Starting phenix.real_space_refine on Wed Nov 19 11:19:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uza_20954/11_2025/6uza_20954.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uza_20954/11_2025/6uza_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 { model { file = "/net/cci-nas-00/data/ceres_data/6uza_20954/11_2025/6uza_20954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uza_20954/11_2025/6uza_20954.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uza_20954/11_2025/6uza_20954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uza_20954/11_2025/6uza_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23284 Number of models: 1 Model: "" Number of chains: 5 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: "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} Restraints were copied for chains: B, C, D Time building chain proxies: 6.67, per 1000 atoms: 0.29 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: 2.06 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: 0.76 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: 3.93 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3600 1.30 - 1.43: 6440 1.43 - 1.56: 13436 1.56 - 1.69: 88 1.69 - 1.83: 248 Bond restraints: 23812 Sorted by residual: bond pdb=" O5 S9Y C1003 " pdb=" P S9Y C1003 " ideal model delta sigma weight residual 1.648 1.799 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O5 S9Y A1002 " pdb=" P S9Y A1002 " ideal model delta sigma weight residual 1.648 1.799 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O5 S9Y B1003 " pdb=" P S9Y B1003 " ideal model delta sigma weight residual 1.648 1.799 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O5 S9Y D1003 " pdb=" P S9Y D1003 " ideal model delta sigma weight residual 1.648 1.799 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C21 R0G B1002 " pdb=" C22 R0G B1002 " ideal model delta sigma weight residual 1.423 1.556 -0.133 2.00e-02 2.50e+03 4.44e+01 ... (remaining 23807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 31835 3.66 - 7.32: 365 7.32 - 10.98: 76 10.98 - 14.64: 4 14.64 - 18.30: 12 Bond angle restraints: 32292 Sorted by residual: angle pdb=" N VAL A 576 " pdb=" CA VAL A 576 " pdb=" C VAL A 576 " ideal model delta sigma weight residual 113.20 104.60 8.60 9.60e-01 1.09e+00 8.03e+01 angle pdb=" N VAL B 576 " pdb=" CA VAL B 576 " pdb=" C VAL B 576 " ideal model delta sigma weight residual 113.20 104.60 8.60 9.60e-01 1.09e+00 8.03e+01 angle pdb=" N VAL D 576 " pdb=" CA VAL D 576 " pdb=" C VAL D 576 " ideal model delta sigma weight residual 113.20 104.60 8.60 9.60e-01 1.09e+00 8.03e+01 angle pdb=" N VAL C 576 " pdb=" CA VAL C 576 " pdb=" C VAL C 576 " ideal model delta sigma weight residual 113.20 104.60 8.60 9.60e-01 1.09e+00 8.03e+01 angle pdb=" O3P S9Y A1002 " pdb=" P S9Y A1002 " pdb=" O5 S9Y A1002 " ideal model delta sigma weight residual 94.12 112.42 -18.30 3.00e+00 1.11e-01 3.72e+01 ... (remaining 32287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.12: 14064 30.12 - 60.24: 536 60.24 - 90.36: 28 90.36 - 120.48: 0 120.48 - 150.60: 4 Dihedral angle restraints: 14632 sinusoidal: 5984 harmonic: 8648 Sorted by residual: dihedral pdb=" CA ASN B 256 " pdb=" C ASN B 256 " pdb=" N ASP B 257 " pdb=" CA ASP B 257 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ASN A 256 " pdb=" C ASN A 256 " pdb=" N ASP A 257 " pdb=" CA ASP A 257 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ASN C 256 " pdb=" C ASN C 256 " pdb=" N ASP C 257 " pdb=" CA ASP C 257 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 14629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3448 0.103 - 0.206: 184 0.206 - 0.309: 36 0.309 - 0.412: 8 0.412 - 0.515: 8 Chirality restraints: 3684 Sorted by residual: chirality pdb=" C2 SBJ A1003 " pdb=" C1 SBJ A1003 " pdb=" C3 SBJ A1003 " pdb=" O2 SBJ A1003 " both_signs ideal model delta sigma weight residual False 2.37 2.88 -0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" C2 SBJ B1004 " pdb=" C1 SBJ B1004 " pdb=" C3 SBJ B1004 " pdb=" O2 SBJ B1004 " both_signs ideal model delta sigma weight residual False 2.37 2.88 -0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" C2 SBJ C1004 " pdb=" C1 SBJ C1004 " pdb=" C3 SBJ C1004 " pdb=" O2 SBJ C1004 " both_signs ideal model delta sigma weight residual False 2.37 2.88 -0.52 2.00e-01 2.50e+01 6.64e+00 ... (remaining 3681 not shown) Planarity restraints: 3956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 758 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C ARG C 758 " 0.048 2.00e-02 2.50e+03 pdb=" O ARG C 758 " -0.018 2.00e-02 2.50e+03 pdb=" N THR C 759 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 758 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C ARG A 758 " 0.048 2.00e-02 2.50e+03 pdb=" O ARG A 758 " -0.018 2.00e-02 2.50e+03 pdb=" N THR A 759 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 758 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C ARG B 758 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG B 758 " -0.018 2.00e-02 2.50e+03 pdb=" N THR B 759 " -0.016 2.00e-02 2.50e+03 ... (remaining 3953 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 7748 2.85 - 3.36: 20216 3.36 - 3.88: 36295 3.88 - 4.39: 43364 4.39 - 4.90: 75205 Nonbonded interactions: 182828 Sorted by model distance: nonbonded pdb=" O SER B 589 " pdb=" OG SER B 589 " model vdw 2.338 3.040 nonbonded pdb=" O SER A 589 " pdb=" OG SER A 589 " model vdw 2.338 3.040 nonbonded pdb=" O SER C 589 " pdb=" OG SER C 589 " model vdw 2.338 3.040 nonbonded pdb=" O SER D 589 " pdb=" OG SER D 589 " model vdw 2.338 3.040 nonbonded pdb=" O PRO B 283 " pdb=" OG SER B 287 " model vdw 2.338 3.040 ... (remaining 182823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 85 through 920) selection = (chain 'B' and resid 85 through 920) selection = (chain 'C' and resid 85 through 920) selection = (chain 'D' and resid 85 through 920) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.000 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.930 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.030 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.151 23816 Z= 0.408 Angle : 1.054 18.304 32300 Z= 0.528 Chirality : 0.062 0.515 3684 Planarity : 0.007 0.068 3956 Dihedral : 15.174 150.597 9012 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.12), residues: 2904 helix: -2.47 (0.09), residues: 1920 sheet: None (None), residues: 0 loop : -2.49 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 758 TYR 0.020 0.002 TYR D 209 PHE 0.020 0.002 PHE C 537 TRP 0.031 0.002 TRP B 514 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00831 (23812) covalent geometry : angle 1.05374 (32292) SS BOND : bond 0.00737 ( 4) SS BOND : angle 2.39416 ( 8) hydrogen bonds : bond 0.13583 ( 1240) hydrogen bonds : angle 5.37542 ( 3660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.906 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: 0.8180 (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: 0.1883 time to fit residues: 101.7679 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 : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS A 380 HIS A 384 GLN A 446 HIS A 550 HIS A 728 ASN B 157 ASN B 358 HIS B 380 HIS B 384 GLN B 446 HIS B 550 HIS B 728 ASN C 157 ASN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 HIS C 380 HIS C 384 GLN C 446 HIS C 550 HIS C 728 ASN D 157 ASN D 358 HIS D 380 HIS D 384 GLN D 446 HIS D 550 HIS D 728 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.159351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121804 restraints weight = 25113.581| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.10 r_work: 0.3289 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23816 Z= 0.115 Angle : 0.488 6.182 32300 Z= 0.260 Chirality : 0.037 0.123 3684 Planarity : 0.004 0.046 3956 Dihedral : 9.078 97.143 4076 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.89 % Allowed : 8.87 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.15), residues: 2904 helix: -0.45 (0.11), residues: 1932 sheet: None (None), residues: 0 loop : -2.05 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 437 TYR 0.008 0.001 TYR D 209 PHE 0.009 0.001 PHE D 548 TRP 0.023 0.001 TRP D 514 HIS 0.002 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00271 (23812) covalent geometry : angle 0.48532 (32292) SS BOND : bond 0.01046 ( 4) SS BOND : angle 3.50619 ( 8) hydrogen bonds : bond 0.03982 ( 1240) hydrogen bonds : angle 3.39241 ( 3660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 322 time to evaluate : 0.906 Fit side-chains REVERT: A 116 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7605 (ttpt) REVERT: A 262 GLN cc_start: 0.7923 (tt0) cc_final: 0.7484 (mt0) REVERT: A 441 MET cc_start: 0.8357 (mmm) cc_final: 0.8067 (mmp) REVERT: A 689 LYS cc_start: 0.8609 (ptmt) cc_final: 0.8311 (ptmt) REVERT: A 696 ASN cc_start: 0.8175 (t0) cc_final: 0.7849 (t0) REVERT: A 881 GLU cc_start: 0.8749 (tt0) cc_final: 0.8172 (mt-10) REVERT: B 116 LYS cc_start: 0.7825 (ttpt) cc_final: 0.7594 (ttpt) REVERT: B 262 GLN cc_start: 0.7933 (tt0) cc_final: 0.7493 (mt0) REVERT: B 441 MET cc_start: 0.8368 (mmm) cc_final: 0.8081 (mmp) REVERT: B 689 LYS cc_start: 0.8611 (ptmt) cc_final: 0.8311 (ptmt) REVERT: B 696 ASN cc_start: 0.8160 (t0) cc_final: 0.7832 (t0) REVERT: B 881 GLU cc_start: 0.8756 (tt0) cc_final: 0.8181 (mt-10) REVERT: C 116 LYS cc_start: 0.7817 (ttpt) cc_final: 0.7585 (ttpt) REVERT: C 262 GLN cc_start: 0.7935 (tt0) cc_final: 0.7497 (mt0) REVERT: C 441 MET cc_start: 0.8364 (mmm) cc_final: 0.8075 (mmp) REVERT: C 689 LYS cc_start: 0.8602 (ptmt) cc_final: 0.8300 (ptmt) REVERT: C 696 ASN cc_start: 0.8174 (t0) cc_final: 0.7846 (t0) REVERT: C 881 GLU cc_start: 0.8757 (tt0) cc_final: 0.8184 (mt-10) REVERT: D 116 LYS cc_start: 0.7827 (ttpt) cc_final: 0.7594 (ttpt) REVERT: D 262 GLN cc_start: 0.7928 (tt0) cc_final: 0.7489 (mt0) REVERT: D 441 MET cc_start: 0.8352 (mmm) cc_final: 0.8063 (mmp) REVERT: D 689 LYS cc_start: 0.8609 (ptmt) cc_final: 0.8310 (ptmt) REVERT: D 696 ASN cc_start: 0.8172 (t0) cc_final: 0.7844 (t0) REVERT: D 881 GLU cc_start: 0.8756 (tt0) cc_final: 0.8181 (mt-10) outliers start: 20 outliers final: 16 residues processed: 330 average time/residue: 0.1738 time to fit residues: 88.7888 Evaluate side-chains 318 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 302 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 280 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 251 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 ASN B 580 ASN C 580 ASN D 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.154725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116922 