Starting phenix.real_space_refine on Thu Mar 5 16:03:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uza_20954/03_2026/6uza_20954.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uza_20954/03_2026/6uza_20954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uza_20954/03_2026/6uza_20954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uza_20954/03_2026/6uza_20954.map" model { file = "/net/cci-nas-00/data/ceres_data/6uza_20954/03_2026/6uza_20954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uza_20954/03_2026/6uza_20954.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 140 5.16 5 C 15296 2.51 5 N 3808 2.21 5 O 4032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23284 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5659 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 24, 'GLN:plan1': 5, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 187 Chain: "B" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5659 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 24, 'GLN:plan1': 5, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 187 Chain: "C" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5659 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 24, 'GLN:plan1': 5, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 187 Chain: "D" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5659 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 19, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 24, 'GLN:plan1': 5, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 187 Chain: "A" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 203 Unusual residues: {'R0G': 1, 'S9Y': 1, 'SBJ': 2, 'Y01': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'R0G': 1, 'S9Y': 1, 'SBJ': 1, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'R0G': 1, 'S9Y': 1, 'SBJ': 1, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 121 Unusual residues: {'R0G': 1, 'S9Y': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.91, per 1000 atoms: 0.21 Number of scatterers: 23284 At special positions: 0 Unit cell: (128.96, 128.96, 174.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 8 15.00 O 4032 8.00 N 3808 7.00 C 15296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 258 " distance=2.04 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 258 " distance=2.04 Simple disulfide: pdb=" SG CYS C 255 " - pdb=" SG CYS C 258 " distance=2.04 Simple disulfide: pdb=" SG CYS D 255 " - pdb=" SG CYS D 258 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 867.3 milliseconds 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5608 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 0 sheets defined 65.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 135 through 141 Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 257 through 265 removed outlier: 3.614A pdb=" N GLN A 262 " --> pdb=" O CYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 281 Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.862A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 311 removed outlier: 3.862A pdb=" N ASN A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 334 removed outlier: 3.846A pdb=" N LYS A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 329 " --> pdb=" O CYS A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.767A pdb=" N ILE A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.621A pdb=" N VAL A 378 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 392 removed outlier: 4.141A pdb=" N GLN A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.619A pdb=" N LEU A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 461 removed outlier: 3.699A pdb=" N PHE A 450 " --> pdb=" O HIS A 446 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 517 removed outlier: 3.669A pdb=" N GLU A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 556 removed outlier: 3.940A pdb=" N MET A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 586 removed outlier: 3.731A pdb=" N TRP A 586 " --> pdb=" O ARG A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 606 removed outlier: 3.542A pdb=" N GLY A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.877A pdb=" N ILE A 610 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 611 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU A 614 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Proline residue: A 615 - end of helix Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 637 through 654 Processing helix chain 'A' and resid 670 through 680 removed outlier: 3.536A pdb=" N LEU A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 removed outlier: 3.680A pdb=" N SER A 690 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 691 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 692 " --> pdb=" O LYS A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 687 through 692' Processing helix chain 'A' and resid 697 through 729 removed outlier: 3.523A pdb=" N GLU A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 751 removed outlier: 3.609A pdb=" N VAL A 740 " --> pdb=" O ASP A 736 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 875 Processing helix chain 'A' and resid 880 through 918 removed outlier: 3.969A pdb=" N LEU A 884 " --> pdb=" O ASN A 880 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU A 886 " --> pdb=" O GLY A 882 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 887 " --> pdb=" O GLU A 883 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 916 " --> pdb=" O LEU A 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 145 through 153 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 221 through 229 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 257 through 265 removed outlier: 3.614A pdb=" N GLN B 262 " --> pdb=" O CYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 281 Processing helix chain 'B' and resid 282 through 290 removed outlier: 3.862A pdb=" N LEU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 311 removed outlier: 3.862A pdb=" N ASN B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 334 removed outlier: 3.846A pdb=" N LYS B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 329 " --> pdb=" O CYS B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.767A pdb=" N ILE B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.621A pdb=" N VAL B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 392 removed outlier: 4.141A pdb=" N GLN B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 390 " --> pdb=" O GLN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.619A pdb=" N LEU B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 461 removed outlier: 3.699A pdb=" N PHE B 450 " --> pdb=" O HIS B 446 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE B 453 " --> pdb=" O SER B 449 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 517 removed outlier: 3.669A pdb=" N GLU B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 556 removed outlier: 3.940A pdb=" N MET B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 534 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 586 removed outlier: 