Starting phenix.real_space_refine on Sun Sep 13 13:27:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uza_20954/09_2026/6uza_20954.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uza_20954/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6uza_20954/09_2026/6uza_20954.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uza_20954/09_2026/6uza_20954.cif" model { file = "/net/cci-nas-00/data/ceres_data/6uza_20954/09_2026/6uza_20954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uza_20954/09_2026/6uza_20954.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uza_20954/09_2026/6uza_20954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uza_20954/09_2026/6uza_20954.map" } 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): 0.18s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 4.93, 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: 2.18 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.61 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: 3.83 Time building geometry restraints manager: 2.77 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: 13600 30.12 - 60.24: 464 60.24 - 90.36: 28 90.36 - 120.48: 0 120.48 - 150.60: 4 Dihedral angle restraints: 14096 sinusoidal: 5448 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 14093 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.990 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 : 14.951 150.597 8476 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/Z covalent geometry : bond 0.00831 / 0.41 (23812) covalent geometry : angle 1.05374 / 0.53 (32292) SS BOND : bond 0.00737 / 0.34 ( 4) SS BOND : angle 2.39416 / 1.37 ( 8) hydrogen bonds : bond 0.13583 / 9.03 ( 1240) hydrogen bonds : angle 5.37542 / 3.79 ( 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 : 0.908 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: 0.1802 time to fit residues: 98.6524 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 : 0.810 ------------------------------------------------------------------------------- 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... 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 = 0.159423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121806 restraints weight = 25119.936| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.11 r_work: 0.3292 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23816 Z= 0.114 Angle : 0.487 6.247 32300 Z= 0.260 Chirality : 0.037 0.123 3684 Planarity : 0.004 0.045 3956 Dihedral : 8.951 104.211 3540 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.71 % Allowed : 8.87 % Favored : 90.43 % 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: -1.57 (0.15), residues: 2904 helix: -0.47 (0.11), residues: 1932 sheet: None (None), residues: 0 loop : -2.06 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 437 TYR 0.009 0.001 TYR D 209 PHE 0.009 0.001 PHE B 548 TRP 0.023 0.001 TRP D 514 HIS 0.002 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (23812) covalent geometry : angle 0.48444 / 0.26 (32292) SS BOND : bond 0.01041 / 0.48 ( 4) SS BOND : angle 3.49156 / 2.03 ( 8) hydrogen bonds : bond 0.04017 / 2.73 ( 1240) hydrogen bonds : angle 3.41846 / 2.39 ( 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 340 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 324 time to evaluate : 0.851 Fit side-chains REVERT: A 116 LYS cc_start: 0.7834 (ttpt) cc_final: 0.7605 (ttpt) REVERT: A 262 GLN cc_start: 0.7914 (tt0) cc_final: 0.7475 (mt0) REVERT: A 441 MET cc_start: 0.8341 (mmm) cc_final: 0.8051 (mmp) REVERT: A 689 LYS cc_start: 0.8612 (ptmt) cc_final: 0.8316 (ptmt) REVERT: A 696 ASN cc_start: 0.8176 (t0) cc_final: 0.7844 (t0) REVERT: A 881 GLU cc_start: 0.8749 (tt0) cc_final: 0.8169 (mt-10) REVERT: B 116 LYS cc_start: 0.7771 (ttpt) cc_final: 0.7541 (ttpt) REVERT: B 262 GLN cc_start: 0.7926 (tt0) cc_final: 0.7485 (mt0) REVERT: B 441 MET cc_start: 0.8348 (mmm) cc_final: 0.8064 (mmp) REVERT: B 689 LYS cc_start: 0.8610 (ptmt) cc_final: 0.8311 (ptmt) REVERT: B 696 ASN cc_start: 0.8156 (t0) cc_final: 0.7824 (t0) REVERT: B 881 GLU cc_start: 0.8756 (tt0) cc_final: 0.8176 (mt-10) REVERT: C 116 LYS cc_start: 0.7762 (ttpt) cc_final: 0.7533 (ttpt) REVERT: C 262 GLN cc_start: 0.7935 (tt0) cc_final: 0.7496 (mt0) REVERT: C 441 MET cc_start: 0.8342 (mmm) cc_final: 0.8055 (mmp) REVERT: C 689 LYS cc_start: 0.8603 (ptmt) cc_final: 0.8301 (ptmt) REVERT: C 696 ASN cc_start: 0.8166 (t0) cc_final: 0.7835 (t0) REVERT: C 881 GLU cc_start: 0.8758 (tt0) cc_final: 0.8178 (mt-10) REVERT: D 116 LYS cc_start: 0.7774 (ttpt) cc_final: 0.7543 (ttpt) REVERT: D 262 GLN cc_start: 0.7932 (tt0) cc_final: 0.7492 (mt0) REVERT: D 441 MET cc_start: 0.8334 (mmm) cc_final: 0.8049 (mmp) REVERT: D 689 LYS cc_start: 0.8609 (ptmt) cc_final: 0.8311 (ptmt) REVERT: D 696 ASN cc_start: 0.8169 (t0) cc_final: 0.7838 (t0) REVERT: D 881 GLU cc_start: 0.8756 (tt0) cc_final: 0.8178 (mt-10) outliers start: 16 outliers final: 12 residues processed: 332 average time/residue: 0.1633 time to fit residues: 84.4239 Evaluate side-chains 316 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 304 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 720 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 310 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 720 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 310 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: 0.9990 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: 2.