE D 611 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL D 620 " --> pdb=" O ARG D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 679 removed outlier: 3.587A pdb=" N GLY D 679 " --> pdb=" O LYS D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 688 Processing helix chain 'D' and resid 691 through 709 Processing helix chain 'D' and resid 709 through 728 removed outlier: 4.507A pdb=" N ILE D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA D 716 " --> pdb=" O ASN D 712 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU D 717 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 747 removed outlier: 3.558A pdb=" N SER D 747 " --> pdb=" O ASP D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 756 Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 411 removed outlier: 6.455A pdb=" N LYS A 405 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP A 420 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LYS A 407 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU A 418 " --> pdb=" O LYS A 407 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 411 removed outlier: 6.455A pdb=" N LYS B 405 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP B 420 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS B 407 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU B 418 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 411 removed outlier: 6.456A pdb=" N LYS C 405 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP C 420 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS C 407 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU C 418 " --> pdb=" O LYS C 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 405 through 411 removed outlier: 6.454A pdb=" N LYS D 405 " --> pdb=" O ASP D 420 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP D 420 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LYS D 407 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU D 418 " --> pdb=" O LYS D 407 " (cutoff:3.500A) 1101 hydrogen bonds defined for protein. 3195 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: 9.28 Time building geometry restraints manager: 5.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 19348 1.04 - 1.24: 2638 1.24 - 1.44: 6085 1.44 - 1.65: 11373 1.65 - 1.85: 196 Bond restraints: 39640 Sorted by residual: bond pdb=" C25 XQ3 B1001 " pdb=" N22 XQ3 B1001 " ideal model delta sigma weight residual 1.347 1.493 -0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" C25 XQ3 D1001 " pdb=" N22 XQ3 D1001 " ideal model delta sigma weight residual 1.347 1.493 -0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" C25 XQ3 A1001 " pdb=" N22 XQ3 A1001 " ideal model delta sigma weight residual 1.347 1.493 -0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" C25 XQ3 C1002 " pdb=" N22 XQ3 C1002 " ideal model delta sigma weight residual 1.347 1.492 -0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" C07 XQ3 D1001 " pdb=" N06 XQ3 D1001 " ideal model delta sigma weight residual 1.349 1.472 -0.123 2.00e-02 2.50e+03 3.75e+01 ... (remaining 39635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 71232 3.43 - 6.86: 196 6.86 - 10.28: 20 10.28 - 13.71: 4 13.71 - 17.14: 4 Bond angle restraints: 71456 Sorted by residual: angle pdb=" O31 XQ3 C1002 " pdb=" S30 XQ3 C1002 " pdb=" O40 XQ3 C1002 " ideal model delta sigma weight residual 119.28 102.14 17.14 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O31 XQ3 D1001 " pdb=" S30 XQ3 D1001 " pdb=" O40 XQ3 D1001 " ideal model delta sigma weight residual 119.28 102.16 17.12 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O31 XQ3 A1001 " pdb=" S30 XQ3 A1001 " pdb=" O40 XQ3 A1001 " ideal model delta sigma weight residual 119.28 102.16 17.12 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O31 XQ3 B1001 " pdb=" S30 XQ3 B1001 " pdb=" O40 XQ3 B1001 " ideal model delta sigma weight residual 119.28 102.17 17.11 3.00e+00 1.11e-01 3.25e+01 angle pdb=" CAT Y01 D1002 " pdb=" CBH Y01 D1002 " pdb=" CBF Y01 D1002 " ideal model delta sigma weight residual 108.46 95.35 13.11 3.00e+00 1.11e-01 1.91e+01 ... (remaining 71451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 17674 16.66 - 33.31: 882 33.31 - 49.97: 275 49.97 - 66.62: 161 66.62 - 83.28: 12 Dihedral angle restraints: 19004 sinusoidal: 10212 harmonic: 8792 Sorted by residual: dihedral pdb=" CA MET A 713 " pdb=" C MET A 713 " pdb=" N LEU A 714 " pdb=" CA LEU A 714 " ideal model delta harmonic sigma weight residual 180.00 164.58 15.42 0 5.00e+00 4.00e-02 9.51e+00 dihedral pdb=" CA MET D 713 " pdb=" C MET D 713 " pdb=" N LEU D 714 " pdb=" CA LEU D 714 " ideal model delta harmonic sigma weight residual 180.00 164.60 15.40 0 5.00e+00 4.00e-02 9.49e+00 dihedral pdb=" CA CYS B 353 " pdb=" CB CYS B 353 " pdb=" SG CYS B 353 " pdb=" HG CYS B 353 " ideal model delta sinusoidal sigma weight residual 60.00 119.09 -59.09 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 19001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3035 0.084 - 0.167: 105 0.167 - 0.251: 8 0.251 - 0.335: 4 0.335 - 0.419: 12 Chirality restraints: 3164 Sorted by residual: chirality pdb=" CBH Y01 D1002 " pdb=" CAT Y01 D1002 " pdb=" CAZ Y01 D1002 " pdb=" CBF Y01 D1002 " both_signs ideal model delta sigma weight residual False -2.85 -3.27 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CBH Y01 C1003 " pdb=" CAT Y01 C1003 " pdb=" CAZ Y01 C1003 " pdb=" CBF Y01 C1003 " both_signs ideal model delta sigma weight residual False -2.85 -3.27 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CBH Y01 C1001 " pdb=" CAT Y01 C1001 " pdb=" CAZ Y01 C1001 " pdb=" CBF Y01 C1001 " both_signs ideal model delta sigma weight residual False -2.85 -3.27 0.42 2.00e-01 2.50e+01 4.34e+00 ... (remaining 3161 not shown) Planarity restraints: 5776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 528 " -0.094 2.00e-02 2.50e+03 8.90e-02 1.19e+02 pdb=" CG ASN B 528 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 528 " 0.084 2.00e-02 2.50e+03 pdb=" ND2 ASN B 528 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 528 " -0.128 2.00e-02 2.50e+03 pdb="HD22 ASN B 528 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 528 " 0.094 2.00e-02 2.50e+03 8.89e-02 1.19e+02 pdb=" CG ASN C 528 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN C 528 " -0.084 2.00e-02 2.50e+03 pdb=" ND2 ASN C 528 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN C 528 " 0.128 2.00e-02 2.50e+03 pdb="HD22 ASN C 528 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 528 " 0.094 2.00e-02 2.50e+03 8.88e-02 1.18e+02 pdb=" CG ASN A 528 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 528 " -0.084 2.00e-02 2.50e+03 pdb=" ND2 ASN A 528 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 528 " 0.128 2.00e-02 2.50e+03 pdb="HD22 ASN A 528 " -0.122 2.00e-02 2.50e+03 ... (remaining 5773 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 4298 2.26 - 2.84: 88444 2.84 - 3.43: 97836 3.43 - 4.01: 129223 4.01 - 4.60: 202683 Nonbonded interactions: 522484 Sorted by model distance: nonbonded pdb=" HH TYR D 346 " pdb=" OE2 GLU D 363 " model vdw 1.671 2.450 nonbonded pdb=" HH TYR C 346 " pdb=" OE2 GLU C 363 " model vdw 1.671 2.450 nonbonded pdb=" HH TYR A 346 " pdb=" OE2 GLU A 363 " model vdw 1.672 2.450 nonbonded pdb=" HH TYR B 346 " pdb=" OE2 GLU B 363 " model vdw 1.672 2.450 nonbonded pdb=" OE1 GLU D 495 " pdb=" H GLU D 495 " model vdw 1.682 2.450 ... (remaining 522479 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 150 through 788) selection = (chain 'B' and resid 150 through 788) selection = (chain 'C' and resid 150 through 788) selection = (chain 'D' and resid 150 through 788) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.250 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 44.270 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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 : 0.006 0.146 20256 Z= 0.286 Angle : 0.676 17.139 27556 Z= 0.297 Chirality : 0.044 0.419 3164 Planarity : 0.003 0.038 3408 Dihedral : 11.822 83.280 7544 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.19 % Allowed : 5.44 % Favored : 94.37 % 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 aren not related in a simple way. whole: 1.21 (0.17), residues: 2452 helix: 1.85 (0.14), residues: 1508 sheet: -2.12 (0.61), residues: 76 loop : -0.78 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 224 TYR 0.008 0.001 TYR D 419 PHE 0.011 0.001 PHE B 341 TRP 0.007 0.001 TRP D 733 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00562 (20256) covalent geometry : angle 0.67650 (27556) hydrogen bonds : bond 0.15857 ( 1101) hydrogen bonds : angle 5.30175 ( 3195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 543 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 539 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8159 (mt0) cc_final: 0.7879 (mt0) REVERT: A 605 MET cc_start: 0.7871 (ptt) cc_final: 0.7631 (ptt) REVERT: A 734 LYS cc_start: 0.8172 (tttp) cc_final: 0.7846 (ptmm) REVERT: A 737 TRP cc_start: 0.7769 (t60) cc_final: 0.7405 (t60) REVERT: B 256 LEU cc_start: 0.8894 (tp) cc_final: 0.8661 (mp) REVERT: B 682 ASP cc_start: 0.6590 (t0) cc_final: 0.6383 (p0) REVERT: B 683 LEU cc_start: 0.8455 (mt) cc_final: 0.7940 (mp) REVERT: B 734 LYS cc_start: 0.8074 (tttp) cc_final: 0.7670 (ptmm) REVERT: C 295 THR cc_start: 0.6364 (p) cc_final: 0.5978 (p) REVERT: C 587 MET cc_start: 0.7401 (ttp) cc_final: 0.7142 (ttp) REVERT: C 605 MET cc_start: 0.7746 (ptt) cc_final: 0.7518 (ptt) REVERT: C 682 ASP cc_start: 0.6342 (t0) cc_final: 0.6007 (p0) REVERT: C 734 LYS cc_start: 0.7800 (tttp) cc_final: 0.7185 (ptmm) REVERT: D 244 ILE cc_start: 0.7946 (mt) cc_final: 0.7679 (mt) REVERT: D 256 LEU cc_start: 0.8907 (tp) cc_final: 0.8703 (mp) REVERT: D 365 VAL cc_start: 0.8303 (t) cc_final: 0.8045 (m) REVERT: D 582 LEU cc_start: 0.8261 (tp) cc_final: 0.7863 (tp) REVERT: D 605 MET cc_start: 0.7729 (ptt) cc_final: 0.7445 (ptt) REVERT: D 707 PHE cc_start: 0.6733 (t80) cc_final: 0.6509 (t80) REVERT: D 734 LYS cc_start: 0.8246 (tttp) cc_final: 0.7722 (ptmm) outliers start: 4 outliers final: 3 residues processed: 543 average time/residue: 0.3347 time to fit residues: 277.3714 Evaluate side-chains 324 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 321 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain D residue 341 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 235 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 787 HIS B 492 GLN C 440 ASN C 492 GLN D 492 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.192233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.147923 restraints weight = 83358.664| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.81 