restraints weight = 25308.264| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.08 r_work: 0.3237 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23816 Z= 0.191 Angle : 0.541 6.813 32300 Z= 0.283 Chirality : 0.040 0.139 3684 Planarity : 0.004 0.038 3956 Dihedral : 8.736 75.646 4076 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.77 % Allowed : 10.28 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.15), residues: 2904 helix: 0.19 (0.12), residues: 1924 sheet: None (None), residues: 0 loop : -1.93 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 861 TYR 0.013 0.001 TYR D 209 PHE 0.012 0.002 PHE B 537 TRP 0.022 0.002 TRP A 514 HIS 0.003 0.001 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00483 (23812) covalent geometry : angle 0.53792 (32292) SS BOND : bond 0.01171 ( 4) SS BOND : angle 3.52290 ( 8) hydrogen bonds : bond 0.04874 ( 1240) hydrogen bonds : angle 3.26649 ( 3660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 316 time to evaluate : 0.879 Fit side-chains REVERT: A 262 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: A 441 MET cc_start: 0.8426 (mmm) cc_final: 0.8132 (mmp) REVERT: A 507 TRP cc_start: 0.8482 (t-100) cc_final: 0.8276 (t-100) REVERT: A 689 LYS cc_start: 0.8671 (ptmt) cc_final: 0.8377 (ptmt) REVERT: A 696 ASN cc_start: 0.8139 (t0) cc_final: 0.7834 (t0) REVERT: A 881 GLU cc_start: 0.8793 (tt0) cc_final: 0.8227 (mt-10) REVERT: B 262 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7597 (mt0) REVERT: B 441 MET cc_start: 0.8435 (mmm) cc_final: 0.8142 (mmp) REVERT: B 507 TRP cc_start: 0.8482 (t-100) cc_final: 0.8276 (t-100) REVERT: B 689 LYS cc_start: 0.8669 (ptmt) cc_final: 0.8371 (ptmt) REVERT: B 696 ASN cc_start: 0.8139 (t0) cc_final: 0.7836 (t0) REVERT: B 881 GLU cc_start: 0.8785 (tt0) cc_final: 0.8219 (mt-10) REVERT: C 262 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7596 (mt0) REVERT: C 441 MET cc_start: 0.8434 (mmm) cc_final: 0.8139 (mmp) REVERT: C 507 TRP cc_start: 0.8497 (t-100) cc_final: 0.8290 (t-100) REVERT: C 689 LYS cc_start: 0.8665 (ptmt) cc_final: 0.8366 (ptmt) REVERT: C 696 ASN cc_start: 0.8152 (t0) cc_final: 0.7849 (t0) REVERT: C 881 GLU cc_start: 0.8784 (tt0) cc_final: 0.8215 (mt-10) REVERT: D 262 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7583 (mt0) REVERT: D 441 MET cc_start: 0.8428 (mmm) cc_final: 0.8134 (mmp) REVERT: D 507 TRP cc_start: 0.8482 (t-100) cc_final: 0.8275 (t-100) REVERT: D 689 LYS cc_start: 0.8672 (ptmt) cc_final: 0.8378 (ptmt) REVERT: D 696 ASN cc_start: 0.8145 (t0) cc_final: 0.7842 (t0) REVERT: D 881 GLU cc_start: 0.8786 (tt0) cc_final: 0.8219 (mt-10) outliers start: 40 outliers final: 20 residues processed: 336 average time/residue: 0.1650 time to fit residues: 86.5767 Evaluate side-chains 332 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 308 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 125 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 287 optimal weight: 0.8980 chunk 253 optimal weight: 0.7980 chunk 91 optimal weight: 0.3980 chunk 182 optimal weight: 0.9990 chunk 257 optimal weight: 0.0270 chunk 219 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 165 optimal weight: 0.1980 chunk 231 optimal weight: 3.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 316 ASN B 230 GLN B 316 ASN C 230 GLN C 316 ASN D 230 GLN D 316 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.160965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123531 restraints weight = 24969.197| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.10 r_work: 0.3307 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1638 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= 0.084 Angle : 0.436 5.754 32300 Z= 0.232 Chirality : 0.036 0.128 3684 Planarity : 0.003 0.036 3956 Dihedral : 7.875 65.314 4076 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.60 % Allowed : 11.52 % 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: -0.00 (0.16), residues: 2904 helix: 0.82 (0.12), residues: 1908 sheet: None (None), residues: 0 loop : -1.59 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 437 TYR 0.005 0.001 TYR D 277 PHE 0.011 0.001 PHE B 641 TRP 0.017 0.001 TRP D 514 HIS 0.001 0.000 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00191 (23812) covalent geometry : angle 0.43273 (32292) SS BOND : bond 0.01034 ( 4) SS BOND : angle 3.39395 ( 8) hydrogen bonds : bond 0.03091 ( 1240) hydrogen bonds : angle 2.92186 ( 3660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5808 Ramachandran restraints generated. 