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 251 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3884 r_free = 0.3884 target = 0.154053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116289 restraints weight = 25324.300| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.08 r_work: 0.3229 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23816 Z= 0.214 Angle : 0.559 6.974 32300 Z= 0.292 Chirality : 0.040 0.143 3684 Planarity : 0.004 0.038 3956 Dihedral : 8.874 85.804 3540 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 : 1.99 % Allowed : 10.24 % Favored : 87.77 % 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: -0.89 (0.15), residues: 2904 helix: 0.13 (0.12), residues: 1924 sheet: None (None), residues: 0 loop : -1.96 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 861 TYR 0.013 0.001 TYR A 209 PHE 0.014 0.002 PHE C 407 TRP 0.023 0.002 TRP A 514 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.21 (23812) covalent geometry : angle 0.55587 / 0.29 (32292) SS BOND : bond 0.01208 / 0.56 ( 4) SS BOND : angle 3.54796 / 2.06 ( 8) hydrogen bonds : bond 0.05102 / 3.48 ( 1240) hydrogen bonds : angle 3.30754 / 2.31 ( 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 365 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 320 time to evaluate : 0.823 Fit side-chains REVERT: A 262 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: A 441 MET cc_start: 0.8459 (mmm) cc_final: 0.8169 (mmp) REVERT: A 507 TRP cc_start: 0.8489 (t-100) cc_final: 0.8270 (t-100) REVERT: A 689 LYS cc_start: 0.8676 (ptmt) cc_final: 0.8381 (ptmt) REVERT: A 696 ASN cc_start: 0.8151 (t0) cc_final: 0.7814 (t0) REVERT: A 758 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8084 (ptt-90) REVERT: A 881 GLU cc_start: 0.8810 (tt0) cc_final: 0.8220 (mt-10) REVERT: B 262 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: B 441 MET cc_start: 0.8462 (mmm) cc_final: 0.8173 (mmp) REVERT: B 507 TRP cc_start: 0.8489 (t-100) cc_final: 0.8272 (t-100) REVERT: B 689 LYS cc_start: 0.8675 (ptmt) cc_final: 0.8375 (ptmt) REVERT: B 696 ASN cc_start: 0.8153 (t0) cc_final: 0.7816 (t0) REVERT: B 758 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8078 (ptt-90) REVERT: B 881 GLU cc_start: 0.8803 (tt0) cc_final: 0.8214 (mt-10) REVERT: C 262 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: C 441 MET cc_start: 0.8461 (mmm) cc_final: 0.8173 (mmp) REVERT: C 507 TRP cc_start: 0.8493 (t-100) cc_final: 0.8274 (t-100) REVERT: C 689 LYS cc_start: 0.8671 (ptmt) cc_final: 0.8371 (ptmt) REVERT: C 696 ASN cc_start: 0.8173 (t0) cc_final: 0.7838 (t0) REVERT: C 758 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8074 (ptt-90) REVERT: C 881 GLU cc_start: 0.8807 (tt0) cc_final: 0.8215 (mt-10) REVERT: D 262 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: D 441 MET cc_start: 0.8459 (mmm) cc_final: 0.8170 (mmp) REVERT: D 507 TRP cc_start: 0.8484 (t-100) cc_final: 0.8266 (t-100) REVERT: D 689 LYS cc_start: 0.8683 (ptmt) cc_final: 0.8386 (ptmt) REVERT: D 696 ASN cc_start: 0.8155 (t0) cc_final: 0.7821 (t0) REVERT: D 758 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8090 (ptt-90) REVERT: D 881 GLU cc_start: 0.8801 (tt0) cc_final: 0.8210 (mt-10) outliers start: 45 outliers final: 20 residues processed: 344 average time/residue: 0.1586 time to fit residues: 84.7155 Evaluate side-chains 340 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 312 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 A residue 758 ARG 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 B residue 758 ARG 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 C residue 758 ARG 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 Chi-restraints excluded: chain D residue 758 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 125 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 287 optimal weight: 0.7980 chunk 253 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 182 optimal weight: 0.9980 chunk 257 optimal weight: 0.8980 chunk 219 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 GLN A 316 ASN B 230 GLN B 316 ASN C 230 GLN C 316 