r_work: 0.3633 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20256 Z= 0.173 Angle : 0.568 5.150 27556 Z= 0.304 Chirality : 0.036 0.143 3164 Planarity : 0.005 0.048 3408 Dihedral : 6.831 58.009 3154 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.60 % Allowed : 12.43 % Favored : 85.97 % 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 aren not related in a simple way. whole: 0.86 (0.17), residues: 2452 helix: 1.50 (0.13), residues: 1528 sheet: -2.14 (0.61), residues: 76 loop : -0.86 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 746 TYR 0.017 0.001 TYR C 556 PHE 0.028 0.002 PHE B 751 TRP 0.011 0.001 TRP B 733 HIS 0.005 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00384 (20256) covalent geometry : angle 0.56756 (27556) hydrogen bonds : bond 0.05215 ( 1101) hydrogen bonds : angle 4.51105 ( 3195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 386 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 353 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 201 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7797 (p0) REVERT: A 215 ASP cc_start: 0.8889 (m-30) cc_final: 0.8650 (m-30) REVERT: A 396 ASP cc_start: 0.7878 (t0) cc_final: 0.7591 (t0) REVERT: A 682 ASP cc_start: 0.6938 (t0) cc_final: 0.6223 (p0) REVERT: A 683 LEU cc_start: 0.8708 (mt) cc_final: 0.8234 (mt) REVERT: A 737 TRP cc_start: 0.7894 (t60) cc_final: 0.7675 (t60) REVERT: B 201 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7850 (p0) REVERT: B 365 VAL cc_start: 0.8726 (t) cc_final: 0.8391 (m) REVERT: B 578 MET cc_start: 0.8181 (ttp) cc_final: 0.7591 (ttm) REVERT: B 605 MET cc_start: 0.7749 (ptt) cc_final: 0.7537 (ptt) REVERT: B 682 ASP cc_start: 0.6758 (t0) cc_final: 0.5929 (p0) REVERT: B 683 LEU cc_start: 0.8791 (mt) cc_final: 0.8160 (mp) REVERT: C 201 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7866 (p0) REVERT: C 313 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7901 (p0) REVERT: C 365 VAL cc_start: 0.8747 (t) cc_final: 0.8429 (m) REVERT: C 553 TYR cc_start: 0.8510 (m-80) cc_final: 0.8270 (m-10) REVERT: C 578 MET cc_start: 0.8187 (ttp) cc_final: 0.7610 (ttm) REVERT: C 682 ASP cc_start: 0.6690 (t0) cc_final: 0.5741 (p0) REVERT: D 365 VAL cc_start: 0.8719 (t) cc_final: 0.8392 (m) REVERT: D 396 ASP cc_start: 0.7632 (t0) cc_final: 0.7324 (t0) REVERT: D 582 LEU cc_start: 0.8442 (tp) cc_final: 0.8081 (tp) REVERT: D 676 LEU cc_start: 0.8016 (tp) cc_final: 0.7798 (tp) REVERT: D 682 ASP cc_start: 0.6784 (t0) cc_final: 0.5933 (p0) REVERT: D 707 PHE cc_start: 0.6860 (t80) cc_final: 0.6531 (t80) REVERT: D 713 MET cc_start: 0.7481 (tmm) cc_final: 0.7271 (tmm) outliers start: 33 outliers final: 16 residues processed: 379 average time/residue: 0.2798 time to fit residues: 166.9229 Evaluate side-chains 334 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 314 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 743 ASP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 580 PHE Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 700 VAL Chi-restraints excluded: chain D residue 743 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 120 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.183830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.134303 restraints weight = 83161.010| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.76 r_work: 0.3473 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 20256 Z= 0.284 Angle : 0.633 7.167 27556 Z= 0.342 Chirality : 0.039 0.198 3164 Planarity : 0.005 0.069 3408 Dihedral : 7.006 59.844 3154 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 2.43 % Allowed : 12.72 % Favored : 84.85 % 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 aren not related in a simple way. whole: 0.10 (0.16), residues: 2452 helix: 0.90 (0.13), residues: 1540 sheet: -2.51 (0.58), residues: 76 loop : -1.17 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 271 TYR 0.023 0.002 TYR B 502 PHE 0.021 0.002 PHE C 524 TRP 0.009 0.002 TRP B 733 HIS 0.004 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00654 (20256) covalent geometry : angle 0.63286 (27556) hydrogen bonds : bond 0.05547 ( 1101) hydrogen bonds : angle 4.86961 ( 3195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 389 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 339 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7735 (p0) REVERT: A 215 ASP cc_start: 0.8950 (m-30) cc_final: 0.8696 (m-30) REVERT: A 682 ASP cc_start: 0.6783 (t0) cc_final: 0.6295 (p0) REVERT: A 713 MET cc_start: 0.7986 (tmm) cc_final: 0.7674 (tmm) REVERT: A 743 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8666 (m-30) REVERT: A 781 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7933 (p0) REVERT: B 201 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7815 (p0) REVERT: B 215 ASP cc_start: 0.8945 (m-30) cc_final: 0.8685 (m-30) REVERT: B 396 ASP cc_start: 0.7736 (t0) cc_final: 0.7520 (t0) REVERT: B 578 MET cc_start: 0.8242 (ttp) cc_final: 0.7655 (ttm) REVERT: B 707 PHE cc_start: 0.6745 (t80) cc_final: 0.6287 (t80) REVERT: B 781 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8060 (p0) REVERT: C 201 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7820 (p0) REVERT: C 215 ASP cc_start: 0.8910 (m-30) cc_final: 0.8600 (m-30) REVERT: C 365 VAL cc_start: 0.8809 (t) cc_final: 0.8519 (m) REVERT: C 396 ASP cc_start: 