2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 304 time to evaluate : 0.931 Fit side-chains REVERT: A 262 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: A 339 THR cc_start: 0.8689 (t) cc_final: 0.8411 (m) REVERT: A 441 MET cc_start: 0.8255 (mmm) cc_final: 0.7969 (mmp) REVERT: A 486 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8050 (mmm) REVERT: A 689 LYS cc_start: 0.8555 (ptmt) cc_final: 0.8275 (ptmt) REVERT: A 696 ASN cc_start: 0.7929 (t0) cc_final: 0.7643 (t0) REVERT: A 881 GLU cc_start: 0.8641 (tt0) cc_final: 0.8134 (mt-10) REVERT: B 262 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7352 (mt0) REVERT: B 339 THR cc_start: 0.8688 (t) cc_final: 0.8411 (m) REVERT: B 441 MET cc_start: 0.8266 (mmm) cc_final: 0.7984 (mmp) REVERT: B 486 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8055 (mmm) REVERT: B 689 LYS cc_start: 0.8558 (ptmt) cc_final: 0.8276 (ptmt) REVERT: B 696 ASN cc_start: 0.7924 (t0) cc_final: 0.7637 (t0) REVERT: B 881 GLU cc_start: 0.8643 (tt0) cc_final: 0.8136 (mt-10) REVERT: C 262 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7346 (mt0) REVERT: C 339 THR cc_start: 0.8700 (t) cc_final: 0.8421 (m) REVERT: C 441 MET cc_start: 0.8273 (mmm) cc_final: 0.7988 (mmp) REVERT: C 486 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8055 (mmm) REVERT: C 689 LYS cc_start: 0.8542 (ptmt) cc_final: 0.8259 (ptmt) REVERT: C 696 ASN cc_start: 0.7936 (t0) cc_final: 0.7649 (t0) REVERT: C 881 GLU cc_start: 0.8651 (tt0) cc_final: 0.8143 (mt-10) REVERT: D 262 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7343 (mt0) REVERT: D 339 THR cc_start: 0.8693 (t) cc_final: 0.8419 (m) REVERT: D 441 MET cc_start: 0.8259 (mmm) cc_final: 0.7974 (mmp) REVERT: D 486 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.8044 (mmm) REVERT: D 689 LYS cc_start: 0.8552 (ptmt) cc_final: 0.8272 (ptmt) REVERT: D 696 ASN cc_start: 0.7935 (t0) cc_final: 0.7650 (t0) REVERT: D 881 GLU cc_start: 0.8642 (tt0) cc_final: 0.8135 (mt-10) outliers start: 36 outliers final: 20 residues processed: 312 average time/residue: 0.1574 time to fit residues: 77.7553 Evaluate side-chains 328 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 300 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 629 ARG Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 238 optimal weight: 0.8980 chunk 289 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 252 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 chunk 223 optimal weight: 0.0040 chunk 179 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.156909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119328 restraints weight = 24986.737| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.06 r_work: 0.3269 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1646 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= 0.136 Angle : 0.475 6.346 32300 Z= 0.250 Chirality : 0.038 0.131 3684 Planarity : 0.004 0.039 3956 Dihedral : 7.975 64.347 4076 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.86 % Allowed : 12.50 % 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: 0.20 (0.16), residues: 2904 helix: 0.95 (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 D 437 TYR 0.010 0.001 TYR C 209 PHE 0.010 0.001 PHE B 641 TRP 0.014 0.001 TRP B 514 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00341 (23812) covalent geometry : angle 0.47197 (32292) SS BOND : bond 0.01102 ( 4) SS BOND : angle 3.38429 ( 8) hydrogen bonds : bond 0.03986 ( 1240) hydrogen bonds : angle 2.94747 ( 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 342 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 300 time to evaluate : 1.365 Fit side-chains REVERT: A 262 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7419 (mt0) REVERT: A 339 THR cc_start: 0.8770 (t) cc_final: 0.8489 (m) REVERT: A 437 ARG cc_start: 0.8567 (ttm-80) cc_final: 0.8004 (ttm-80) REVERT: A 441 MET cc_start: 0.8359 (mmm) cc_final: 0.8061 (mmp) REVERT: A 689 LYS cc_start: 0.8619 (ptmt) cc_final: 0.8347 (ptmt) REVERT: A 696 ASN cc_start: 0.7957 (t0) cc_final: 0.7670 (t0) REVERT: A 758 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8111 (ptt-90) REVERT: A 881 GLU cc_start: 0.8778 (tt0) cc_final: 0.8259 (mt-10) REVERT: B 262 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7473 (mt0) REVERT: B 339 THR cc_start: 0.8763 (t) cc_final: 0.8484 (m) REVERT: B 437 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.8019 (ttm-80) REVERT: B 441 MET cc_start: 0.8368 (mmm) cc_final: 0.8076 (mmp) REVERT: B 689 LYS cc_start: 0.8625 (ptmt) cc_final: 0.8336 (ptmt) REVERT: B 696 ASN cc_start: 0.7942 (t0) cc_final: 0.7653 (t0) REVERT: B 758 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8105 (ptt-90) REVERT: B 881 GLU cc_start: 0.8771 (tt0) cc_final: 0.8250 (mt-10) REVERT: C 262 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7430 (mt0) REVERT: C 339 THR cc_start: 0.8771 (t) cc_final: 0.8491 (m) REVERT: C 437 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.8023 (ttm-80) REVERT: C 441 MET cc_start: 0.8366 (mmm) cc_final: 0.8072 (mmp) REVERT: C 689 LYS cc_start: 0.8618 (ptmt) cc_final: 0.8323 (ptmt) REVERT: C 696 ASN cc_start: 0.7963 (t0) cc_final: 0.7674 (t0) REVERT: C 758 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8101 (ptt-90) REVERT: C 881 GLU cc_start: 0.8784 (tt0) cc_final: 0.8264 (mt-10) REVERT: D 262 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7427 (mt0) REVERT: D 339 THR cc_start: 0.8767 (t) cc_final: 0.8487 (m) REVERT: D 437 ARG cc_start: 0.8588 (ttm-80) cc_final: 0.8027 (ttm-80) REVERT: D 441 MET cc_start: 0.8357 (mmm) cc_final: 0.8062 (mmp) REVERT: D 689 LYS cc_start: 0.8614 (ptmt) cc_final: 0.8323 (ptmt) REVERT: D 696 ASN cc_start: 0.7958 (t0) cc_final: 0.7671 (t0) REVERT: D 758 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8110 (ptt-90) REVERT: D 881 GLU cc_start: 0.8773 (tt0) cc_final: 0.8254 (mt-10) outliers start: 42 outliers final: 28 residues processed: 320 average time/residue: 0.1782 time to fit residues: 87.9825 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 : 0.835 ------------------------------------------------------------------------------- 