Starting phenix.real_space_refine on Thu Sep 26 14:32:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/09_2024/7sil_25143.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/09_2024/7sil_25143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/09_2024/7sil_25143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/09_2024/7sil_25143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/09_2024/7sil_25143.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sil_25143/09_2024/7sil_25143.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 ------------------------------------------------------------------------------- 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= 0.060 sd= 0.251 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: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 P 2 5.49 5 S 70 5.16 5 Cl 2 4.86 5 C 8454 2.51 5 N 2036 2.21 5 O 2352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12924 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6206 Classifications: {'peptide': 781} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 749} Chain breaks: 3 Chain: "B" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6206 Classifications: {'peptide': 781} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 749} Chain breaks: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 142 Unusual residues: {' CA': 4, '9IG': 1, 'CLR': 4, 'PO4': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 142 Unusual residues: {' CA': 4, '9IG': 1, 'CLR': 4, 'PO4': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 8.18, per 1000 atoms: 0.63 Number of scatterers: 12924 At special positions: 0 Unit cell: (98.77, 97.11, 172.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 8 19.99 Cl 2 17.00 S 70 16.00 P 2 15.00 O 2352 8.00 N 2036 7.00 C 8454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.04 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 901 " - " ASN A 261 " " NAG A 902 " - " ASN A 287 " " NAG A 903 " - " ASN A 468 " " NAG B 901 " - " ASN B 261 " " NAG B 902 " - " ASN B 287 " " NAG B 903 " - " ASN B 468 " " NAG C 1 " - " ASN A 488 " " NAG D 1 " - " ASN A 541 " " NAG E 1 " - " ASN B 488 " " NAG F 1 " - " ASN B 541 " Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.6 seconds 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 51.7% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 146 through 160 removed outlier: 3.737A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 190 through 204 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.638A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 272 through 287 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.703A pdb=" N VAL A 455 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.545A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 610 through 637 Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.540A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 669 removed outlier: 3.845A pdb=" N PHE A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 679 Processing helix chain 'A' and resid 680 through 703 removed outlier: 3.594A pdb=" N PHE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 746 Processing helix chain 'A' and resid 769 through 794 Processing helix chain 'A' and resid 802 through 821 removed outlier: 4.264A pdb=" N PHE A 806 " --> pdb=" O ASN A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 831 through 861 removed outlier: 3.969A pdb=" N ALA A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 146 through 160 removed outlier: 3.732A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 190 through 204 Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.618A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 262 Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 347 through 356 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 415 through 436 Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.723A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.516A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 610 through 637 Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.689A pdb=" N THR B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 669 removed outlier: 3.754A pdb=" N PHE B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 679 Processing helix chain 'B' and resid 680 through 703 removed outlier: 3.625A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 746 removed outlier: 3.514A pdb=" N ALA B 746 " --> pdb=" O TRP B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 794 removed outlier: 3.513A pdb=" N SER B 794 " --> pdb=" O PHE B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 821 removed outlier: 4.107A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 831 through 861 removed outlier: 4.010A pdb=" N ALA B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.160A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 33 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.967A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 267 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AA5, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AA7, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.148A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL B 165 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.963A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 267 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AB1, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AB2, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AB3, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AB4, first strand: chain 'B' and resid 602 through 604 628 hydrogen bonds defined for protein. 