0.7653 (t0) cc_final: 0.7423 (t0) REVERT: C 578 MET cc_start: 0.8218 (ttp) cc_final: 0.7704 (ttm) REVERT: D 201 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7877 (p0) REVERT: D 215 ASP cc_start: 0.8914 (m-30) cc_final: 0.8579 (m-30) REVERT: D 365 VAL cc_start: 0.8795 (t) cc_final: 0.8487 (m) REVERT: D 396 ASP cc_start: 0.7771 (t0) cc_final: 0.7568 (t0) REVERT: D 743 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8735 (m-30) REVERT: D 781 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8052 (p0) outliers start: 50 outliers final: 27 residues processed: 373 average time/residue: 0.3112 time to fit residues: 183.1734 Evaluate side-chains 354 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 318 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 PHE Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 700 VAL Chi-restraints excluded: chain D residue 743 ASP Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 26 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 220 optimal weight: 0.5980 chunk 181 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.186752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.140989 restraints weight = 82771.757| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.07 r_work: 0.3516 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20256 Z= 0.124 Angle : 0.511 4.654 27556 Z= 0.273 Chirality : 0.034 0.134 3164 Planarity : 0.004 0.060 3408 Dihedral : 6.578 58.863 3154 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.80 % Allowed : 14.03 % Favored : 84.17 % 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 aren not related in a simple way. whole: 0.61 (0.17), residues: 2452 helix: 1.35 (0.13), residues: 1528 sheet: -2.15 (0.60), residues: 76 loop : -1.05 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 249 TYR 0.010 0.001 TYR D 556 PHE 0.015 0.001 PHE C 751 TRP 0.012 0.001 TRP B 733 HIS 0.004 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00278 (20256) covalent geometry : angle 0.51091 (27556) hydrogen bonds : bond 0.04498 ( 1101) hydrogen bonds : angle 4.44026 ( 3195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 335 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7629 (p0) REVERT: A 215 ASP cc_start: 0.8894 (m-30) cc_final: 0.8634 (m-30) REVERT: A 365 VAL cc_start: 0.8789 (t) cc_final: 0.8505 (m) REVERT: A 396 ASP cc_start: 0.7452 (t0) cc_final: 0.7230 (t0) REVERT: A 553 TYR cc_start: 0.8244 (m-80) cc_final: 0.7980 (m-80) REVERT: A 682 ASP cc_start: 0.6813 (t0) cc_final: 0.6285 (p0) REVERT: A 683 LEU cc_start: 0.8787 (mt) cc_final: 0.8272 (mt) REVERT: A 713 MET cc_start: 0.8031 (tmm) cc_final: 0.7571 (tmm) REVERT: A 781 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7993 (p0) REVERT: B 201 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7822 (p0) REVERT: B 206 ARG cc_start: 0.6244 (mmp-170) cc_final: 0.6007 (mmm160) REVERT: B 215 ASP cc_start: 0.8850 (m-30) cc_final: 0.8494 (m-30) REVERT: B 365 VAL cc_start: 0.8733 (t) cc_final: 0.8416 (m) REVERT: B 396 ASP cc_start: 0.7670 (t0) cc_final: 0.7412 (t0) REVERT: B 578 MET cc_start: 0.8176 (ttp) cc_final: 0.7630 (ttm) REVERT: B 707 PHE cc_start: 0.6914 (t80) cc_final: 0.6425 (t80) REVERT: C 201 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7961 (p0) REVERT: C 215 ASP cc_start: 0.8899 (m-30) cc_final: 0.8540 (m-30) REVERT: C 365 VAL cc_start: 0.8744 (t) cc_final: 0.8433 (m) REVERT: C 396 ASP cc_start: 0.7616 (t0) cc_final: 0.7371 (t0) REVERT: C 482 MET cc_start: 0.7502 (mmt) cc_final: 0.7065 (mmp) REVERT: C 578 MET cc_start: 0.8144 (ttp) cc_final: 0.7626 (ttm) REVERT: C 628 TYR cc_start: 0.8418 (m-80) cc_final: 0.8168 (m-80) REVERT: D 201 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7812 (p0) REVERT: D 215 ASP cc_start: 0.8859 (m-30) cc_final: 0.8526 (m-30) REVERT: D 365 VAL cc_start: 0.8730 (t) cc_final: 0.8416 (m) outliers start: 37 outliers final: 22 residues processed: 361 average time/residue: 0.2613 time to fit residues: 154.1214 Evaluate side-chains 345 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 318 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 PHE Chi-restraints excluded: chain C residue 743 ASP Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 558 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 49 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 492 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.179580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131994 restraints weight = 82518.909| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.76 r_work: 0.3430 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 20256 Z= 0.305 Angle : 0.647 6.921 27556 Z= 0.349 Chirality : 0.040 0.212 3164 Planarity : 0.006 0.073 3408 Dihedral : 6.968 59.840 3154 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.51 % Favored : 94.37 % Rotamer: Outliers : 2.91 % Allowed : 13.35 % Favored : 83.74 % 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 aren not related in a simple way. whole: -0.16 (0.16), residues: 2452 helix: 0.74 (0.13), residues: 1520 sheet: -2.11 (0.61), residues: 76 loop : -1.40 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 271 TYR 0.022 0.002 TYR D 556 PHE 0.023 0.002 PHE C 341 TRP 0.013 0.002 TRP C 409 HIS 0.004 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00710 (20256) covalent geometry : angle 0.64696 (27556) hydrogen bonds : bond 0.05427 ( 1101) hydrogen bonds : angle 4.93689 ( 3195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 381 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 321 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7533 (p0) REVERT: A 215 ASP cc_start: 0.9002 (m-30) cc_final: 0.8754 (m-30) REVERT: A 235 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7266 (m-10) REVERT: A 271 ARG cc_start: 0.8343 (mtt-85) cc_final: 0.7960 (mtp180) REVERT: A 365 VAL cc_start: 0.9060 (t) cc_final: 0.8830 (m) REVERT: A 396 ASP cc_start: 0.7693 (t0) cc_final: 0.7477 (t0) REVERT: A 682 ASP cc_start: 0.7105 (t0) cc_final: 0.6375 (p0) REVERT: A 683 LEU cc_start: 0.8801 (mt) cc_final: 0.8425 (mt) REVERT: A 781 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8107 (p0) REVERT: B 215 ASP cc_start: 0.8963 (m-30) cc_final: 0.8647 (m-30) REVERT: B 235 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.7184 (m-10) REVERT: B 365 VAL cc_start: 0.9024 (t) cc_final: 0.8785 (m) REVERT: B 578 MET cc_start: 0.8307 (ttp) cc_final: 0.7752 (ttm) REVERT: B 682 ASP cc_start: 0.6757 (t0) cc_final: 0.5898 (p0) REVERT: B 781 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8202 (p0) REVERT: C 215 ASP cc_start: 0.9027 (m-30) cc_final: 0.8726 (m-30) REVERT: C 235 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7305 (m-10) REVERT: C 365 VAL cc_start: 0.9027 (t) cc_final: 0.8768 (m) REVERT: C 396 ASP cc_start: 0.7788 (t0) cc_final: 0.7561 (t0) REVERT: C 578 MET cc_start: 0.8337 (ttp) cc_final: 0.7817 (ttm) REVERT: C 682 ASP cc_start: 0.6626 (t0) cc_final: 0.6357 (t0) REVERT: C 781 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8192 (p0) REVERT: D 201 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7473 (p0) REVERT: D 235 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7121 (m-10) REVERT: D 365 VAL cc_start: 0.9049 (t) cc_final: 0.8806 (m) REVERT: D 396 ASP cc_start: 0.7677 (t0) cc_final: 0.7460 (t0) REVERT: D 578 MET cc_start: 0.8463 (ttp) cc_final: 0.7826 (ttm) REVERT: D 682 ASP cc_start: 0.6839 (t0) cc_final: 0.6119 (p0) REVERT: D 781 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8146 (p0) outliers start: 60 outliers final: 36 residues processed: 366 average time/residue: 0.2554 time to fit residues: 151.1809 Evaluate side-chains 359 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 674 PHE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 PHE Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 672 ASP Chi-restraints excluded: chain D residue 700 VAL Chi-restraints excluded: chain D residue 710 LEU Chi-restraints excluded: chain D residue 781 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 209 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 62 optimal weight: 30.0000 chunk 137 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 184 optimal weight: 30.0000 chunk 96 optimal weight: 6.9990 chunk 202 optimal weight: 0.5980 chunk 225 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.182692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.134060 restraints weight = 82878.749| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.70 r_work: 0.3475 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20256 Z= 0.147 Angle : 0.526 6.712 27556 Z= 0.280 Chirality : 0.035 0.124 3164 Planarity : 0.005 0.078 3408 Dihedral : 6.454 58.573 3154 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.14 % Allowed : 15.15 % Favored : 82.72 % 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 aren not related in a simple way. whole: 0.60 (0.17), residues: 2452 helix: 1.30 (0.13), residues: 1520 sheet: -2.12 (0.61), residues: 76 loop : -0.94 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 271 TYR 0.012 0.001 TYR A 411 PHE 0.015 0.001 PHE C 544 TRP 0.012 0.001 TRP B 733 HIS 0.005 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00338 (20256) covalent geometry : angle 0.52613 (27556) hydrogen bonds : bond 0.04425 ( 1101) hydrogen bonds : angle 4.44162 ( 3195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 328 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.7434 (p0) REVERT: A 215 ASP cc_start: 0.8931 (m-30) cc_final: 0.8687 (m-30) REVERT: A 235 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6950 (m-10) REVERT: A 365 VAL cc_start: 0.8852 (t) cc_final: 0.8582 (m) REVERT: A 682 ASP cc_start: 0.7086 (t0) cc_final: 0.6350 (p0) REVERT: A 683 LEU cc_start: 0.8756 (mt) cc_final: 0.8454 (mt) REVERT: A 781 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8066 (p0) REVERT: B 215 ASP cc_start: 0.8804 (m-30) cc_final: 0.8478 (m-30) REVERT: B 235 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6921 (m-10) REVERT: B 365 VAL cc_start: 0.8836 (t) cc_final: 0.8571 (m) REVERT: B 578 MET cc_start: 0.8164 (ttp) cc_final: 0.7635 (ttm) REVERT: B 628 TYR cc_start: 0.8412 (m-80) cc_final: 0.8157 (m-80) REVERT: B 682 ASP cc_start: 0.6760 (t0) cc_final: 0.5888 (p0) REVERT: C 215 ASP cc_start: 0.8898 (m-30) cc_final: 0.8506 (m-30) REVERT: C 229 SER cc_start: 0.9047 (t) cc_final: 0.8632 (m) REVERT: C 235 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.7004 (m-10) REVERT: C 365 VAL cc_start: 0.8841 (t) cc_final: 0.8559 (m) REVERT: C 578 MET cc_start: 0.8117 (ttp) cc_final: 0.7619 (ttm) REVERT: C 682 ASP cc_start: 0.6579 (t0) cc_final: 0.6336 (t0) REVERT: D 201 