3.731A pdb=" N TRP B 586 " --> pdb=" O ARG B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 606 removed outlier: 3.542A pdb=" N GLY B 597 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE B 601 " --> pdb=" O GLY B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 removed outlier: 3.877A pdb=" N ILE B 610 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 611 " --> pdb=" O SER B 608 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU B 614 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Proline residue: B 615 - end of helix Processing helix chain 'B' and resid 620 through 629 Processing helix chain 'B' and resid 637 through 654 Processing helix chain 'B' and resid 670 through 680 removed outlier: 3.536A pdb=" N LEU B 678 " --> pdb=" O SER B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 removed outlier: 3.680A pdb=" N SER B 690 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 691 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 692 " --> pdb=" O LYS B 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 687 through 692' Processing helix chain 'B' and resid 697 through 729 removed outlier: 3.523A pdb=" N GLU B 701 " --> pdb=" O HIS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 751 removed outlier: 3.609A pdb=" N VAL B 740 " --> pdb=" O ASP B 736 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP B 742 " --> pdb=" O ALA B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 875 Processing helix chain 'B' and resid 880 through 918 removed outlier: 3.969A pdb=" N LEU B 884 " --> pdb=" O ASN B 880 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS B 885 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU B 886 " --> pdb=" O GLY B 882 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE B 887 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 916 " --> pdb=" O LEU B 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 110 through 118 Processing helix chain 'C' and resid 135 through 141 Processing helix chain 'C' and resid 145 through 153 Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 221 through 229 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 257 through 265 removed outlier: 3.614A pdb=" N GLN C 262 " --> pdb=" O CYS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.862A pdb=" N LEU C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 311 removed outlier: 3.862A pdb=" N ASN C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 334 removed outlier: 3.846A pdb=" N LYS C 320 " --> pdb=" O ASN C 316 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 329 " --> pdb=" O CYS C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.767A pdb=" N ILE C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.621A pdb=" N VAL C 378 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 392 removed outlier: 4.141A pdb=" N GLN C 386 " --> pdb=" O ASN C 382 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 390 " --> pdb=" O GLN C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 416 Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.619A pdb=" N LEU C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 461 removed outlier: 3.699A pdb=" N PHE C 450 " --> pdb=" O HIS C 446 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE C 453 " --> pdb=" O SER C 449 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA C 461 " --> pdb=" O LEU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 517 removed outlier: 3.669A pdb=" N GLU C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 556 removed outlier: 3.940A pdb=" N MET C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 534 " --> pdb=" O ASP C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 586 removed outlier: 3.731A pdb=" N TRP C 586 " --> pdb=" O ARG C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 606 removed outlier: 3.542A pdb=" N GLY C 597 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE C 601 " --> pdb=" O GLY C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 617 removed outlier: 3.877A pdb=" N ILE C 610 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 611 " --> pdb=" O SER C 608 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU C 614 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Proline residue: C 615 - end of helix Processing helix chain 'C' and resid 620 through 629 Processing helix chain 'C' and resid 637 through 654 Processing helix chain 'C' and resid 670 through 680 removed outlier: 3.536A pdb=" N LEU C 678 " --> pdb=" O SER C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 692 removed outlier: 3.680A pdb=" N SER C 690 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 691 " --> pdb=" O VAL C 688 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C 692 " --> pdb=" O LYS C 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 687 through 692' Processing helix chain 'C' and resid 697 through 729 removed outlier: 3.523A pdb=" N GLU C 701 " --> pdb=" O HIS C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 751 removed outlier: 3.609A pdb=" N VAL C 740 " --> pdb=" O ASP C 736 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP C 742 " --> pdb=" O ALA C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 875 Processing helix chain 'C' and resid 880 through 918 removed outlier: 3.969A pdb=" N LEU C 884 " --> pdb=" O ASN C 880 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS C 885 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU C 886 " --> pdb=" O GLY C 882 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 887 " --> pdb=" O GLU C 883 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 916 " --> pdb=" O LEU C 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 110 through 118 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 145 through 153 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 257 through 265 removed outlier: 3.614A pdb=" N GLN D 262 " --> pdb=" O CYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 281 Processing helix chain 'D' and resid 282 through 290 removed outlier: 3.862A pdb=" N LEU D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 311 removed outlier: 3.862A pdb=" N ASN D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 334 removed outlier: 3.846A pdb=" N LYS D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL D 329 " --> pdb=" O CYS D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 347 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 364 through 372 removed outlier: 3.767A pdb=" N ILE D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.621A pdb=" N VAL D 378 " --> pdb=" O VAL D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 392 removed outlier: 4.141A pdb=" N GLN D 386 " --> pdb=" O ASN D 382 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER D 389 " --> pdb=" O GLN D 385 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 390 " --> pdb=" O GLN D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.619A pdb=" N LEU D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 461 removed outlier: 3.699A pdb=" N PHE D 450 " --> pdb=" O HIS D 446 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE D 453 " --> pdb=" O SER D 449 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 517 removed outlier: 3.669A pdb=" N GLU D 512 " --> pdb=" O ALA D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 556 removed outlier: 3.940A pdb=" N MET D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 534 " --> pdb=" O ASP D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 586 removed outlier: 3.731A pdb=" N TRP D 586 " --> pdb=" O ARG D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 606 removed outlier: 3.542A pdb=" N GLY D 597 " --> pdb=" O ILE D 593 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA D 600 " --> pdb=" O GLU D 596 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 617 removed outlier: 3.877A pdb=" N ILE D 610 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 611 " --> pdb=" O SER D 608 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU D 614 " --> pdb=" O ALA D 611 " (cutoff:3.500A) Proline residue: D 615 - end of helix Processing helix chain 'D' and resid 620 through 629 Processing helix chain 'D' and resid 637 through 654 Processing helix chain 'D' and resid 670 through 680 removed outlier: 3.536A pdb=" N LEU D 678 " --> pdb=" O SER D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 692 removed outlier: 3.680A pdb=" N SER D 690 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 691 " --> pdb=" O VAL D 688 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 692 " --> pdb=" O LYS D 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 687 through 692' Processing helix chain 'D' and resid 697 through 729 removed outlier: 3.523A pdb=" N GLU D 701 " --> pdb=" O HIS D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 751 removed outlier: 3.609A pdb=" N VAL D 740 " --> pdb=" O ASP D 736 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP D 742 " --> pdb=" O ALA D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 875 Processing helix chain 'D' and resid 880 through 918 removed outlier: 3.969A pdb=" N LEU D 884 " --> pdb=" O ASN D 880 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS D 885 " --> pdb=" O GLU D 881 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU D 886 " --> pdb=" O GLY D 882 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE D 887 " --> pdb=" O GLU D 883 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU D 916 " --> pdb=" O LEU D 912 " (cutoff:3.500A) 1240 hydrogen bonds defined for protein. 3660 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3600 1.30 - 1.43: 6440 1.43 - 1.56: 13436 1.56 - 1.69: 88 1.69 - 1.83: 248 Bond restraints: 23812 Sorted by residual: bond pdb=" O5 S9Y C1003 " pdb=" P S9Y C1003 " ideal model delta sigma weight residual 1.648 1.799 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O5 S9Y A1002 " pdb=" P S9Y A1002 " ideal model delta sigma weight residual 1.648 1.799 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O5 S9Y B1003 " pdb=" P S9Y B1003 " ideal model delta sigma weight residual 1.648 1.799 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O5 S9Y D1003 " pdb=" P S9Y D1003 " ideal model delta sigma weight residual 1.648 1.799 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C21 R0G B1002 " pdb=" C22 R0G B1002 " ideal model delta sigma weight residual 1.423 1.556 -0.133 2.00e-02 2.50e+03 4.44e+01 ... (remaining 23807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 31835 3.66 - 7.32: 365 7.32 - 10.98: 76 10.98 - 14.64: 4 14.64 - 18.30: 12 Bond angle restraints: 32292 Sorted by residual: angle pdb=" N VAL A 576 " pdb=" CA VAL A 576 " pdb=" C VAL A 576 " ideal model delta sigma weight residual 113.20 104.60 8.60 9.60e-01 1.09e+00 8.03e+01 angle pdb=" N VAL B 576 " pdb=" CA VAL B 576 " pdb=" C VAL B 576 " ideal model delta sigma weight residual 113.20 104.60 8.60 9.60e-01 1.09e+00 8.03e+01 angle pdb=" N VAL D 576 " pdb=" CA VAL D 576 " pdb=" C VAL D 576 " ideal model delta sigma weight residual 113.20 104.60 8.60 9.60e-01 1.09e+00 8.03e+01 angle pdb=" N VAL C 576 " pdb=" CA VAL C 576 " pdb=" C VAL C 576 " ideal model delta sigma weight residual 113.20 104.60 8.60 9.60e-01 1.09e+00 8.03e+01 angle pdb=" O3P S9Y A1002 " pdb=" P S9Y A1002 " pdb=" O5 S9Y A1002 " ideal model delta sigma weight residual 94.12 112.42 -18.30 3.00e+00 1.11e-01 3.72e+01 ... (remaining 32287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.12: 14064 30.12 - 60.24: 536 60.24 - 90.36: 28 90.36 - 120.48: 0 120.48 - 150.60: 4 Dihedral angle restraints: 14632 sinusoidal: 5984 harmonic: 8648 Sorted by residual: dihedral pdb=" CA ASN B 256 " pdb=" C ASN B 256 " pdb=" N ASP B 257 " pdb=" CA ASP B 257 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ASN A 256 " pdb=" C ASN A 256 " pdb=" N ASP A 257 " pdb=" CA ASP A 257 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ASN C 256 " pdb=" C ASN C 256 " pdb=" N ASP C 257 " pdb=" CA ASP C 257 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 14629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3448 0.103 - 0.206: 184 0.206 - 0.309: 36 0.309 - 0.412: 8 0.412 - 0.515: 8 Chirality restraints: 3684 Sorted by residual: chirality pdb=" C2 SBJ A1003 " pdb=" C1 SBJ A1003 " pdb=" C3 SBJ A1003 " pdb=" O2 SBJ A1003 " both_signs ideal model delta sigma weight residual False 2.37 2.88 -0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" C2 SBJ B1004 " pdb=" C1 SBJ B1004 " pdb=" C3 SBJ B1004 " pdb=" O2 SBJ B1004 " both_signs ideal model delta sigma weight residual False 2.37 2.88 -0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" C2 SBJ C1004 " pdb=" C1 SBJ C1004 " pdb=" C3 SBJ C1004 " pdb=" O2 SBJ C1004 " both_signs ideal model delta sigma weight residual False 2.37 2.88 -0.52 2.00e-01 2.50e+01 6.64e+00 ... (remaining 3681 not shown) Planarity restraints: 3956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 758 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C ARG C 758 " 0.048 2.00e-02 2.50e+03 pdb=" O ARG C 758 " -0.018 2.00e-02 2.50e+03 pdb=" N THR C 759 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 758 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C ARG A 758 " 0.048 2.00e-02 2.50e+03 pdb=" O ARG A 758 " -0.018 2.00e-02 2.50e+03 pdb=" N THR A 759 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 758 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C ARG B 758 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG B 758 " -0.018 2.00e-02 2.50e+03 pdb=" N THR B 759 " -0.016 2.00e-02 2.50e+03 ... (remaining 3953 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 7748 2.85 - 3.36: 20216 3.36 - 3.88: 36295 3.88 - 4.39: 43364 4.39 - 4.90: 75205 Nonbonded interactions: 182828 Sorted by model distance: nonbonded pdb=" O SER B 589 " pdb=" OG SER B 589 " model vdw 2.338 3.040 nonbonded pdb=" O SER A 589 " pdb=" OG SER A 589 " model vdw 2.338 3.040 nonbonded pdb=" O SER C 589 " pdb=" OG SER C 589 " model vdw 2.338 3.040 nonbonded pdb=" O SER D 589 " pdb=" OG SER D 589 " model vdw 2.338 3.040 nonbonded pdb=" O PRO B 283 " pdb=" OG SER B 287 " model vdw 2.338 3.040 ... (remaining 182823 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 85 