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 A residue 758 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 629 ARG Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 274 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 280 optimal weight: 0.8980 chunk 156 optimal weight: 0.5980 chunk 212 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN B 316 ASN C 316 ASN D 316 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.155664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117912 restraints weight = 25175.001| |-----------------------------------------------------------------------------| 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: 0.3087 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23816 Z= 0.165 Angle : 0.501 6.530 32300 Z= 0.262 Chirality : 0.039 0.133 3684 Planarity : 0.004 0.036 3956 Dihedral : 8.199 66.090 4076 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.30 % Allowed : 12.06 % 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: 0.24 (0.16), residues: 2904 helix: 0.96 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.38 (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 C 209 PHE 0.010 0.001 PHE B 377 TRP 0.013 0.001 TRP D 514 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00418 (23812) covalent geometry : angle 0.49835 (32292) SS BOND : bond 0.01127 ( 4) SS BOND : angle 3.39922 ( 8) hydrogen bonds : bond 0.04386 ( 1240) hydrogen bonds : angle 3.00966 ( 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 376 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 324 time to evaluate : 1.010 Fit side-chains REVERT: A 262 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7487 (mt0) REVERT: A 339 THR cc_start: 0.8804 (t) cc_final: 0.8508 (m) REVERT: A 441 MET cc_start: 0.8387 (mmm) cc_final: 0.8080 (mmp) REVERT: A 689 LYS cc_start: 0.8681 (ptmt) cc_final: 0.8393 (ptmt) REVERT: A 696 ASN cc_start: 0.7929 (t0) cc_final: 0.7635 (t0) REVERT: A 758 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8135 (ptt-90) REVERT: A 881 GLU cc_start: 0.8784 (tt0) cc_final: 0.8241 (mt-10) REVERT: B 262 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: B 339 THR cc_start: 0.8800 (t) cc_final: 0.8504 (m) REVERT: B 441 MET cc_start: 0.8393 (mmm) cc_final: 0.8092 (mmp) REVERT: B 689 LYS cc_start: 0.8690 (ptmt) cc_final: 0.8402 (ptmt) REVERT: B 696 ASN cc_start: 0.7917 (t0) cc_final: 0.7620 (t0) REVERT: B 758 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8129 (ptt-90) REVERT: B 881 GLU cc_start: 0.8774 (tt0) cc_final: 0.8231 (mt-10) REVERT: C 262 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7500 (mt0) REVERT: C 339 THR cc_start: 0.8808 (t) cc_final: 0.8511 (m) REVERT: C 441 MET cc_start: 0.8392 (mmm) cc_final: 0.8089 (mmp) REVERT: C 689 LYS cc_start: 0.8676 (ptmt) cc_final: 0.8382 (ptmt) REVERT: C 696 ASN cc_start: 0.7934 (t0) cc_final: 0.7637 (t0) REVERT: C 758 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8122 (ptt-90) REVERT: C 881 GLU cc_start: 0.8789 (tt0) cc_final: 0.8244 (mt-10) REVERT: D 262 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7495 (mt0) REVERT: D 339 THR cc_start: 0.8800 (t) cc_final: 0.8505 (m) REVERT: D 441 MET cc_start: 0.8384 (mmm) cc_final: 0.8079 (mmp) REVERT: D 689 LYS cc_start: 0.8686 (ptmt) cc_final: 0.8396 (ptmt) REVERT: D 696 ASN cc_start: 0.7933 (t0) cc_final: 0.7638 (t0) REVERT: D 758 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8132 (ptt-90) REVERT: D 881 GLU cc_start: 0.8783 (tt0) cc_final: 0.8240 (mt-10) outliers start: 52 outliers final: 36 residues processed: 348 average time/residue: 0.1643 time to fit residues: 89.0286 Evaluate side-chains 368 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 324 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 758 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 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 758 ARG Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 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 758 ARG Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 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 758 ARG Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 100 optimal weight: 4.9990 chunk 276 optimal weight: 0.8980 chunk 68 optimal weight: 0.0000 chunk 67 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3946 r_free = 0.3946 target = 0.159895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122228 restraints weight = 25134.382| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.11 r_work: 0.3294 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1796 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= 0.100 Angle : 0.446 6.483 32300 Z= 0.237 Chirality : 0.037 0.132 3684 Planarity : 0.003 0.036 3956 Dihedral : 7.765 61.972 4076 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.95 % Allowed : 13.12 % 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: 0.62 (0.16), residues: 2904 helix: 1.26 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.23 (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 B 209 PHE 0.013 0.001 PHE D 641 TRP 0.014 0.001 TRP C 514 HIS 0.002 0.000 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00242 (23812) covalent geometry : angle 0.44248 (32292) SS BOND : bond 0.01044 ( 4) SS BOND : angle 3.32413 ( 8) hydrogen bonds : bond 0.03410 ( 1240) hydrogen bonds : angle 2.86165 ( 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 356 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 312 time to evaluate : 1.023 Fit side-chains REVERT: A 262 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7267 (mt0) REVERT: A 339 THR cc_start: 0.8720 (t) cc_final: 0.8445 (m) REVERT: A 437 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.7892 (ttm-80) REVERT: A 441 MET cc_start: 0.8308 (mmm) cc_final: 0.7982 (mmp) REVERT: A 689 LYS cc_start: 0.8579 (ptmt) cc_final: 0.8264 (ptmt) REVERT: A 696 ASN cc_start: 0.7854 (t0) cc_final: 0.7574 (t0) REVERT: A 758 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8090 (ptt-90) REVERT: A 881 GLU cc_start: 0.8716 (tt0) cc_final: 0.8244 (mt-10) REVERT: B 262 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7267 (mt0) REVERT: B 339 THR cc_start: 0.8715 (t) cc_final: 0.8442 (m) REVERT: B 437 ARG cc_start: 0.8474 (ttm-80) cc_final: 0.7903 (ttm-80) REVERT: B 441 MET cc_start: 0.8324 (mmm) cc_final: 0.8003 (mmp) REVERT: B 689 LYS cc_start: 0.8588 (ptmt) cc_final: 0.8268 (ptmt) REVERT: B 696 ASN cc_start: 0.7866 (t0) cc_final: 0.7580 (t0) REVERT: B 758 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8090 (ptt-90) REVERT: B 881 GLU cc_start: 0.8712 (tt0) cc_final: 0.8241 (mt-10) REVERT: C 262 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7277 (mt0) REVERT: C 339 THR cc_start: 0.8726 (t) cc_final: 0.8451 (m) REVERT: C 437 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.7909 (ttm-80) REVERT: C 441 MET cc_start: 0.8324 (mmm) cc_final: 0.8000 (mmp) REVERT: C 689 LYS cc_start: 0.8577 (ptmt) cc_final: 0.8256 (ptmt) REVERT: C 696 ASN cc_start: 0.7879 (t0) cc_final: 0.7595 (t0) REVERT: C 758 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8084 (ptt-90) REVERT: C 881 GLU cc_start: 0.8722 (tt0) cc_final: 0.8250 (mt-10) REVERT: D 262 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7268 (mt0) REVERT: D 339 THR cc_start: 0.8720 (t) cc_final: 0.8448 (m) REVERT: D 437 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.7906 (ttm-80) REVERT: D 441 MET cc_start: 0.8312 (mmm) cc_final: 0.7989 (mmp) REVERT: D 689 LYS cc_start: 0.8587 (ptmt) cc_final: 0.8268 (ptmt) REVERT: D 696 ASN cc_start: 0.7879 (t0) cc_final: 0.7597 (t0) REVERT: D 758 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8090 (ptt-90) REVERT: D 881 GLU cc_start: 0.8708 (tt0) cc_final: 0.8238 (mt-10) outliers start: 44 outliers final: 32 residues processed: 328 average time/residue: 0.1706 time to fit residues: 87.2050 Evaluate side-chains 344 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 304 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 629 ARG Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 629 ARG Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 71 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 247 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 246 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 chunk 213 optimal weight: 0.9980 chunk 277 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3926 r_free = 0.3926 target = 0.156544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.121214 restraints weight = 24658.460| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.89 r_work: 0.3295 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1840 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= 0.108 Angle : 0.447 6.789 32300 Z= 0.237 Chirality : 0.037 0.132 3684 Planarity : 0.003 0.036 3956 Dihedral : 7.693 60.490 4076 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.77 % Allowed : 13.48 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.16), residues: 2904 helix: 1.37 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.14 (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 0.012 0.001 PHE D 641 TRP 0.013 0.001 TRP A 514 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00264 (23812) covalent geometry : angle 0.44359 (32292) SS BOND : bond 0.01053 ( 4) SS BOND : angle 3.33764 ( 8) hydrogen bonds : bond 0.03536 ( 1240) hydrogen bonds : angle 2.84362 ( 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 340 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 1.002 Fit side-chains REVERT: A 262 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7379 (mt0) REVERT: A 339 THR cc_start: 0.8840 (t) cc_final: 0.8584 (m) REVERT: A 437 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8005 (ttm-80) REVERT: A 441 MET cc_start: 0.8459 (mmm) cc_final: 0.8147 (mmp) REVERT: A 643 MET cc_start: 0.8280 (mtt) cc_final: 0.7971 (mtt) REVERT: A 689 LYS cc_start: 0.8685 (ptmt) cc_final: 0.8386 (ptmt) REVERT: A 696 ASN cc_start: 0.7959 (t0) cc_final: 0.7695 (t0) REVERT: A 758 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8258 (ptt-90) REVERT: A 881 GLU cc_start: 0.8799 (tt0) cc_final: 0.8385 (mt-10) REVERT: B 262 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7395 (mt0) REVERT: B 339 THR cc_start: 0.8821 (t) cc_final: 0.8571 (m) REVERT: B 437 ARG cc_start: 0.8546 (ttm-80) cc_final: 0.8010 (ttm-80) REVERT: B 441 MET cc_start: 0.8467 (mmm) cc_final: 0.8159 (mmp) REVERT: B 689 LYS cc_start: 0.8696 (ptmt) cc_final: 0.8399 (ptmt) REVERT: B 696 ASN cc_start: 0.7957 (t0) cc_final: 0.7694 (t0) REVERT: B 758 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8256 (ptt-90) REVERT: B 881 GLU cc_start: 0.8795 (tt0) cc_final: 0.8383 (mt-10) REVERT: C 262 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7384 (mt0) REVERT: C 339 THR cc_start: 0.8833 (t) cc_final: 0.8581 (m) REVERT: C 437 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8021 (ttm-80) REVERT: C 441 MET cc_start: 0.8459 (mmm) cc_final: 0.8148 (mmp) REVERT: C 689 LYS cc_start: 0.8684 (ptmt) cc_final: 0.8383 (ptmt) REVERT: C 696 ASN cc_start: 0.7969 (t0) cc_final: 0.7707 (t0) REVERT: C 758 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8252 (ptt-90) REVERT: C 881 GLU cc_start: 0.8810 (tt0) cc_final: 0.8397 (mt-10) REVERT: D 262 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7386 (mt0) REVERT: D 339 THR cc_start: 0.8832 (t) cc_final: 0.8581 (m) REVERT: D 437 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8006 (ttm-80) REVERT: D 441 MET cc_start: 0.8455 (mmm) cc_final: 0.8143 (mmp) REVERT: D 689 LYS cc_start: 0.8689 (ptmt) cc_final: 0.8390 (ptmt) REVERT: D 696 ASN cc_start: 0.7957 (t0) cc_final: 0.7698 (t0) REVERT: D 758 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8258 (ptt-90) REVERT: D 881 GLU cc_start: 0.8795 (tt0) cc_final: 0.8382 (mt-10) outliers start: 40 outliers final: 32 residues processed: 320 average time/residue: 0.1721 time to fit residues: 85.6445 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 : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain 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 720 LEU Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 44 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 284 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN B 316 ASN C 316 ASN D 316 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.157848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120200 restraints weight = 25156.726| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.06 r_work: 0.3283 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1864 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= 0.116 Angle : 0.456 6.361 32300 Z= 0.242 Chirality : 0.037 0.132 3684 Planarity : 0.003 0.036 3956 Dihedral : 7.702 59.925 4076 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % 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: 0.86 (0.16), residues: 2904 helix: 1.42 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -1.07 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 437 TYR 0.010 0.001 TYR C 209 PHE 0.013 0.001 PHE D 641 TRP 0.013 0.001 TRP A 514 HIS 0.002 0.000 HIS D 183 Details of bonding type rmsd covalent geometry : bond 0.00287 (23812) covalent geometry : angle 0.45267 (32292) SS BOND : bond 0.01055 ( 4) SS BOND : angle 3.31787 ( 8) hydrogen bonds : bond 0.03669 ( 1240) hydrogen bonds : angle 2.85774 ( 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 343 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 303 time to evaluate : 0.946 Fit side-chains REVERT: A 262 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7082 (mt0) REVERT: A 339 THR cc_start: 0.8761 (t) cc_final: 0.8498 (m) REVERT: A 437 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.7929 (ttm-80) REVERT: A 441 MET cc_start: 0.8378 (mmm) cc_final: 0.8056 (mmp) REVERT: A 689 LYS cc_start: 0.8628 (ptmt) cc_final: 0.8296 (ptmt) REVERT: A 696 ASN cc_start: 0.7900 (t0) cc_final: 0.7629 (t0) REVERT: A 758 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8237 (ptt-90) REVERT: A 881 GLU cc_start: 0.8768 (tt0) cc_final: 0.8316 (mt-10) REVERT: B 262 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7104 (mt0) REVERT: B 339 THR cc_start: 0.8750 (t) cc_final: 0.8485 (m) REVERT: B 437 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.7932 (ttm-80) REVERT: B 441 MET cc_start: 0.8389 (mmm) cc_final: 0.8069 (mmp) REVERT: B 689 LYS cc_start: 0.8642 (ptmt) cc_final: 0.8306 (ptmt) REVERT: B 696 ASN cc_start: 0.7885 (t0) cc_final: 0.7615 (t0) REVERT: B 758 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8237 (ptt-90) REVERT: B 881 GLU cc_start: 0.8765 (tt0) cc_final: 0.8316 (mt-10) REVERT: C 262 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7088 (mt0) REVERT: C 339 THR cc_start: 0.8762 (t) cc_final: 0.8496 (m) REVERT: C 437 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.7935 (ttm-80) REVERT: C 441 MET cc_start: 0.8383 (mmm) cc_final: 0.8063 (mmp) REVERT: C 689 LYS cc_start: 0.8633 (ptmt) cc_final: 0.8295 (ptmt) REVERT: C 696 ASN cc_start: 0.7902 (t0) cc_final: 0.7633 (t0) REVERT: C 758 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8231 (ptt-90) REVERT: C 881 GLU cc_start: 0.8775 (tt0) cc_final: 0.8325 (mt-10) REVERT: D 262 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7096 (mt0) REVERT: D 339 THR cc_start: 0.8754 (t) cc_final: 0.8491 (m) REVERT: D 437 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.7935 (ttm-80) REVERT: D 441 MET cc_start: 0.8371 (mmm) cc_final: 0.8049 (mmp) REVERT: D 689 LYS cc_start: 0.8636 (ptmt) cc_final: 0.8301 (ptmt) REVERT: D 696 ASN cc_start: 0.7895 (t0) cc_final: 0.7628 (t0) REVERT: D 758 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8243 (ptt-90) REVERT: D 881 GLU cc_start: 0.8760 (tt0) cc_final: 0.8310 (mt-10) outliers start: 40 outliers final: 32 residues processed: 323 average time/residue: 0.1709 time to fit residues: 86.1044 Evaluate