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7495 (p0) REVERT: D 215 ASP cc_start: 0.8880 (m-30) cc_final: 0.8562 (m-30) REVERT: D 365 VAL cc_start: 0.8834 (t) cc_final: 0.8560 (m) REVERT: D 578 MET cc_start: 0.8281 (ttp) cc_final: 0.7763 (ttm) REVERT: D 628 TYR cc_start: 0.8507 (m-80) cc_final: 0.8256 (m-80) REVERT: D 682 ASP cc_start: 0.6826 (t0) cc_final: 0.6066 (p0) outliers start: 44 outliers final: 30 residues processed: 359 average time/residue: 0.2840 time to fit residues: 165.7718 Evaluate side-chains 355 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 319 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 674 PHE Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 PHE Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 577 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 192 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.182661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133917 restraints weight = 82684.960| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.74 r_work: 0.3465 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20256 Z= 0.150 Angle : 0.517 7.458 27556 Z= 0.274 Chirality : 0.035 0.128 3164 Planarity : 0.005 0.075 3408 Dihedral : 6.186 56.207 3154 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.04 % Allowed : 15.83 % Favored : 82.14 % 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 aren not related in a simple way. whole: 0.80 (0.17), residues: 2452 helix: 1.49 (0.13), residues: 1520 sheet: -2.13 (0.61), residues: 76 loop : -0.93 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 271 TYR 0.010 0.001 TYR A 556 PHE 0.015 0.001 PHE C 544 TRP 0.011 0.001 TRP B 733 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00346 (20256) covalent geometry : angle 0.51719 (27556) hydrogen bonds : bond 0.04250 ( 1101) hydrogen bonds : angle 4.34585 ( 3195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 330 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7336 (p0) REVERT: A 215 ASP cc_start: 0.8932 (m-30) cc_final: 0.8696 (m-30) REVERT: A 235 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.7039 (m-10) REVERT: A 271 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.7748 (mtp180) REVERT: A 365 VAL cc_start: 0.8859 (t) cc_final: 0.8585 (m) REVERT: A 628 TYR cc_start: 0.8435 (m-80) cc_final: 0.8185 (m-80) REVERT: A 682 ASP cc_start: 0.7197 (t0) cc_final: 0.6397 (p0) REVERT: A 683 LEU cc_start: 0.8848 (mt) cc_final: 0.8512 (mt) REVERT: A 781 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8097 (p0) REVERT: B 215 ASP cc_start: 0.8829 (m-30) cc_final: 0.8496 (m-30) REVERT: B 235 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.7004 (m-10) REVERT: B 365 VAL cc_start: 0.8853 (t) cc_final: 0.8561 (m) REVERT: B 578 MET cc_start: 0.8164 (ttp) cc_final: 0.7648 (ttm) REVERT: B 628 TYR cc_start: 0.8414 (m-80) cc_final: 0.8115 (m-80) REVERT: B 682 ASP cc_start: 0.6905 (t0) cc_final: 0.5986 (p0) REVERT: B 683 LEU cc_start: 0.8665 (mt) cc_final: 0.8273 (mt) REVERT: C 215 ASP cc_start: 0.8943 (m-30) cc_final: 0.8548 (m-30) REVERT: C 229 SER cc_start: 0.9095 (t) cc_final: 0.8709 (m) REVERT: C 235 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.7000 (m-10) REVERT: C 365 VAL cc_start: 0.8836 (t) cc_final: 0.8543 (m) REVERT: C 578 MET cc_start: 0.8149 (ttp) cc_final: 0.7640 (ttm) REVERT: C 682 ASP cc_start: 0.6711 (t0) cc_final: 0.6401 (t0) REVERT: D 201 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7440 (p0) REVERT: D 215 ASP cc_start: 0.8889 (m-30) cc_final: 0.8572 (m-30) REVERT: D 365 VAL cc_start: 0.8841 (t) cc_final: 0.8556 (m) REVERT: D 578 MET cc_start: 0.8292 (ttp) cc_final: 0.7762 (ttm) REVERT: D 628 TYR cc_start: 0.8519 (m-80) cc_final: 0.8273 (m-80) REVERT: D 682 ASP cc_start: 0.6834 (t0) cc_final: 0.6000 (p0) outliers start: 42 outliers final: 28 residues processed: 359 average time/residue: 0.2467 time to fit residues: 143.2582 Evaluate side-chains 357 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 323 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 674 PHE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 PHE Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 710 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 117 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 242 optimal weight: 0.0050 chunk 207 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.184543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139660 restraints weight = 82398.880| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.89 r_work: 0.3507 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20256 Z= 0.108 Angle : 0.495 7.985 27556 Z= 0.260 Chirality : 0.034 0.153 3164 Planarity : 0.004 0.072 3408 Dihedral : 5.868 54.474 3154 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.65 % Allowed : 16.17 % Favored : 82.18 % 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 aren not related in a simple way. whole: 1.05 (0.17), residues: 2452 helix: 1.71 (0.14), residues: 1512 sheet: -2.15 (0.61), residues: 76 loop : -0.84 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 271 TYR 0.010 0.001 TYR A 411 PHE 0.014 0.001 PHE C 544 TRP 0.011 0.001 TRP B 409 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00241 (20256) covalent geometry : angle 0.49529 (27556) hydrogen bonds : bond 0.03876 ( 1101) hydrogen bonds : angle 4.15423 ( 3195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 369 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 335 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7338 (p0) REVERT: A 215 ASP cc_start: 0.8884 (m-30) cc_final: 0.8647 (m-30) REVERT: A 235 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6927 (m-10) REVERT: A 365 VAL cc_start: 0.8812 (t) cc_final: 0.8515 (m) REVERT: A 682 ASP cc_start: 0.7217 (t0) cc_final: 0.6443 (p0) REVERT: A 683 LEU cc_start: 0.8851 (mt) cc_final: 0.8512 (mt) REVERT: B 215 ASP cc_start: 0.8781 (m-30) cc_final: 0.8442 (m-30) REVERT: B 229 SER cc_start: 0.8983 (t) cc_final: 0.8582 (m) REVERT: B 365 VAL cc_start: 0.8795 (t) cc_final: 0.8497 (m) REVERT: B 578 MET cc_start: 0.8185 (ttp) cc_final: 0.7675 (ttm) REVERT: B 682 ASP cc_start: 0.6893 (t0) cc_final: 0.6003 (p0) REVERT: B 683 LEU cc_start: 0.8700 (mt) cc_final: 0.8303 (mt) REVERT: C 215 ASP cc_start: 0.8898 (m-30) cc_final: 0.8474 (m-30) REVERT: C 229 SER cc_start: 0.9062 (t) cc_final: 0.8685 (m) REVERT: C 365 VAL cc_start: 0.8797 (t) cc_final: 0.8492 (m) REVERT: C 578 MET cc_start: 0.8085 (ttp) cc_final: 0.7552 (ttm) REVERT: C 682 ASP cc_start: 0.6728 (t0) cc_final: 0.6432 (t0) REVERT: D 201 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7566 (p0) REVERT: D 215 ASP cc_start: 0.8851 (m-30) cc_final: 0.8535 (m-30) REVERT: D 365 VAL cc_start: 0.8791 (t) cc_final: 0.8486 (m) REVERT: D 578 MET cc_start: 0.8227 (ttp) cc_final: 0.7704 (ttm) REVERT: D 682 ASP cc_start: 0.6820 (t0) cc_final: 0.6000 (p0) outliers start: 34 outliers final: 24 residues processed: 358 average time/residue: 0.2525 time to fit residues: 148.0371 Evaluate side-chains 354 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 327 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 674 PHE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 PHE Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 441 SER Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain D residue 577 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 21 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.182201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.138254 restraints weight = 82551.874| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.67 r_work: 0.3492 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20256 Z= 0.174 Angle : 0.529 7.151 27556 Z= 0.280 Chirality : 0.035 0.133 3164 Planarity : 0.005 0.076 3408 Dihedral : 6.000 53.792 3154 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.75 % Allowed : 16.55 % Favored : 81.70 % 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 aren not related in a simple way. whole: 0.94 (0.17), residues: 2452 helix: 1.61 (0.13), residues: 1524 sheet: -2.10 (0.62), residues: 76 loop : -0.90 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 271 TYR 0.012 0.001 TYR D 628 PHE 0.015 0.001 PHE C 544 TRP 0.009 0.001 TRP B 733 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00406 (20256) covalent geometry : angle 0.52942 (27556) hydrogen bonds : bond 0.04158 ( 1101) hydrogen bonds : angle 4.33723 ( 3195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 364 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 328 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7261 (p0) REVERT: A 215 ASP cc_start: 0.8949 (m-30) cc_final: 0.8692 (m-30) REVERT: A 235 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.7180 (m-10) REVERT: A 365 VAL cc_start: 0.8976 (t) cc_final: 0.8677 (m) REVERT: A 682 ASP cc_start: 0.7194 (t0) cc_final: 0.6398 (p0) REVERT: A 683 LEU cc_start: 0.8870 (mt) cc_final: 0.8580 (mt) REVERT: B 215 ASP cc_start: 0.8834 (m-30) cc_final: 0.8497 (m-30) REVERT: B 229 SER cc_start: 0.9055 (t) cc_final: 0.8685 (m) REVERT: B 235 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.7154 (m-10) REVERT: B 365 VAL cc_start: 0.8964 (t) cc_final: 0.8656 (m) REVERT: B 578 MET cc_start: 0.8294 (ttp) cc_final: 0.7789 (ttm) REVERT: B 682 ASP cc_start: 0.7015 (t0) cc_final: 0.5990 (p0) REVERT: B 683 LEU cc_start: 0.8730 (mt) cc_final: 0.8355 (mt) REVERT: C 215 ASP cc_start: 0.8972 (m-30) cc_final: 0.8545 (m-30) REVERT: C 229 SER cc_start: 0.9122 (t) cc_final: 0.8764 (m) REVERT: C 235 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.7107 (m-10) REVERT: C 365 VAL cc_start: 0.8981 (t) cc_final: 0.8669 (m) REVERT: C 578 MET cc_start: 0.8224 (ttp) cc_final: 0.7697 (ttm) REVERT: C 682 ASP cc_start: 0.6776 (t0) cc_final: 0.6546 (t0) REVERT: D 201 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7451 (p0) REVERT: D 215 ASP cc_start: 0.8887 (m-30) cc_final: 0.8561 (m-30) REVERT: D 235 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6999 (m-10) REVERT: D 365 VAL cc_start: 0.8950 (t) cc_final: 0.8644 (m) REVERT: D 578 MET cc_start: 0.8334 (ttp) cc_final: 0.7823 (ttm) outliers start: 36 outliers final: 25 residues processed: 350 average time/residue: 0.2780 time to fit residues: 158.8324 Evaluate side-chains 349 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 318 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 674 PHE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 PHE Chi-restraints excluded: chain C residue 672 ASP Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 674 PHE Chi-restraints excluded: chain D residue 710 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 67 optimal