through 920) selection = (chain 'B' and resid 85 through 920) selection = (chain 'C' and resid 85 through 920) selection = (chain 'D' and resid 85 through 920) } 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: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.850 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.008 0.151 23816 Z= 0.408 Angle : 1.054 18.304 32300 Z= 0.528 Chirality : 0.062 0.515 3684 Planarity : 0.007 0.068 3956 Dihedral : 15.174 150.597 9012 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.12), residues: 2904 helix: -2.47 (0.09), residues: 1920 sheet: None (None), residues: 0 loop : -2.49 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 758 TYR 0.020 0.002 TYR D 209 PHE 0.020 0.002 PHE C 537 TRP 0.031 0.002 TRP B 514 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00831 (23812) covalent geometry : angle 1.05374 (32292) SS BOND : bond 0.00737 ( 4) SS BOND : angle 2.39416 ( 8) hydrogen bonds : bond 0.13583 ( 1240) hydrogen bonds : angle 5.37542 ( 3660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.829 Fit side-chains REVERT: A 441 MET cc_start: 0.7995 (mmm) cc_final: 0.7746 (mmp) REVERT: A 689 LYS cc_start: 0.8440 (ptmt) cc_final: 0.8178 (ptmt) REVERT: A 696 ASN cc_start: 0.8072 (t0) cc_final: 0.7871 (t0) REVERT: A 881 GLU cc_start: 0.8157 (tt0) cc_final: 0.7757 (mt-10) REVERT: B 441 MET cc_start: 0.7997 (mmm) cc_final: 0.7751 (mmp) REVERT: B 689 LYS cc_start: 0.8445 (ptmt) cc_final: 0.8183 (ptmt) REVERT: B 696 ASN cc_start: 0.8077 (t0) cc_final: 0.7875 (t0) REVERT: B 881 GLU cc_start: 0.8166 (tt0) cc_final: 0.7764 (mt-10) REVERT: C 441 MET cc_start: 0.7995 (mmm) cc_final: 0.7748 (mmp) REVERT: C 689 LYS cc_start: 0.8442 (ptmt) cc_final: 0.8181 (ptmt) REVERT: C 696 ASN cc_start: 0.8076 (t0) cc_final: 0.7872 (t0) REVERT: C 881 GLU cc_start: 0.8166 (tt0) cc_final: 0.7764 (mt-10) REVERT: D 441 MET cc_start: 0.7993 (mmm) cc_final: 0.7742 (mmp) REVERT: D 689 LYS cc_start: 0.8443 (ptmt) cc_final: 0.8178 (ptmt) REVERT: D 696 ASN cc_start: 0.8076 (t0) cc_final: 0.7873 (t0) REVERT: D 881 GLU cc_start: 0.8160 (tt0) cc_final: 0.7759 (mt-10) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.1723 time to fit residues: 93.8075 Evaluate side-chains 288 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS A 380 HIS A 384 GLN A 446 HIS A 550 HIS A 728 ASN B 157 ASN B 358 HIS B 380 HIS B 384 GLN B 446 HIS B 550 HIS B 728 ASN C 157 ASN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 HIS C 380 HIS C 384 GLN C 446 HIS C 550 HIS C 728 ASN D 157 ASN D 358 HIS D 380 HIS D 384 GLN D 446 HIS D 550 HIS D 728 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.159351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121804 restraints weight = 25113.581| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.10 r_work: 0.3289 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23816 Z= 0.115 Angle : 0.488 6.182 32300 Z= 0.260 Chirality : 0.037 0.123 3684 Planarity : 0.004 0.046 3956 Dihedral : 9.078 97.143 4076 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.89 % Allowed : 8.87 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.15), residues: 2904 helix: -0.45 (0.11), residues: 1932 sheet: None (None), residues: 0 loop : -2.05 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 437 TYR 0.008 0.001 TYR D 209 PHE 0.009 0.001 PHE D 548 TRP 0.023 0.001 TRP D 514 HIS 0.002 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00271 (23812) covalent geometry : angle 0.48532 (32292) SS BOND : bond 0.01046 ( 4) SS BOND : angle 3.50619 ( 8) hydrogen bonds : bond 0.03982 ( 1240) hydrogen bonds : angle 3.39241 ( 3660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 322 time to evaluate : 0.827 Fit side-chains REVERT: A 116 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7605 (ttpt) REVERT: A 262 GLN cc_start: 0.7923 (tt0) cc_final: 0.7484 (mt0) REVERT: A 441 MET cc_start: 0.8357 (mmm) cc_final: 0.8067 (mmp) REVERT: A 689 LYS cc_start: 0.8609 (ptmt) cc_final: 0.8311 (ptmt) REVERT: A 696 ASN cc_start: 0.8175 (t0) cc_final: 0.7848 (t0) REVERT: A 881 GLU cc_start: 0.8749 (tt0) cc_final: 0.8172 (mt-10) REVERT: B 116 LYS cc_start: 0.7826 (ttpt) cc_final: 0.7594 (ttpt) REVERT: B 262 GLN cc_start: 0.7933 (tt0) cc_final: 0.7493 (mt0) REVERT: B 441 MET cc_start: 0.8368 (mmm) cc_final: 0.8081 (mmp) REVERT: B 689 LYS cc_start: 0.8611 (ptmt) cc_final: 0.8311 (ptmt) REVERT: B 696 ASN cc_start: 0.8160 (t0) cc_final: 0.7832 (t0) REVERT: B 881 GLU cc_start: 0.8756 (tt0) cc_final: 0.8181 (mt-10) REVERT: C 116 LYS cc_start: 0.7817 (ttpt) cc_final: 0.7585 (ttpt) REVERT: C 262 GLN cc_start: 0.7935 (tt0) cc_final: 0.7497 (mt0) REVERT: C 441 MET cc_start: 0.8364 (mmm) cc_final: 0.8075 (mmp) REVERT: C 689 LYS cc_start: 0.8602 (ptmt) cc_final: 0.8300 (ptmt) REVERT: C 696 ASN cc_start: 0.8174 (t0) cc_final: 0.7846 (t0) REVERT: C 881 GLU cc_start: 0.8757 (tt0) cc_final: 0.8184 (mt-10) REVERT: D 116 LYS cc_start: 0.7827 (ttpt) cc_final: 0.7594 (ttpt) REVERT: D 262 GLN cc_start: 0.7928 (tt0) cc_final: 0.7489 (mt0) REVERT: D 441 MET cc_start: 0.8351 (mmm) cc_final: 0.8064 (mmp) REVERT: D 689 LYS cc_start: 0.8609 (ptmt) cc_final: 0.8310 (ptmt) REVERT: D 696 ASN cc_start: 0.8172 (t0) cc_final: 0.7844 (t0) REVERT: D 881 GLU cc_start: 0.8756 (tt0) cc_final: 0.8181 (mt-10) outliers start: 20 outliers final: 16 residues processed: 330 average time/residue: 0.1656 time to fit residues: 84.6354 Evaluate side-chains 318 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 302 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 280 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 251 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 ASN B 580 ASN C 580 ASN D 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.154725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.116912 restraints weight = 25308.265| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.08 r_work: 0.3235 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23816 Z= 0.191 Angle : 0.541 6.813 32300 Z= 0.283 Chirality : 0.040 0.139 3684 Planarity : 0.004 0.038 3956 Dihedral : 8.736 75.646 4076 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.77 % Allowed : 10.28 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.15), residues: 2904 helix: 0.19 (0.12), residues: 1924 sheet: None (None), residues: 0 loop : -1.93 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 861 TYR 0.013 0.001 TYR D 209 PHE 0.012 0.002 PHE B 537 TRP 0.022 0.002 TRP A 514 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00483 (23812) covalent geometry : angle 0.53792 (32292) SS BOND : bond 0.01171 ( 4) SS BOND : angle 3.52290 ( 8) hydrogen bonds : bond 0.04874 ( 1240) hydrogen bonds : angle 3.26649 ( 3660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 316 time to evaluate : 0.905 Fit side-chains REVERT: A 262 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7588 (mt0) REVERT: A 441 MET cc_start: 0.8424 (mmm) cc_final: 0.8130 (mmp) REVERT: A 507 TRP cc_start: 0.8478 (t-100) cc_final: 0.8272 (t-100) REVERT: A 689 LYS cc_start: 0.8669 (ptmt) cc_final: 0.8374 (ptmt) REVERT: A 696 ASN cc_start: 0.8137 (t0) cc_final: 0.7832 (t0) REVERT: A 881 GLU cc_start: 0.8793 (tt0) cc_final: 0.8226 (mt-10) REVERT: B 262 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: B 441 MET cc_start: 0.8434 (mmm) cc_final: 0.8141 (mmp) REVERT: B 507 TRP cc_start: 0.8479 (t-100) cc_final: 0.8273 (t-100) REVERT: B 689 LYS cc_start: 0.8666 (ptmt) cc_final: 0.8369 (ptmt) REVERT: B 696 ASN cc_start: 0.8137 (t0) cc_final: 0.7833 (t0) REVERT: B 881 GLU cc_start: 0.8784 (tt0) cc_final: 0.8219 (mt-10) REVERT: C 262 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: C 441 MET cc_start: 0.8433 (mmm) cc_final: 0.8138 (mmp) REVERT: C 507 TRP cc_start: 0.8494 (t-100) cc_final: 0.8287 (t-100) REVERT: C 689 LYS cc_start: 0.8663 (ptmt) cc_final: 0.8363 (ptmt) REVERT: C 696 ASN cc_start: 0.8149 (t0) cc_final: 0.7846 (t0) REVERT: C 881 GLU cc_start: 0.8784 (tt0) cc_final: 0.8215 (mt-10) REVERT: D 262 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: D 441 MET cc_start: 0.8429 (mmm) cc_final: 0.8136 (mmp) REVERT: D 507 TRP cc_start: 0.8479 (t-100) cc_final: 0.8272 (t-100) REVERT: D 689 LYS cc_start: 0.8671 (ptmt) cc_final: 0.8376 (ptmt) REVERT: D 696 ASN cc_start: 0.8142 (t0) cc_final: 0.7839 (t0) REVERT: D 881 GLU cc_start: 0.8786 (tt0) cc_final: 0.8218 (mt-10) outliers start: 40 outliers final: 20 residues processed: 336 average time/residue: 0.1592 time to fit residues: 83.9531 Evaluate side-chains 332 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 308 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 125 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 287 optimal weight: 0.6980 chunk 253 optimal weight: 0.7980 chunk 91 optimal weight: 0.0980 chunk 182 optimal weight: 0.9990 chunk 257 optimal weight: 7.9990 chunk 219 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 165 optimal weight: 0.0570 chunk 231 optimal weight: 3.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 316 ASN B 230 GLN B 316 ASN C 230 GLN C 316 ASN D 230 GLN D 316 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.160921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123489 restraints weight = 24971.358| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.10 r_work: 0.3307 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23816 Z= 0.086 Angle : 0.437 5.778 32300 Z= 0.232 Chirality : 0.036 0.127 3684 Planarity : 0.003 0.036 3956 Dihedral : 7.877 65.232 4076 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.60 % Allowed : 11.70 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.16), residues: 2904 helix: 0.83 (0.12), residues: 1908 sheet: None (None), residues: 0 loop : -1.59 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 437 TYR 0.005 0.001 TYR D 277 PHE 0.013 0.001 PHE B 641 TRP 0.017 0.001 TRP D 514 HIS 0.001 0.000 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00196 (23812) covalent geometry : angle 0.43349 (32292) SS BOND : bond 0.01025 ( 4) SS BOND : angle 3.38280 ( 8) hydrogen bonds : bond 0.03095 ( 1240) hydrogen bonds : angle 2.92046 ( 3660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 304 time to evaluate : 0.879 Fit side-chains REVERT: A 262 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7336 (mt0) REVERT: A 339 THR cc_start: 0.8689 (t) cc_final: 0.8411 (m) REVERT: A 441 MET cc_start: 0.8259 (mmm) cc_final: 0.7973 (mmp) REVERT: A 486 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8048 (mmm) REVERT: A 689 LYS cc_start: 0.8557 (ptmt) cc_final: 0.8275 (ptmt) REVERT: A 696 ASN cc_start: 0.7917 (t0) cc_final: 0.7630 (t0) REVERT: A 881 GLU cc_start: 0.8643 (tt0) cc_final: 0.8175 (mt-10) REVERT: B 262 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7359 (mt0) REVERT: B 339 THR cc_start: 0.8690 (t) cc_final: 0.8413 (m) REVERT: B 441 MET cc_start: 0.8270 (mmm) cc_final: 0.7988 (mmp) REVERT: B 486 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.8052 (mmm) REVERT: B 689 LYS cc_start: 0.8562 (ptmt) cc_final: 0.8277 (ptmt) REVERT: B 696 ASN cc_start: 0.7914 (t0) cc_final: 0.7626 (t0) REVERT: B 881 GLU cc_start: 0.8644 (tt0) cc_final: 0.8176 (mt-10) REVERT: C 262 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7353 (mt0) REVERT: C 339 THR cc_start: 0.8699 (t) cc_final: 0.8420 (m) REVERT: C 441 MET cc_start: 0.8275 (mmm) cc_final: 0.7991 (mmp) REVERT: C 486 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8053 (mmm) REVERT: C 689 LYS cc_start: 0.8544 (ptmt) cc_final: 0.8259 (ptmt) REVERT: C 696 ASN cc_start: 0.7924 (t0) cc_final: 0.7635 (t0) REVERT: C 881 GLU cc_start: 0.8650 (tt0) cc_final: 0.8182 (mt-10) REVERT: D 262 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7348 (mt0) REVERT: D 339 THR cc_start: 0.8693 (t) cc_final: 0.8419 (m) REVERT: D 441 MET cc_start: 0.8265 (mmm) cc_final: 0.7980 (mmp) REVERT: D 486 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.8042 (mmm) REVERT: D 689 LYS cc_start: 0.8555 (ptmt) cc_final: 0.8272 (ptmt) REVERT: D 696 ASN cc_start: 0.7923 (t0) cc_final: 0.7637 (t0) REVERT: D 881 GLU cc_start: 0.8641 (tt0) cc_final: 0.8175 (mt-10) outliers start: 36 outliers final: 20 residues processed: 312 average time/residue: 0.1541 time to fit residues: 76.3235 Evaluate side-chains 328 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 300 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 629 ARG Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 238 optimal weight: 0.9990 chunk 289 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 252 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 chunk 223 optimal weight: 0.0040 chunk 179 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.160700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.123326 restraints weight = 24810.245| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.08 r_work: 0.3303 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23816 Z= 0.097 Angle : 0.437 5.937 32300 Z= 0.232 Chirality : 0.036 0.128 3684 Planarity : 0.003 0.039 3956 Dihedral : 7.637 61.112 4076 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.82 % Allowed : 11.84 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.16), residues: 2904 helix: 1.11 (0.12), residues: 1896 sheet: None (None), residues: 0 loop : -1.39 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 437 TYR 0.007 0.001 TYR C 209 PHE 0.008 0.001 PHE D 548 TRP 0.015 0.001 TRP B 514 HIS 0.002 0.000 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00232 (23812) covalent geometry : angle 0.43365 (32292) SS BOND : bond 0.01018 ( 4) SS BOND : angle 3.35588 ( 8) hydrogen bonds : bond 0.03308 ( 1240) hydrogen bonds : angle 2.83262 ( 3660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 312 time to evaluate : 0.785 Fit side-chains REVERT: A 262 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7351 (mt0) REVERT: A 339 THR cc_start: 0.8730 (t) cc_final: 0.8457 (m) REVERT: A 441 MET cc_start: 0.8294 (mmm) cc_final: 0.8000 (mmp) REVERT: A 689 LYS cc_start: 0.8574 (ptmt) cc_final: 0.8296 (ptmt) REVERT: A 696 ASN cc_start: 0.7922 (t0) cc_final: 0.7653 (t0) REVERT: A 758 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8096 (ptt-90) REVERT: A 881 GLU cc_start: 0.8699 (tt0) cc_final: 0.8248 (mt-10) REVERT: B 262 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7370 (mt0) REVERT: B 339 THR cc_start: 0.8718 (t) cc_final: 0.8448 (m) REVERT: B 441 MET cc_start: 0.8302 (mmm) cc_final: 0.8011 (mmp) REVERT: B 689 LYS cc_start: 0.8575 (ptmt) cc_final: 0.8294 (ptmt) REVERT: B 696 ASN cc_start: 0.7911 (t0) cc_final: 0.7639 (t0) REVERT: B 758 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8086 (ptt-90) REVERT: B 881 GLU cc_start: 0.8699 (tt0) cc_final: 0.8251 (mt-10) REVERT: C 262 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7368 (mt0) REVERT: C 339 THR cc_start: 0.8735 (t) cc_final: 0.8462 (m) REVERT: C 441 MET cc_start: 0.8304 (mmm) cc_final: 0.8012 (mmp) REVERT: C 689 LYS cc_start: 0.8567 (ptmt) cc_final: 0.8283 (ptmt) REVERT: C 696 ASN cc_start: 0.7925 (t0) cc_final: 0.7654 (t0) REVERT: C 758 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8088 (ptt-90) REVERT: C 881 GLU cc_start: 0.8709 (tt0) cc_final: 0.8259 (mt-10) REVERT: D 262 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7362 (mt0) REVERT: D 339 THR cc_start: 0.8731 (t) cc_final: 0.8461 (m) REVERT: D 441 MET cc_start: 0.8293 (mmm) cc_final: 0.8002 (mmp) REVERT: D 689 LYS cc_start: 0.8570 (ptmt) cc_final: 0.8290 (ptmt) REVERT: D 696 ASN cc_start: 0.7921 (t0) cc_final: 0.7652 (t0) REVERT: D 758 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8090 (ptt-90) REVERT: D 881 GLU cc_start: 0.8696 (tt0) cc_final: 0.8247 (mt-10) outliers start: 41 outliers final: 32 residues processed: 332 average time/residue: 0.1623 time to fit residues: 84.5289 Evaluate side-chains 344 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 304 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 629 ARG Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 274 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 192 optimal weight: 0.0060 chunk 280 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 212 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN B 316 ASN C 316 ASN D 316 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.162085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.124673 restraints weight = 24884.636| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.08 r_work: 0.3323 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23816 Z= 0.085 Angle : 0.422 6.163 32300 Z= 0.224 Chirality : 0.036 0.127 3684 Planarity : 0.003 0.036 3956 Dihedral : 7.360 57.424 4076 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.77 % Allowed : 12.94 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.16), residues: 2904 helix: 1.45 (0.12), residues: 1884 sheet: None (None), residues: 0 loop : -1.25 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 437 TYR 0.008 0.001 TYR C 209 PHE 0.010 0.001 PHE B 641 TRP 0.014 0.001 TRP B 514 HIS 0.001 0.000 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00196 (23812) covalent geometry : angle 0.41899 (32292) SS BOND : bond 0.00999 ( 4) SS BOND : angle 3.29354 ( 8) hydrogen bonds : bond 0.03012 ( 1240) hydrogen bonds : angle 2.74873 ( 3660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 328 time to evaluate : 0.914 Fit side-chains REVERT: A 262 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7077 (mt0) REVERT: A 339 THR cc_start: 0.8694 (t) cc_final: 0.8432 (m) REVERT: A 432 MET cc_start: 0.7352 (mmt) cc_final: 0.7036 (mmt) REVERT: A 441 MET cc_start: 0.8303 (mmm) cc_final: 0.8015 (mmp) REVERT: A 643 MET cc_start: 0.8063 (mtt) cc_final: 0.7746 (mtt) REVERT: A 689 LYS cc_start: 0.8547 (ptmt) cc_final: 0.8293 (ptmt) REVERT: A 696 ASN cc_start: 0.7888 (t0) cc_final: 0.7638 (t0) REVERT: A 881 GLU cc_start: 0.8703 (tt0) cc_final: 0.8307 (mt-10) REVERT: B 262 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7100 (mt0) REVERT: B 339 THR cc_start: 0.8685 (t) cc_final: 0.8425 (m) REVERT: B 432 MET cc_start: 0.7361 (mmt) cc_final: 0.7047 (mmt) REVERT: B 441 MET cc_start: 0.8313 (mmm) cc_final: 0.8029 (mmp) REVERT: B 643 MET cc_start: 0.8104 (mtt) cc_final: 0.7824 (mtt) REVERT: B 689 LYS cc_start: 0.8546 (ptmt) cc_final: 0.8292 (ptmt) REVERT: B 696 ASN cc_start: 0.7887 (t0) cc_final: 0.7635 (t0) REVERT: B 881 GLU cc_start: 0.8702 (tt0) cc_final: 0.8309 (mt-10) REVERT: C 262 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7091 (mt0) REVERT: C 339 THR cc_start: 0.8698 (t) cc_final: 0.8434 (m) REVERT: C 432 MET cc_start: 0.7390 (mmt) cc_final: 0.7073 (mmt) REVERT: C 441 MET cc_start: 0.8309 (mmm) cc_final: 0.8022 (mmp) REVERT: C 643 MET cc_start: 0.8100 (mtt) cc_final: 0.7820 (mtt) REVERT: C 689 LYS cc_start: 0.8537 (ptmt) cc_final: 0.8282 (ptmt) REVERT: C 696 ASN cc_start: 0.7890 (t0) cc_final: 0.7640 (t0) REVERT: C 881 GLU cc_start: 0.8710 (tt0) cc_final: 0.8315 (mt-10) REVERT: D 262 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.7087 (mt0) REVERT: D 339 THR cc_start: 0.8695 (t) cc_final: 0.8437 (m) REVERT: D 432 MET cc_start: 0.7376 (mmt) cc_final: 0.7059 (mmt) REVERT: D 441 MET cc_start: 0.8299 (mmm) cc_final: 0.8015 (mmp) REVERT: D 643 MET cc_start: 0.8095 (mtt) cc_final: 0.7814 (mtt) REVERT: D 689 LYS cc_start: 0.8539 (ptmt) cc_final: 0.8283 (ptmt) REVERT: D 696 ASN cc_start: 0.7895 (t0) cc_final: 0.7647 (t0) REVERT: D 881 GLU cc_start: 0.8695 (tt0) cc_final: 0.8301 (mt-10) outliers start: 40 outliers final: 32 residues processed: 344 average time/residue: 0.1486 time to fit residues: 81.6807 Evaluate side-chains 348 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 312 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 629 ARG Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 100 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.159565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121977 restraints weight = 25222.703| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.06 r_work: 0.3311 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23816 Z= 0.097 Angle : 0.434 6.545 32300 Z= 0.230 Chirality : 0.037 0.128 3684 Planarity : 0.003 0.035 3956 Dihedral : 7.335 57.342 4076 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.04 % Allowed : 12.68 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.16), residues: 2904 helix: 1.53 (0.12), residues: 1892 sheet: None (None), residues: 0 loop : -1.21 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 437 TYR 0.010 0.001 TYR D 209 PHE 0.011 0.001 PHE D 641 TRP 0.012 0.001 TRP D 514 HIS 0.002 0.000 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00233 (23812) covalent geometry : angle 0.43141 (32292) SS BOND : bond 0.01032 ( 4) SS BOND : angle 3.25755 ( 8) hydrogen bonds : bond 0.03215 ( 1240) hydrogen bonds : angle 2.74652 ( 3660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 312 time to evaluate : 0.891 Fit side-chains REVERT: A 262 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7035 (mt0) REVERT: A 339 THR cc_start: 0.8714 (t) cc_final: 0.8451 (m) REVERT: A 432 MET cc_start: 0.7345 (mmt) cc_final: 0.7019 (mmt) REVERT: A 441 MET cc_start: 0.8317 (mmm) cc_final: 0.8018 (mmp) REVERT: A 689 LYS cc_start: 0.8553 (ptmt) cc_final: 0.8287 (ptmt) REVERT: A 696 