1794 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: 4.38 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3957 1.34 - 1.46: 3211 1.46 - 1.58: 6002 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 13256 Sorted by residual: bond pdb=" CG TCR A 904 " pdb=" CD1 TCR A 904 " ideal model delta sigma weight residual 1.364 1.477 -0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" CG TCR B 904 " pdb=" CD1 TCR B 904 " ideal model delta sigma weight residual 1.364 1.476 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CD2 TCR A 904 " pdb=" CE2 TCR A 904 " ideal model delta sigma weight residual 1.416 1.479 -0.063 2.00e-02 2.50e+03 9.86e+00 bond pdb=" CD2 TCR B 904 " pdb=" CE2 TCR B 904 " ideal model delta sigma weight residual 1.416 1.478 -0.062 2.00e-02 2.50e+03 9.47e+00 bond pdb=" O3 PO4 A 905 " pdb=" P PO4 A 905 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.25e+00 ... (remaining 13251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 17440 1.67 - 3.34: 463 3.34 - 5.01: 87 5.01 - 6.68: 27 6.68 - 8.35: 15 Bond angle restraints: 18032 Sorted by residual: angle pdb=" C PHE B 762 " pdb=" N ILE B 763 " pdb=" CA ILE B 763 " ideal model delta sigma weight residual 122.43 118.02 4.41 1.26e+00 6.30e-01 1.22e+01 angle pdb=" C ASN B 468 " pdb=" N PHE B 469 " pdb=" CA PHE B 469 " ideal model delta sigma weight residual 122.21 116.69 5.52 1.62e+00 3.81e-01 1.16e+01 angle pdb=" C ASN A 468 " pdb=" N PHE A 469 " pdb=" CA PHE A 469 " ideal model delta sigma weight residual 121.75 115.99 5.76 1.73e+00 3.34e-01 1.11e+01 angle pdb=" C GLU B 604 " pdb=" N PHE B 605 " pdb=" CA PHE B 605 " ideal model delta sigma weight residual 122.32 127.79 -5.47 1.76e+00 3.23e-01 9.67e+00 angle pdb=" N VAL A 508 " pdb=" CA VAL A 508 " pdb=" C VAL A 508 " ideal model delta sigma weight residual 113.47 110.41 3.06 1.01e+00 9.80e-01 9.16e+00 ... (remaining 18027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7559 17.77 - 35.53: 643 35.53 - 53.30: 112 53.30 - 71.06: 36 71.06 - 88.83: 12 Dihedral angle restraints: 8362 sinusoidal: 3816 harmonic: 4546 Sorted by residual: dihedral pdb=" CB CYS A 546 " pdb=" SG CYS A 546 " pdb=" SG CYS A 565 " pdb=" CB CYS A 565 " ideal model delta sinusoidal sigma weight residual -86.00 -174.83 88.83 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS B 546 " pdb=" SG CYS B 546 " pdb=" SG CYS B 565 " pdb=" CB CYS B 565 " ideal model delta sinusoidal sigma weight residual 93.00 -179.25 -87.75 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 101 " pdb=" CB CYS B 101 " ideal model delta sinusoidal sigma weight residual -86.00 -23.86 -62.14 1 1.00e+01 1.00e-02 5.11e+01 ... (remaining 8359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1944 0.097 - 0.194: 100 0.194 - 0.291: 13 0.291 - 0.388: 8 0.388 - 0.485: 1 Chirality restraints: 2066 Sorted by residual: chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 261 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C14 CLR B 913 " pdb=" C13 CLR B 913 " pdb=" C15 CLR B 913 " pdb=" C8 CLR B 913 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C14 CLR A 912 " pdb=" C13 CLR A 912 " pdb=" C15 CLR A 912 " pdb=" C8 CLR A 912 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 2063 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 746 " -0.054 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO B 747 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 747 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 747 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 438 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO A 439 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 439 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 439 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 438 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO B 439 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 439 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 439 " -0.033 5.00e-02 4.00e+02 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 276 2.71 - 3.26: 13040 3.26 - 3.80: 21747 3.80 - 4.35: 28134 4.35 - 4.90: 45612 Nonbonded interactions: 108809 Sorted by model distance: nonbonded pdb=" OG SER B 657 " pdb=" O SER B 687 " model vdw 2.160 3.040 nonbonded pdb=" OG SER A 657 " pdb=" O SER A 687 " model vdw 2.173 3.040 nonbonded pdb=" OE2 GLU B 232 " pdb=" NH1 ARG B 233 " model vdw 2.232 3.120 nonbonded pdb=" OD2 ASP B 238 " pdb=" OG SER B 262 " model vdw 2.239 3.040 nonbonded pdb=" OG SER B 175 " pdb=" NH2 ARG B 185 " model vdw 2.249 3.120 ... (remaining 108804 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.090 