weight: 5.9990 chunk 204 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 132 optimal weight: 0.0470 chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.184354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138307 restraints weight = 82418.625| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.92 r_work: 0.3497 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20256 Z= 0.110 Angle : 0.504 8.479 27556 Z= 0.265 Chirality : 0.034 0.144 3164 Planarity : 0.004 0.071 3408 Dihedral : 5.745 51.802 3154 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.50 % Allowed : 17.09 % Favored : 81.41 % 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 aren not related in a simple way. whole: 1.12 (0.17), residues: 2452 helix: 1.77 (0.13), residues: 1520 sheet: -2.35 (0.56), residues: 84 loop : -0.80 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 271 TYR 0.009 0.001 TYR A 411 PHE 0.016 0.001 PHE C 525 TRP 0.011 0.001 TRP B 409 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00248 (20256) covalent geometry : angle 0.50405 (27556) hydrogen bonds : bond 0.03814 ( 1101) hydrogen bonds : angle 4.13609 ( 3195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4904 Ramachandran restraints generated. 2452 Oldfield, 0 Emsley, 2452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue LYS 340 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue SER 557 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 363 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 332 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 201 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.7305 (p0) REVERT: A 215 ASP cc_start: 0.8901 (m-30) cc_final: 0.8664 (m-30) REVERT: A 235 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.6976 (m-10) REVERT: A 365 VAL cc_start: 0.8814 (t) cc_final: 0.8517 (m) REVERT: A 682 ASP cc_start: 0.7226 (t0) cc_final: 0.6409 (p0) REVERT: A 683 LEU cc_start: 0.8813 (mt) cc_final: 0.8564 (mt) REVERT: B 215 ASP cc_start: 0.8794 (m-30) cc_final: 0.8459 (m-30) REVERT: B 229 SER cc_start: 0.9048 (t) cc_final: 0.8675 (m) REVERT: B 235 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.6923 (m-10) REVERT: B 365 VAL cc_start: 0.8799 (t) cc_final: 0.8497 (m) REVERT: B 578 MET cc_start: 0.8168 (ttp) cc_final: 0.7673 (ttm) REVERT: B 682 ASP cc_start: 0.7044 (t0) cc_final: 0.6013 (p0) REVERT: B 683 LEU cc_start: 0.8702 (mt) cc_final: 0.8333 (mt) REVERT: C 215 ASP cc_start: 0.8904 (m-30) cc_final: 0.8468 (m-30) REVERT: C 229 SER cc_start: 0.9053 (t) cc_final: 0.8683 (m) REVERT: C 235 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6936 (m-10) REVERT: C 365 VAL cc_start: 0.8838 (t) cc_final: 0.8531 (m) REVERT: C 578 MET cc_start: 0.8092 (ttp) cc_final: 0.7540 (ttm) REVERT: C 626 ILE cc_start: 0.8779 (mm) cc_final: 0.8146 (tp) REVERT: C 682 ASP cc_start: 0.6898 (t0) cc_final: 0.6574 (t0) REVERT: D 201 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7453 (p0) REVERT: D 215 ASP cc_start: 0.8875 (m-30) cc_final: 0.8536 (m-30) REVERT: D 229 SER cc_start: 0.8957 (t) cc_final: 0.8569 (m) REVERT: D 365 VAL cc_start: 0.8799 (t) cc_final: 0.8485 (m) REVERT: D 578 MET cc_start: 0.8250 (ttp) cc_final: 0.7753 (ttm) REVERT: D 682 ASP cc_start: 0.7029 (t0) cc_final: 0.6138 (p0) outliers start: 31 outliers final: 22 residues processed: 351 average time/residue: 0.2784 time to fit residues: 160.4438 Evaluate side-chains 352 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 325 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 580 PHE Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 674 PHE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain B residue 235 TYR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 341 PHE Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 PHE Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 PHE Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 341 PHE Chi-restraints excluded: chain D residue 674 PHE Chi-restraints excluded: chain D residue 710 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 134 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 184 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 712 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.183961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139149 restraints weight = 82619.519| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.89 r_work: 0.3491 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20256 Z= 0.119 Angle : 0.500 8.265 27556 Z= 0.263 Chirality : 0.034 0.139 3164 Planarity : 0.004 0.073 3408 Dihedral : 5.647 52.054 3154 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.46 % Allowed : 17.09 % Favored : 81.46 % 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 aren not related in a simple way. whole: 1.25 (0.17), residues: 2452 helix: 1.84 (0.13), residues: 1536 sheet: -2.30 (0.56), residues: 84 loop : -0.73 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 271 TYR 0.009 0.001 TYR A 411 PHE 0.015 0.001 PHE C 544 TRP 0.009 0.001 TRP B 409 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00272 (20256) covalent geometry : angle 0.50005 (27556) hydrogen bonds : bond 0.03778 ( 1101) hydrogen bonds : angle 4.12784 ( 3195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8431.22 seconds wall clock time: 143 minutes 41.44 seconds (8621.44 seconds total)