ASN cc_start: 0.7874 (t0) cc_final: 0.7619 (t0) REVERT: A 881 GLU cc_start: 0.8704 (tt0) cc_final: 0.8264 (mt-10) REVERT: B 262 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.7060 (mt0) REVERT: B 339 THR cc_start: 0.8705 (t) cc_final: 0.8444 (m) REVERT: B 432 MET cc_start: 0.7348 (mmt) cc_final: 0.7021 (mmt) REVERT: B 441 MET cc_start: 0.8324 (mmm) cc_final: 0.8029 (mmp) REVERT: B 689 LYS cc_start: 0.8557 (ptmt) cc_final: 0.8290 (ptmt) REVERT: B 696 ASN cc_start: 0.7869 (t0) cc_final: 0.7613 (t0) REVERT: B 881 GLU cc_start: 0.8702 (tt0) cc_final: 0.8264 (mt-10) REVERT: C 262 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7044 (mt0) REVERT: C 339 THR cc_start: 0.8714 (t) cc_final: 0.8448 (m) REVERT: C 432 MET cc_start: 0.7377 (mmt) cc_final: 0.7051 (mmt) REVERT: C 441 MET cc_start: 0.8314 (mmm) cc_final: 0.8019 (mmp) REVERT: C 689 LYS cc_start: 0.8548 (ptmt) cc_final: 0.8278 (ptmt) REVERT: C 696 ASN cc_start: 0.7874 (t0) cc_final: 0.7619 (t0) REVERT: C 881 GLU cc_start: 0.8708 (tt0) cc_final: 0.8266 (mt-10) REVERT: D 262 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7038 (mt0) REVERT: D 339 THR cc_start: 0.8713 (t) cc_final: 0.8453 (m) REVERT: D 432 MET cc_start: 0.7372 (mmt) cc_final: 0.7044 (mmt) REVERT: D 441 MET cc_start: 0.8311 (mmm) cc_final: 0.8015 (mmp) REVERT: D 689 LYS cc_start: 0.8548 (ptmt) cc_final: 0.8282 (ptmt) REVERT: D 696 ASN cc_start: 0.7883 (t0) cc_final: 0.7630 (t0) REVERT: D 881 GLU cc_start: 0.8698 (tt0) cc_final: 0.8258 (mt-10) outliers start: 46 outliers final: 32 residues processed: 336 average time/residue: 0.1497 time to fit residues: 80.2022 Evaluate side-chains 344 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 308 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 629 ARG Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 71 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 233 optimal weight: 0.6980 chunk 213 optimal weight: 0.6980 chunk 277 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.158693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121410 restraints weight = 24956.787| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.03 r_work: 0.3302 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23816 Z= 0.106 Angle : 0.443 6.713 32300 Z= 0.235 Chirality : 0.037 0.129 3684 Planarity : 0.003 0.035 3956 Dihedral : 7.385 58.286 4076 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.35 % Allowed : 12.54 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.16), residues: 2904 helix: 1.58 (0.12), residues: 1896 sheet: None (None), residues: 0 loop : -1.16 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 437 TYR 0.010 0.001 TYR B 209 PHE 0.012 0.001 PHE D 641 TRP 0.012 0.001 TRP D 514 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00259 (23812) covalent geometry : angle 0.44040 (32292) SS BOND : bond 0.01039 ( 4) SS BOND : angle 3.25047 ( 8) hydrogen bonds : bond 0.03457 ( 1240) hydrogen bonds : angle 2.77659 ( 3660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 308 time to evaluate : 0.890 Fit side-chains REVERT: A 262 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7023 (mt0) REVERT: A 339 THR cc_start: 0.8734 (t) cc_final: 0.8473 (m) REVERT: A 437 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.8114 (ttm-80) REVERT: A 441 MET cc_start: 0.8347 (mmm) cc_final: 0.8024 (mmp) REVERT: A 643 MET cc_start: 0.8113 (mtt) cc_final: 0.7802 (mtt) REVERT: A 689 LYS cc_start: 0.8592 (ptmt) cc_final: 0.8307 (ptmt) REVERT: A 696 ASN cc_start: 0.7921 (t0) cc_final: 0.7662 (t0) REVERT: A 758 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8223 (ptt-90) REVERT: A 881 GLU cc_start: 0.8717 (tt0) cc_final: 0.8249 (mt-10) REVERT: B 262 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7045 (mt0) REVERT: B 339 THR cc_start: 0.8716 (t) cc_final: 0.8459 (m) REVERT: B 437 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.8122 (ttm-80) REVERT: B 441 MET cc_start: 0.8344 (mmm) cc_final: 0.8024 (mmp) REVERT: B 689 LYS cc_start: 0.8592 (ptmt) cc_final: 0.8308 (ptmt) REVERT: B 696 ASN cc_start: 0.7918 (t0) cc_final: 0.7657 (t0) REVERT: B 758 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8219 (ptt-90) REVERT: B 881 GLU cc_start: 0.8713 (tt0) cc_final: 0.8247 (mt-10) REVERT: C 262 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.7025 (mt0) REVERT: C 339 THR cc_start: 0.8724 (t) cc_final: 0.8464 (m) REVERT: C 437 ARG cc_start: 0.8436 (ttm-80) cc_final: 0.8121 (ttm-80) REVERT: C 441 MET cc_start: 0.8344 (mmm) cc_final: 0.8022 (mmp) REVERT: C 689 LYS cc_start: 0.8584 (ptmt) cc_final: 0.8295 (ptmt) REVERT: C 696 ASN cc_start: 0.7934 (t0) cc_final: 0.7676 (t0) REVERT: C 758 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8224 (ptt-90) REVERT: C 881 GLU cc_start: 0.8723 (tt0) cc_final: 0.8254 (mt-10) REVERT: D 262 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.7023 (mt0) REVERT: D 339 THR cc_start: 0.8725 (t) cc_final: 0.8470 (m) REVERT: D 437 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.8131 (ttm-80) REVERT: D 441 MET cc_start: 0.8336 (mmm) cc_final: 0.8017 (mmp) REVERT: D 689 LYS cc_start: 0.8584 (ptmt) cc_final: 0.8297 (ptmt) REVERT: D 696 ASN cc_start: 0.7932 (t0) cc_final: 0.7674 (t0) REVERT: D 758 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8230 (ptt-90) REVERT: D 881 GLU cc_start: 0.8709 (tt0) cc_final: 0.8241 (mt-10) outliers start: 53 outliers final: 36 residues processed: 336 average time/residue: 0.1618 time to fit residues: 85.3110 Evaluate side-chains 352 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 308 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 44 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 284 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 chunk 42 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 ASN B 580 ASN C 580 ASN D 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.155515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117767 restraints weight = 25319.498| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.07 r_work: 0.3248 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23816 Z= 0.181 Angle : 0.515 6.824 32300 Z= 0.269 Chirality : 0.040 0.131 3684 Planarity : 0.004 0.036 3956 Dihedral : 8.000 64.988 4076 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.82 % Allowed : 13.43 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.16), residues: 2904 helix: 1.30 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.31 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 437 TYR 0.014 0.001 TYR C 209 PHE 0.014 0.001 PHE B 641 TRP 0.012 0.002 TRP C 514 HIS 0.004 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00459 (23812) covalent geometry : angle 0.51269 (32292) SS BOND : bond 0.01153 ( 4) SS BOND : angle 3.23883 ( 8) hydrogen bonds : bond 0.04571 ( 1240) hydrogen bonds : angle 2.98513 ( 3660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 320 time to evaluate : 0.866 Fit side-chains REVERT: A 262 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7192 (mt0) REVERT: A 339 THR cc_start: 0.8795 (t) cc_final: 0.8521 (m) REVERT: A 441 