ASN D 316 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.159088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.121549 restraints weight = 24987.814| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.10 r_work: 0.3281 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23816 Z= 0.104 Angle : 0.453 6.056 32300 Z= 0.241 Chirality : 0.037 0.131 3684 Planarity : 0.003 0.037 3956 Dihedral : 8.304 75.125 3540 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.42 % Allowed : 11.70 % Favored : 86.88 % 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: -0.13 (0.16), residues: 2904 helix: 0.70 (0.12), residues: 1920 sheet: None (None), residues: 0 loop : -1.60 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 437 TYR 0.006 0.001 TYR B 209 PHE 0.010 0.001 PHE B 548 TRP 0.018 0.001 TRP B 514 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.10 (23812) covalent geometry : angle 0.45012 / 0.24 (32292) SS BOND : bond 0.01072 / 0.49 ( 4) SS BOND : angle 3.43556 / 2.00 ( 8) hydrogen bonds : bond 0.03528 / 2.41 ( 1240) hydrogen bonds : angle 2.98228 / 2.07 ( 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 328 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 296 time to evaluate : 0.828 Fit side-chains REVERT: A 262 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7435 (mt0) REVERT: A 339 THR cc_start: 0.8736 (t) cc_final: 0.8442 (m) REVERT: A 441 MET cc_start: 0.8313 (mmm) cc_final: 0.8022 (mmp) REVERT: A 689 LYS cc_start: 0.8576 (ptmt) cc_final: 0.8296 (ptmt) REVERT: A 696 ASN cc_start: 0.7942 (t0) cc_final: 0.7644 (t0) REVERT: A 881 GLU cc_start: 0.8698 (tt0) cc_final: 0.8180 (mt-10) REVERT: B 262 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7454 (mt0) REVERT: B 339 THR cc_start: 0.8726 (t) cc_final: 0.8430 (m) REVERT: B 441 MET cc_start: 0.8323 (mmm) cc_final: 0.8035 (mmp) REVERT: B 689 LYS cc_start: 0.8583 (ptmt) cc_final: 0.8297 (ptmt) REVERT: B 696 ASN cc_start: 0.7933 (t0) cc_final: 0.7634 (t0) REVERT: B 881 GLU cc_start: 0.8699 (tt0) cc_final: 0.8181 (mt-10) REVERT: C 262 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7452 (mt0) REVERT: C 339 THR cc_start: 0.8736 (t) cc_final: 0.8440 (m) REVERT: C 441 MET cc_start: 0.8324 (mmm) cc_final: 0.8037 (mmp) REVERT: C 689 LYS cc_start: 0.8576 (ptmt) cc_final: 0.8295 (ptmt) REVERT: C 696 ASN cc_start: 0.7952 (t0) cc_final: 0.7653 (t0) REVERT: C 881 GLU cc_start: 0.8704 (tt0) cc_final: 0.8184 (mt-10) REVERT: D 262 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7436 (mt0) REVERT: D 339 THR cc_start: 0.8727 (t) cc_final: 0.8436 (m) REVERT: D 441 MET cc_start: 0.8318 (mmm) cc_final: 0.8028 (mmp) REVERT: D 689 LYS cc_start: 0.8574 (ptmt) cc_final: 0.8291 (ptmt) REVERT: D 696 ASN cc_start: 0.7950 (t0) cc_final: 0.7651 (t0) REVERT: D 881 GLU cc_start: 0.8699 (tt0) cc_final: 0.8183 (mt-10) outliers start: 32 outliers final: 24 residues processed: 304 average time/residue: 0.1510 time to fit residues: 72.5477 Evaluate side-chains 324 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 296 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 629 ARG Chi-restraints excluded: chain A residue 720 LEU 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 629 ARG Chi-restraints excluded: chain B residue 720 LEU 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 629 ARG Chi-restraints excluded: chain C residue 720 LEU 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 629 ARG Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 238 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 252 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 223 optimal weight: 0.0670 chunk 179 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 338 ASN D 230 GLN D 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.156549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118925 restraints weight = 24982.178| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.06 r_work: 0.3265 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23816 Z= 0.142 Angle : 0.479 6.489 32300 Z= 0.252 Chirality : 0.038 0.133 3684 Planarity : 0.004 0.038 3956 Dihedral : 8.308 72.632 3540 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.13 % Allowed : 12.23 % Favored : 85.64 % 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: 0.09 (0.16), residues: 2904 helix: 0.87 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.48 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 437 TYR 0.009 0.001 TYR D 209 PHE 0.009 0.001 PHE A 548 TRP 0.013 0.001 TRP C 514 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.14 (23812) covalent geometry : angle 0.47566 / 0.25 (32292) SS BOND : bond 0.01109 / 0.51 ( 4) SS BOND : angle 3.44652 / 2.01 ( 8) hydrogen bonds : bond 0.04060 / 2.77 ( 1240) hydrogen bonds : angle 2.97535 / 2.07 ( 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 352 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 304 time to evaluate : 0.646 Fit side-chains REVERT: A 262 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7459 (mt0) REVERT: A 339 THR cc_start: 0.8760 (t) cc_final: 0.8464 (m) REVERT: A 437 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.7856 (ttm-80) REVERT: A 441 MET cc_start: 0.8322 (mmm) cc_final: 0.8022 (mmp) REVERT: A 689 LYS cc_start: 0.8600 (ptmt) cc_final: 0.8307 (ptmt) REVERT: A 696 ASN cc_start: 0.7920 (t0) cc_final: 0.7623 (t0) REVERT: A 881 GLU cc_start: 0.8734 (tt0) cc_final: 0.8186 (mt-10) REVERT: B 262 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7468 (mt0) REVERT: B 339 THR cc_start: 0.8743 (t) cc_final: 0.8453 (m) REVERT: B 437 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.7864 (ttm-80) REVERT: B 441 MET cc_start: 0.8329 (mmm) cc_final: 0.8031 (mmp) REVERT: B 689 LYS cc_start: 0.8603 (ptmt) cc_final: 0.8310 (ptmt) REVERT: B 696 ASN cc_start: 0.7914 (t0) cc_final: 0.7617 (t0) REVERT: B 881 GLU cc_start: 0.8731 (tt0) cc_final: 0.8183 (mt-10) REVERT: C 262 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7469 (mt0) REVERT: C 339 THR cc_start: 0.8760 (t) cc_final: 0.8463 (m) REVERT: C 437 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.7869 (ttm-80) REVERT: C 441 MET cc_start: 0.8332 (mmm) cc_final: 0.8034 (mmp) REVERT: C 689 LYS cc_start: 0.8598 (ptmt) cc_final: 0.8299 (ptmt) REVERT: C 696 ASN cc_start: 0.7935 (t0) cc_final: 0.7638 (t0) REVERT: C 881 GLU cc_start: 0.8740 (tt0) cc_final: 0.8191 (mt-10) REVERT: D 262 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7467 (mt0) REVERT: D 339 THR cc_start: 0.8751 (t) cc_final: 0.8464 (m) REVERT: D 437 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.7882 (ttm-80) REVERT: D 441 MET cc_start: 0.8326 (mmm) cc_final: 0.8027 (mmp) REVERT: D 689 LYS cc_start: 0.8605 (ptmt) cc_final: 0.8308 (ptmt) REVERT: D 696 ASN cc_start: 0.7928 (t0) cc_final: 0.7630 (t0) REVERT: D 881 GLU cc_start: 0.8728 (tt0) cc_final: 0.8181 (mt-10) outliers start: 48 outliers final: 36 residues processed: 328 average time/residue: 0.1475 time to fit residues: 76.7789 Evaluate side-chains 340 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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 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 537 PHE 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 537 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 274 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.0670 chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 156 optimal weight: 0.3980 chunk 212 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 overall best weight: 1.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3901 r_free = 0.3901 target = 0.155711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117890 restraints weight = 25161.679| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.07 r_work: 0.3251 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23816 Z= 0.161 Angle : 0.496 6.575 32300 Z= 0.260 Chirality : 0.039 0.133 3684 Planarity : 0.004 0.036 3956 Dihedral : 8.325 71.925 3540 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.39 % Allowed : 12.68 % Favored : 84.93 % 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: 0.18 (0.16), residues: 2904 helix: 0.93 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.43 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 861 TYR 0.009 0.001 TYR D 209 PHE 0.010 0.001 PHE B 377 TRP 0.012 0.001 TRP B 514 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.16 (23812) covalent geometry : angle 0.49262 / 0.26 (32292) SS BOND : bond 0.01144 / 0.53 ( 4) SS BOND : angle 3.44483 / 2.00 ( 8) hydrogen bonds : bond 0.04341 / 2.96 ( 1240) hydrogen bonds : angle 3.00025 / 2.09 ( 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 375 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 321 time to evaluate : 1.225 Fit side-chains REVERT: A 262 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7504 (mt0) REVERT: A 339 THR cc_start: 0.8799 (t) cc_final: 0.8502 (m) REVERT: A 441 MET cc_start: 0.8380 (mmm) cc_final: 0.8073 (mmp) REVERT: A 507 TRP cc_start: 0.8469 (t-100) cc_final: 0.8251 (t-100) REVERT: A 689 LYS cc_start: 0.8661 (ptmt) cc_final: 0.8361 (ptmt) REVERT: A 696 ASN cc_start: 0.7916 (t0) cc_final: 0.7623 (t0) REVERT: A 758 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8120 (ptt-90) REVERT: A 881 GLU cc_start: 0.8775 (tt0) cc_final: 0.8230 (mt-10) REVERT: B 262 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: B 339 THR cc_start: 0.8798 (t) cc_final: 0.8496 (m) REVERT: B 441 MET cc_start: 0.8383 (mmm) cc_final: 0.8081 (mmp) REVERT: B 507 TRP cc_start: 0.8463 (t-100) cc_final: 