side-chains 339 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain 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 720 LEU Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 112 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 279 optimal weight: 0.9980 chunk 229 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN B 316 ASN C 316 ASN D 316 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.159176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.121696 restraints weight = 25128.659| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.05 r_work: 0.3305 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1959 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= 0.100 Angle : 0.438 6.394 32300 Z= 0.234 Chirality : 0.037 0.131 3684 Planarity : 0.003 0.035 3956 Dihedral : 7.549 57.863 4076 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.77 % Allowed : 14.01 % Favored : 84.22 % 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 B 437 TYR 0.010 0.001 TYR A 209 PHE 0.012 0.001 PHE B 641 TRP 0.013 0.001 TRP D 514 HIS 0.002 0.000 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00241 (23812) covalent geometry : angle 0.43541 (32292) SS BOND : bond 0.01025 ( 4) SS BOND : angle 3.32720 ( 8) hydrogen bonds : bond 0.03361 ( 1240) hydrogen bonds : angle 2.81371 ( 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 334 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 294 time to evaluate : 0.892 Fit side-chains REVERT: A 262 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7002 (mt0) REVERT: A 339 THR cc_start: 0.8726 (t) cc_final: 0.8454 (m) REVERT: A 441 MET cc_start: 0.8342 (mmm) cc_final: 0.8022 (mmp) REVERT: A 689 LYS cc_start: 0.8600 (ptmt) cc_final: 0.8265 (ptmt) REVERT: A 696 ASN cc_start: 0.7865 (t0) cc_final: 0.7603 (t0) REVERT: A 758 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8191 (ptt-90) REVERT: A 881 GLU cc_start: 0.8741 (tt0) cc_final: 0.8308 (mt-10) REVERT: B 262 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7142 (mt0) REVERT: B 339 THR cc_start: 0.8716 (t) cc_final: 0.8444 (m) REVERT: B 441 MET cc_start: 0.8351 (mmm) cc_final: 0.8032 (mmp) REVERT: B 689 LYS cc_start: 0.8609 (ptmt) cc_final: 0.8274 (ptmt) REVERT: B 696 ASN cc_start: 0.7852 (t0) cc_final: 0.7588 (t0) REVERT: B 758 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8191 (ptt-90) REVERT: B 881 GLU cc_start: 0.8739 (tt0) cc_final: 0.8310 (mt-10) REVERT: C 262 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7007 (mt0) REVERT: C 339 THR cc_start: 0.8727 (t) cc_final: 0.8455 (m) REVERT: C 441 MET cc_start: 0.8351 (mmm) cc_final: 0.8031 (mmp) REVERT: C 689 LYS cc_start: 0.8604 (ptmt) cc_final: 0.8265 (ptmt) REVERT: C 696 ASN cc_start: 0.7862 (t0) cc_final: 0.7601 (t0) REVERT: C 758 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8191 (ptt-90) REVERT: C 881 GLU cc_start: 0.8744 (tt0) cc_final: 0.8312 (mt-10) REVERT: D 262 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.7013 (mt0) REVERT: D 339 THR cc_start: 0.8722 (t) cc_final: 0.8451 (m) REVERT: D 441 MET cc_start: 0.8339 (mmm) cc_final: 0.8020 (mmp) REVERT: D 689 LYS cc_start: 0.8603 (ptmt) cc_final: 0.8265 (ptmt) REVERT: D 696 ASN cc_start: 0.7863 (t0) cc_final: 0.7598 (t0) REVERT: D 758 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8195 (ptt-90) REVERT: D 881 GLU cc_start: 0.8733 (tt0) cc_final: 0.8301 (mt-10) outliers start: 40 outliers final: 32 residues processed: 314 average time/residue: 0.1731 time to fit residues: 84.5059 Evaluate side-chains 331 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 291 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 758 ARG Chi-restraints excluded: chain 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 720 LEU Chi-restraints excluded: chain B residue 758 ARG Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 486 MET Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 758 ARG Chi-restraints excluded: chain D residue 762 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 226 optimal weight: 0.0020 chunk 22 optimal weight: 2.9990 chunk 276 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.159155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.121709 restraints weight = 25011.896| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.05 r_work: 0.3303 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1981 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= 0.103 Angle : 0.443 6.121 32300 Z= 0.236 Chirality : 0.037 0.131 3684 Planarity : 0.003 0.035 3956 Dihedral : 7.491 57.858 4076 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.77 % Allowed : 14.18 % Favored : 84.04 % 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: 1.13 (0.16), residues: 2904 helix: 1.65 (0.12), residues: 1900 sheet: None (None), residues: 0 loop : -0.99 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 437 TYR 0.010 0.001 TYR A 209 PHE 0.011 0.001 PHE B 641 TRP 0.013 0.001 TRP D 514 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00250 (23812) covalent geometry : angle 0.44022 (32292) SS BOND : bond 0.01039 ( 4) SS BOND : angle 3.32735 ( 8) hydrogen bonds : bond 0.03445 ( 1240) hydrogen bonds : angle 2.81046 ( 3660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6204.27 seconds wall clock time: 106 minutes 35.91 seconds (6395.91 seconds total)