MET cc_start: 0.8411 (mmm) cc_final: 0.8099 (mmp) REVERT: A 689 LYS cc_start: 0.8686 (ptmt) cc_final: 0.8386 (ptmt) REVERT: A 696 ASN cc_start: 0.7968 (t0) cc_final: 0.7676 (t0) REVERT: A 758 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8229 (ptt-90) REVERT: A 881 GLU cc_start: 0.8792 (tt0) cc_final: 0.8235 (mt-10) REVERT: B 262 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7194 (mt0) REVERT: B 339 THR cc_start: 0.8786 (t) cc_final: 0.8516 (m) REVERT: B 441 MET cc_start: 0.8407 (mmm) cc_final: 0.8097 (mmp) REVERT: B 643 MET cc_start: 0.8284 (mtt) cc_final: 0.8050 (mtt) REVERT: B 689 LYS cc_start: 0.8689 (ptmt) cc_final: 0.8387 (ptmt) REVERT: B 696 ASN cc_start: 0.7964 (t0) cc_final: 0.7672 (t0) REVERT: B 758 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8234 (ptt-90) REVERT: B 881 GLU cc_start: 0.8793 (tt0) cc_final: 0.8234 (mt-10) REVERT: C 262 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7191 (mt0) REVERT: C 339 THR cc_start: 0.8798 (t) cc_final: 0.8525 (m) REVERT: C 441 MET cc_start: 0.8408 (mmm) cc_final: 0.8098 (mmp) REVERT: C 643 MET cc_start: 0.8285 (mtt) cc_final: 0.8053 (mtt) REVERT: C 689 LYS cc_start: 0.8684 (ptmt) cc_final: 0.8375 (ptmt) REVERT: C 696 ASN cc_start: 0.7981 (t0) cc_final: 0.7691 (t0) REVERT: C 758 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8240 (ptt-90) REVERT: C 881 GLU cc_start: 0.8803 (tt0) cc_final: 0.8248 (mt-10) REVERT: D 262 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7186 (mt0) REVERT: D 339 THR cc_start: 0.8796 (t) cc_final: 0.8523 (m) REVERT: D 441 MET cc_start: 0.8401 (mmm) cc_final: 0.8091 (mmp) REVERT: D 643 MET cc_start: 0.8282 (mtt) cc_final: 0.8047 (mtt) REVERT: D 689 LYS cc_start: 0.8693 (ptmt) cc_final: 0.8389 (ptmt) REVERT: D 696 ASN cc_start: 0.7974 (t0) cc_final: 0.7685 (t0) REVERT: D 758 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8242 (ptt-90) REVERT: D 881 GLU cc_start: 0.8794 (tt0) cc_final: 0.8239 (mt-10) outliers start: 41 outliers final: 28 residues processed: 340 average time/residue: 0.1585 time to fit residues: 84.4285 Evaluate side-chains 348 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 312 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 758 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 112 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 chunk 249 optimal weight: 9.9990 chunk 216 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 279 optimal weight: 1.9990 chunk 229 optimal weight: 0.0020 chunk 134 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN B 316 ASN C 316 ASN D 316 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.158885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121355 restraints weight = 25161.916| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.06 r_work: 0.3300 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23816 Z= 0.098 Angle : 0.445 7.282 32300 Z= 0.237 Chirality : 0.037 0.130 3684 Planarity : 0.003 0.035 3956 Dihedral : 7.530 60.955 4076 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.55 % Allowed : 13.87 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.16), residues: 2904 helix: 1.58 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.11 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 437 TYR 0.010 0.001 TYR C 209 PHE 0.013 0.001 PHE C 641 TRP 0.014 0.001 TRP C 514 HIS 0.002 0.000 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00233 (23812) covalent geometry : angle 0.44211 (32292) SS BOND : bond 0.01051 ( 4) SS BOND : angle 3.23957 ( 8) hydrogen bonds : bond 0.03407 ( 1240) hydrogen bonds : angle 2.84156 ( 3660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 306 time to evaluate : 1.454 Fit side-chains REVERT: A 262 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7003 (mt0) REVERT: A 339 THR cc_start: 0.8741 (t) cc_final: 0.8470 (m) REVERT: A 441 MET cc_start: 0.8341 (mmm) cc_final: 0.8036 (mmp) REVERT: A 643 MET cc_start: 0.8158 (mtt) cc_final: 0.7846 (mtt) REVERT: A 689 LYS cc_start: 0.8563 (ptmt) cc_final: 0.8265 (ptmt) REVERT: A 696 ASN cc_start: 0.7876 (t0) cc_final: 0.7593 (t0) REVERT: A 758 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8208 (ptt-90) REVERT: A 881 GLU cc_start: 0.8625 (tt0) cc_final: 0.8142 (mt-10) REVERT: B 262 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7116 (mt0) REVERT: B 339 THR cc_start: 0.8726 (t) cc_final: 0.8457 (m) REVERT: B 441 MET cc_start: 0.8338 (mmm) cc_final: 0.8032 (mmp) REVERT: B 689 LYS cc_start: 0.8575 (ptmt) cc_final: 0.8279 (ptmt) REVERT: B 696 ASN cc_start: 0.7867 (t0) cc_final: 0.7584 (t0) REVERT: B 758 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8209 (ptt-90) REVERT: B 881 GLU cc_start: 0.8628 (tt0) cc_final: 0.8214 (mt-10) REVERT: C 262 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.7001 (mt0) REVERT: C 339 THR cc_start: 0.8734 (t) cc_final: 0.8459 (m) REVERT: C 441 MET cc_start: 0.8336 (mmm) cc_final: 0.8032 (mmp) REVERT: C 689 LYS cc_start: 0.8564 (ptmt) cc_final: 0.8264 (ptmt) REVERT: C 696 ASN cc_start: 0.7875 (t0) cc_final: 0.7594 (t0) REVERT: C 758 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8242 (ptt-90) REVERT: C 881 GLU cc_start: 0.8633 (tt0) cc_final: 0.8218 (mt-10) REVERT: D 262 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.7010 (mt0) REVERT: D 339 THR cc_start: 0.8735 (t) cc_final: 0.8466 (m) REVERT: D 441 MET cc_start: 0.8331 (mmm) cc_final: 0.8027 (mmp) REVERT: D 689 LYS cc_start: 0.8568 (ptmt) cc_final: 0.8271 (ptmt) REVERT: D 696 ASN cc_start: 0.7874 (t0) cc_final: 0.7592 (t0) REVERT: D 758 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8218 (ptt-90) REVERT: D 881 GLU cc_start: 0.8625 (tt0) cc_final: 0.8210 (mt-10) outliers start: 35 outliers final: 24 residues processed: 318 average time/residue: 0.1584 time to fit residues: 78.5391 Evaluate side-chains 334 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 758 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 276 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.156751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119757 restraints weight = 24934.803| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.03 r_work: 0.3284 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23816 Z= 0.121 Angle : 0.463 7.094 32300 Z= 0.245 Chirality : 0.038 0.129 3684 Planarity : 0.004 0.037 3956 Dihedral : 7.555 61.221 4076 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.60 % Allowed : 13.83 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 2904 helix: 1.57 (0.12), residues: 1896 sheet: None (None), residues: 0 loop : -1.10 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 437 TYR 0.012 0.001 TYR B 209 PHE 0.024 0.001 PHE B 641 TRP 0.013 0.001 TRP D 514 HIS 0.002 0.000 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00300 (23812) covalent geometry : angle 0.45981 (32292) SS BOND : bond 0.01068 ( 4) SS BOND : angle 3.24805 ( 8) hydrogen bonds : bond 0.03727 ( 1240) hydrogen bonds : angle 2.86882 ( 3660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6000.30 seconds wall clock time: 102 minutes 52.72 seconds (6172.72 seconds total)