0.8246 (t-100) REVERT: B 689 LYS cc_start: 0.8673 (ptmt) cc_final: 0.8372 (ptmt) REVERT: B 696 ASN cc_start: 0.7915 (t0) cc_final: 0.7620 (t0) REVERT: B 758 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8111 (ptt-90) REVERT: B 881 GLU cc_start: 0.8776 (tt0) cc_final: 0.8232 (mt-10) REVERT: C 262 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7505 (mt0) REVERT: C 339 THR cc_start: 0.8805 (t) cc_final: 0.8506 (m) REVERT: C 441 MET cc_start: 0.8383 (mmm) cc_final: 0.8082 (mmp) REVERT: C 507 TRP cc_start: 0.8474 (t-100) cc_final: 0.8256 (t-100) REVERT: C 689 LYS cc_start: 0.8669 (ptmt) cc_final: 0.8362 (ptmt) REVERT: C 696 ASN cc_start: 0.7936 (t0) cc_final: 0.7642 (t0) REVERT: C 758 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8107 (ptt-90) REVERT: C 881 GLU cc_start: 0.8782 (tt0) cc_final: 0.8237 (mt-10) REVERT: D 262 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: D 339 THR cc_start: 0.8796 (t) cc_final: 0.8499 (m) REVERT: D 441 MET cc_start: 0.8376 (mmm) cc_final: 0.8073 (mmp) REVERT: D 507 TRP cc_start: 0.8466 (t-100) cc_final: 0.8247 (t-100) REVERT: D 689 LYS cc_start: 0.8671 (ptmt) cc_final: 0.8368 (ptmt) REVERT: D 696 ASN cc_start: 0.7920 (t0) cc_final: 0.7626 (t0) REVERT: D 758 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8108 (ptt-90) REVERT: D 881 GLU cc_start: 0.8771 (tt0) cc_final: 0.8226 (mt-10) outliers start: 54 outliers final: 32 residues processed: 345 average time/residue: 0.1737 time to fit residues: 93.4499 Evaluate side-chains 353 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 313 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 435 ILE 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 435 ILE 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 435 ILE 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 435 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 100 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 68 optimal weight: 0.0570 chunk 67 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.0670 chunk 25 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN A 580 ASN B 316 ASN B 580 ASN C 316 ASN C 580 ASN D 316 ASN D 580 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.159531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122038 restraints weight = 25050.948| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.10 r_work: 0.3287 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23816 Z= 0.098 Angle : 0.441 6.547 32300 Z= 0.235 Chirality : 0.037 0.132 3684 Planarity : 0.003 0.036 3956 Dihedral : 7.716 67.659 3540 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.77 % Allowed : 13.83 % Favored : 84.40 % 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: 0.57 (0.16), residues: 2904 helix: 1.24 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.28 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 437 TYR 0.006 0.001 TYR D 579 PHE 0.007 0.001 PHE A 186 TRP 0.013 0.001 TRP A 514 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (23812) covalent geometry : angle 0.43741 / 0.23 (32292) SS BOND : bond 0.01035 / 0.48 ( 4) SS BOND : angle 3.37500 / 1.97 ( 8) hydrogen bonds : bond 0.03406 / 2.32 ( 1240) hydrogen bonds : angle 2.84925 / 1.97 ( 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 340 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 0.848 Fit side-chains REVERT: A 262 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7272 (mt0) REVERT: A 339 THR cc_start: 0.8743 (t) cc_final: 0.8459 (m) REVERT: A 437 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.8096 (ttm110) REVERT: A 441 MET cc_start: 0.8305 (mmm) cc_final: 0.8003 (mmp) REVERT: A 507 TRP cc_start: 0.8451 (t-100) cc_final: 0.8231 (t-100) REVERT: A 689 LYS cc_start: 0.8581 (ptmt) cc_final: 0.8252 (ptmt) REVERT: A 696 ASN cc_start: 0.7840 (t0) cc_final: 0.7567 (t0) REVERT: A 881 GLU cc_start: 0.8711 (tt0) cc_final: 0.8246 (mt-10) REVERT: B 262 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7280 (mt0) REVERT: B 339 THR cc_start: 0.8733 (t) cc_final: 0.8458 (m) REVERT: B 437 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.8107 (ttm110) REVERT: B 441 MET cc_start: 0.8315 (mmm) cc_final: 0.8018 (mmp) REVERT: B 507 TRP cc_start: 0.8442 (t-100) cc_final: 0.8223 (t-100) REVERT: B 689 LYS cc_start: 0.8587 (ptmt) cc_final: 0.8257 (ptmt) REVERT: B 696 ASN cc_start: 0.7830 (t0) cc_final: 0.7552 (t0) REVERT: B 881 GLU cc_start: 0.8715 (tt0) cc_final: 0.8252 (mt-10) REVERT: C 262 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7283 (mt0) REVERT: C 339 THR cc_start: 0.8749 (t) cc_final: 0.8465 (m) REVERT: C 437 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.8107 (ttm110) REVERT: C 441 MET cc_start: 0.8310 (mmm) cc_final: 0.8013 (mmp) REVERT: C 507 TRP cc_start: 0.8455 (t-100) cc_final: 0.8235 (t-100) REVERT: C 689 LYS cc_start: 0.8585 (ptmt) cc_final: 0.8253 (ptmt) REVERT: C 696 ASN cc_start: 0.7851 (t0) cc_final: 0.7575 (t0) REVERT: C 881 GLU cc_start: 0.8715 (tt0) cc_final: 0.8250 (mt-10) REVERT: D 262 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7288 (mt0) REVERT: D 339 THR cc_start: 0.8734 (t) cc_final: 0.8461 (m) REVERT: D 437 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8111 (ttm110) REVERT: D 441 MET cc_start: 0.8301 (mmm) cc_final: 0.8001 (mmp) REVERT: D 507 TRP cc_start: 0.8449 (t-100) cc_final: 0.8228 (t-100) REVERT: D 689 LYS cc_start: 0.8586 (ptmt) cc_final: 0.8258 (ptmt) REVERT: D 696 ASN cc_start: 0.7840 (t0) cc_final: 0.7566 (t0) REVERT: D 881 GLU cc_start: 0.8706 (tt0) cc_final: 0.8243 (mt-10) outliers start: 40 outliers final: 32 residues processed: 312 average time/residue: 0.1578 time to fit residues: 78.6379 Evaluate side-chains 332 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 296 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- 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: 0.4980 chunk 247 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 246 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 213 optimal weight: 0.9980 chunk 277 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3931 r_free = 0.3931 target = 0.158407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.120678 restraints weight = 24940.716| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.06 r_work: 0.3287 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23816 Z= 0.108 Angle : 0.446 6.730 32300 Z= 0.237 Chirality : 0.037 0.131 3684 Planarity : 0.003 0.036 3956 Dihedral : 7.550 65.771 3540 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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: 0.78 (0.16), residues: 2904 helix: 1.38 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.16 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 437 TYR 0.009 0.001 TYR D 209 PHE 0.007 0.001 PHE A 377 TRP 0.012 0.001 TRP B 514 HIS 0.002 0.000 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (23812) covalent geometry : angle 0.44303 / 0.24 (32292) SS BOND : bond 0.01060 / 0.49 ( 4) SS BOND : angle 3.37273 / 1.96 ( 8) hydrogen bonds : bond 0.03560 / 2.43 ( 1240) hydrogen bonds : angle 2.83356 / 1.96 ( 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 336 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 300 time to evaluate : 0.888 Fit side-chains REVERT: A 262 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7248 (mt0) REVERT: A 339 THR cc_start: 0.8761 (t) cc_final: 0.8489 (m) REVERT: A 437 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.7841 (ttm-80) REVERT: A 441 MET cc_start: 0.8377 (mmm) cc_final: 0.8059 (mmp) REVERT: A 507 TRP cc_start: 0.8475 (t-100) cc_final: 0.8267 (t-100) REVERT: A 643 MET cc_start: 0.8196 (mtt) cc_final: 0.7885 (mtt) REVERT: A 689 LYS cc_start: 0.8621 (ptmt) cc_final: 0.8293 (ptmt) REVERT: A 696 ASN cc_start: 0.7864 (t0) cc_final: 0.7595 (t0) REVERT: A 881 GLU cc_start: 0.8777 (tt0) cc_final: 0.8316 (mt-10) REVERT: B 262 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7254 (mt0) REVERT: B 339 THR cc_start: 0.8750 (t) cc_final: 0.8479 (m) REVERT: B 437 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.7850 (ttm-80) REVERT: B 441 MET cc_start: 0.8385 (mmm) cc_final: 0.8071 (mmp) REVERT: B 507 TRP cc_start: 0.8467 (t-100) cc_final: 0.8261 (t-100) REVERT: B 643 MET cc_start: 0.8203 (mtt) cc_final: 0.7890 (mtt) REVERT: B 689 LYS cc_start: 0.8631 (ptmt) cc_final: 0.8300 (ptmt) REVERT: B 696 ASN cc_start: 0.7853 (t0) cc_final: 0.7582 (t0) REVERT: B 881 GLU cc_start: 0.8783 (tt0) cc_final: 0.8324 (mt-10) REVERT: C 262 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7258 (mt0) REVERT: C 339 THR cc_start: 0.8764 (t) cc_final: 0.8488 (m) REVERT: C 437 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.7850 (ttm-80) REVERT: C 441 MET cc_start: 0.8380 (mmm) cc_final: 0.8064 (mmp) REVERT: C 507 TRP cc_start: 0.8478 (t-100) cc_final: 0.8271 (t-100) REVERT: C 643 MET cc_start: 0.8197 (mtt) cc_final: 0.7885 (mtt) REVERT: C 689 LYS cc_start: 0.8625 (ptmt) cc_final: 0.8292 (ptmt) REVERT: C 696 ASN cc_start: 0.7869 (t0) cc_final: 0.7600 (t0) REVERT: C 881 GLU cc_start: 0.8789 (tt0) cc_final: 0.8328 (mt-10) REVERT: D 262 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7244 (mt0) REVERT: D 339 THR cc_start: 0.8757 (t) cc_final: 0.8486 (m) REVERT: D 437 ARG cc_start: 0.8429 (ttm-80) cc_final: 0.7850 (ttm-80) REVERT: D 441 MET cc_start: 0.8369 (mmm) cc_final: 0.8050 (mmp) REVERT: D 507 TRP cc_start: 0.8477 (t-100) cc_final: 0.8269 (t-100) REVERT: D 643 MET cc_start: 0.8206 (mtt) cc_final: 0.7894 (mtt) REVERT: D 689 LYS cc_start: 0.8628 (ptmt) cc_final: 0.8298 (ptmt) REVERT: D 696 ASN cc_start: 0.7862 (t0) cc_final: 0.7595 (t0) REVERT: D 881 GLU cc_start: 0.8776 (tt0) cc_final: 0.8316 (mt-10) outliers start: 36 outliers final: 28 residues processed: 312 average time/residue: 0.1609 time to fit residues: 80.3171 Evaluate side-chains 332 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 537 PHE Chi-restraints excluded: chain A residue 584 ILE 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 537 PHE Chi-restraints excluded: chain B residue 584 ILE 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 537 PHE Chi-restraints excluded: chain C residue 584 ILE 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 537 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 720 LEU 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: 0.6980 chunk 284 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 185 optimal weight: 0.0000 chunk 92 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3953 r_free = 0.3953 target = 0.160179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122775 restraints weight = 24921.085| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.08 r_work: 0.3299 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 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 : 0.002 0.039 23816 Z= 0.095 Angle : 0.435 6.465 32300 Z= 0.232 Chirality : 0.037 0.131 3684 Planarity : 0.003 0.035 3956 Dihedral : 7.263 63.215 3540 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.42 % Allowed : 14.01 % 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: 1.56 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.09 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 437 TYR 0.009 0.001 TYR A 209 PHE 0.016 0.001 PHE C 407 TRP 0.012 0.001 TRP B 514 HIS 0.002 0.000 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (23812) covalent geometry : angle 0.43193 / 0.23 (32292) SS BOND : bond 0.01004 / 0.46 ( 4) SS BOND : angle 3.36898 / 1.96 ( 8) hydrogen bonds : bond 0.03282 / 2.24 ( 1240) hydrogen bonds : angle 2.78302 / 1.93 ( 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 328 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 296 time to evaluate : 0.825 Fit side-chains REVERT: A 262 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7015 (mt0) REVERT: A 339 THR cc_start: 0.8719 (t) cc_final: 0.8452 (m) REVERT: A 437 ARG cc_start: 0.8392 (ttm-80) cc_final: 0.7819 (ttm-80) REVERT: A 441 MET cc_start: 0.8339 (mmm) cc_final: 0.8030 (mmp) REVERT: A 643 MET cc_start: 0.8142 (mtt) cc_final: 0.7832 (mtt) REVERT: A 689 LYS cc_start: 0.8598 (ptmt) cc_final: 0.8268 (ptmt) REVERT: A 696 ASN cc_start: 0.7837 (t0) cc_final: 0.7579 (t0) REVERT: A 881 GLU cc_start: 0.8737 (tt0) cc_final: 0.8310 (mt-10) REVERT: B 262 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7052 (mt0) REVERT: B 339 THR cc_start: 0.8713 (t) cc_final: 0.8445 (m) REVERT: B 437 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.7836 (ttm-80) REVERT: B 441 MET cc_start: 0.8347 (mmm) cc_final: 0.8039 (mmp) REVERT: B 643 MET cc_start: 0.8146 (mtt) cc_final: 0.7835 (mtt) REVERT: B 689 LYS cc_start: 0.8605 (ptmt) cc_final: 0.8276 (ptmt) REVERT: B 696 ASN cc_start: 0.7829 (t0) cc_final: 0.7569 (t0) REVERT: B 881 GLU cc_start: 0.8739 (tt0) cc_final: 0.8315 (mt-10) REVERT: C 262 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.7028 (mt0) REVERT: C 339 THR cc_start: 0.8728 (t) cc_final: 0.8454 (m) REVERT: C 437 ARG cc_start: 0.8407 (ttm-80) cc_final: 0.7837 (ttm-80) REVERT: C 441 MET cc_start: 0.8349 (mmm) cc_final: 0.8038 (mmp) REVERT: C 643 MET cc_start: 0.8150 (mtt) cc_final: 0.7841 (mtt) REVERT: C 689 LYS cc_start: 0.8602 (ptmt) cc_final: 0.8270 (ptmt) REVERT: C 696 ASN cc_start: 0.7846 (t0) cc_final: 0.7589 (t0) REVERT: C 881 GLU cc_start: 0.8739 (tt0) cc_final: 0.8312 (mt-10) REVERT: D 262 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.7019 (mt0) REVERT: D 339 THR cc_start: 0.8722 (t) cc_final: 0.8454 (m) REVERT: D 437 ARG cc_start: 0.8407 (ttm-80) cc_final: 0.7841 (ttm-80) REVERT: D 441 MET cc_start: 0.8336 (mmm) cc_final: 0.8025 (mmp) REVERT: D 643 MET cc_start: 0.8146 (mtt) cc_final: 0.7834 (mtt) REVERT: D 689 LYS cc_start: 0.8599 (ptmt) cc_final: 0.8269 (ptmt) REVERT: D 696 ASN cc_start: 0.7840 (t0) cc_final: 0.7582 (t0) REVERT: D 881 GLU cc_start: 0.8731 (tt0) cc_final: 0.8306 (mt-10) outliers start: 32 outliers final: 28 residues processed: 308 average time/residue: 0.1610 time to fit residues: 79.0487 Evaluate side-chains 324 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 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 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 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 720 LEU Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 112 optimal weight: 0.0770 chunk 137 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 142 optimal weight: 0.3980 overall best weight: 1.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3919 r_free = 0.3919 target = 0.157378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119680 restraints weight = 25240.087| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.07 r_work: 0.3275 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23816 Z= 0.130 Angle : 0.464 6.238 32300 Z= 0.245 Chirality : 0.038 0.131 3684 Planarity : 0.003 0.036 3956 Dihedral : 7.466 65.283 3540 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.42 % Allowed : 14.23 % Favored : 84.35 % 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: 0.95 (0.16), residues: 2904 helix: 1.51 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.08 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 437 TYR 0.011 0.001 TYR D 209 PHE 0.009 0.001 PHE C 377 TRP 0.011 0.001 TRP B 514 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.13 (23812) covalent geometry : angle 0.46151 / 0.24 (32292) SS BOND : bond 0.01065 / 0.49 ( 4) SS BOND : angle 3.35540 / 1.95 ( 8) hydrogen bonds : bond 0.03853 / 2.63 ( 1240) hydrogen bonds : angle 2.85693 / 1.98 ( 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 328 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 296 time to evaluate : 0.911 Fit side-chains REVERT: A 262 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.7039 (mt0) REVERT: A 339 THR cc_start: 0.8761 (t) cc_final: 0.8486 (m) REVERT: A 441 MET cc_start: 0.8388 (mmm) cc_final: 0.8072 (mmp) REVERT: A 689 LYS cc_start: 0.8627 (ptmt) cc_final: 0.8311 (ptmt) REVERT: A 696 ASN cc_start: 0.7889 (t0) cc_final: 0.7612 (t0) REVERT: A 881 GLU cc_start: 0.8756 (tt0) cc_final: 0.8312 (mt-10) REVERT: B 262 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7069 (mt0) REVERT: B 339 THR cc_start: 0.8756 (t) cc_final: 0.8481 (m) REVERT: B 441 MET cc_start: 0.8393 (mmm) cc_final: 0.8080 (mmp) REVERT: B 689 LYS cc_start: 0.8640 (ptmt) cc_final: 0.8322 (ptmt) REVERT: B 696 ASN cc_start: 0.7883 (t0) cc_final: 0.7603 (t0) REVERT: B 881 GLU cc_start: 0.8760 (tt0) cc_final: 0.8320 (mt-10) REVERT: C 262 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7049 (mt0) REVERT: C 339 THR cc_start: 0.8765 (t) cc_final: 0.8487 (m) REVERT: C 441 MET cc_start: 0.8386 (mmm) cc_final: 0.8074 (mmp) REVERT: C 689 LYS cc_start: 0.8636 (ptmt) cc_final: 0.8317 (ptmt) REVERT: C 696 ASN cc_start: 0.7898 (t0) cc_final: 0.7619 (t0) REVERT: C 881 GLU cc_start: 0.8763 (tt0) cc_final: 0.8322 (mt-10) REVERT: D 262 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.7035 (mt0) REVERT: D 339 THR cc_start: 0.8759 (t) cc_final: 0.8483 (m) REVERT: D 441 MET cc_start: 0.8375 (mmm) cc_final: 0.8059 (mmp) REVERT: D 689 LYS cc_start: 0.8636 (ptmt) cc_final: 0.8317 (ptmt) REVERT: D 696 ASN cc_start: 0.7894 (t0) cc_final: 0.7618 (t0) REVERT: D 881 GLU cc_start: 0.8761 (tt0) cc_final: 0.8320 (mt-10) outliers start: 32 outliers final: 28 residues processed: 308 average time/residue: 0.1616 time to fit residues: 79.2163 Evaluate side-chains 327 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 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 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 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 720 LEU Chi-restraints excluded: chain D residue 762 VAL 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: 6.9990 chunk 188 optimal weight: 0.2980 chunk 226 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 276 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3924 r_free = 0.3924 target = 0.157912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120441 restraints weight = 25075.611| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.06 r_work: 0.3294 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23816 Z= 0.112 Angle : 0.449 6.169 32300 Z= 0.239 Chirality : 0.037 0.130 3684 Planarity : 0.003 0.036 3956 Dihedral : 7.343 64.972 3540 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.60 % Allowed : 14.49 % Favored : 83.91 % 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: 1.07 (0.16), residues: 2904 helix: 1.59 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.01 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 437 TYR 0.011 0.001 TYR B 209 PHE 0.007 0.001 PHE B 186 TRP 0.012 0.001 TRP A 514 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.11 (23812) covalent geometry : angle 0.44631 / 0.24 (32292) SS BOND : bond 0.01057 / 0.49 ( 4) SS BOND : angle 3.33984 / 1.94 ( 8) hydrogen bonds : bond 0.03598 / 2.45 ( 1240) hydrogen bonds : angle 2.83961 / 1.97 ( 3660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6120.92 seconds wall clock time: 105 minutes 16.68 seconds (6316.68 seconds total)