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 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 : 0.004 0.113 13256 Z= 0.252 Angle : 0.698 8.346 18032 Z= 0.352 Chirality : 0.053 0.485 2066 Planarity : 0.004 0.082 2212 Dihedral : 13.548 86.088 5368 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.15 % Allowed : 0.07 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1546 helix: 1.27 (0.19), residues: 716 sheet: -0.67 (0.36), residues: 198 loop : -0.12 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 742 HIS 0.003 0.001 HIS A 463 PHE 0.019 0.001 PHE A 619 TYR 0.025 0.001 TYR A 425 ARG 0.003 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 226 time to evaluate : 2.995 Fit side-chains REVERT: A 285 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7409 (ttp80) REVERT: B 285 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7376 (ttp80) REVERT: B 536 GLU cc_start: 0.6952 (pm20) cc_final: 0.6697 (pm20) outliers start: 2 outliers final: 0 residues processed: 228 average time/residue: 1.1000 time to fit residues: 276.3683 Evaluate side-chains 205 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 253 GLN A 338 HIS A 466 HIS B 27 GLN B 253 GLN B 338 HIS B 466 HIS B 802 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13256 Z= 0.184 Angle : 0.562 10.334 18032 Z= 0.294 Chirality : 0.043 0.306 2066 Planarity : 0.004 0.053 2212 Dihedral : 8.470 59.671 2514 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.40 % Allowed : 8.70 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1546 helix: 1.54 (0.19), residues: 722 sheet: -0.64 (0.34), residues: 228 loop : 0.02 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 742 HIS 0.003 0.001 HIS B 463 PHE 0.022 0.001 PHE A 789 TYR 0.020 0.001 TYR A 425 ARG 0.002 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 207 time to evaluate : 1.407 Fit side-chains revert: symmetry clash REVERT: A 285 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7486 (ttp80) REVERT: B 285 ARG cc_start: 0.7699 (ttp80) cc_final: 0.7412 (ttp80) REVERT: B 536 GLU cc_start: 0.6976 (pm20) cc_final: 0.6775 (pm20) outliers start: 19 outliers final: 3 residues processed: 213 average time/residue: 1.1291 time to fit residues: 264.2887 Evaluate side-chains 195 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 619 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 113 optimal weight: 8.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS ** B 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13256 Z= 0.252 Angle : 0.571 10.183 18032 Z= 0.300 Chirality : 0.043 0.252 2066 Planarity : 0.004 0.047 2212 Dihedral : 8.008 59.202 2514 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.21 % Allowed : 10.25 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1546 helix: 1.55 (0.19), residues: 722 sheet: -0.85 (0.33), residues: 228 loop : -0.00 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 742 HIS 0.006 0.001 HIS A 312 PHE 0.016 0.002 PHE B 226 TYR 0.018 0.002 TYR A 425 ARG 0.004 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 208 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7474 (ttp80) REVERT: B 285 ARG cc_start: 0.7756 (ttp80) cc_final: 0.7346 (ttp80) REVERT: B 743 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6349 (mp) outliers start: 30 outliers final: 9 residues processed: 214 average time/residue: 1.0382 time to fit residues: 245.5944 Evaluate side-chains 206 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 743 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS A 493 ASN A 594 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN B 338 HIS B 466 HIS B 493 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 13256 Z= 0.464 Angle : 0.684 9.693 18032 Z= 0.360 Chirality : 0.049 0.379 2066 Planarity : 0.005 0.048 2212 Dihedral : 8.321 56.043 2514 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.24 % Allowed : 12.39 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1546 helix: 1.42 (0.19), residues: 706 sheet: -1.29 (0.31), residues: 228 loop : -0.30 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 742 HIS 0.006 0.001 HIS A 338 PHE 0.021 0.002 PHE A 789 TYR 0.019 0.003 TYR B 425 ARG 0.007 0.001 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 209 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: A 409 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7760 (tp) REVERT: B 270 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: B 409 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7747 (tp) outliers start: 44 outliers final: 16 residues processed: 227 average time/residue: 1.1199 time to fit residues: 281.8801 Evaluate side-chains 224 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 738 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN A 253 GLN A 338 HIS A 466 HIS A 493 ASN A 594 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS B 493 ASN B 766 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13256 Z= 0.211 Angle : 0.563 8.177 18032 Z= 0.297 Chirality : 0.043 0.266 2066 Planarity : 0.004 0.044 2212 Dihedral : 7.847 58.601 2514 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.43 % Allowed : 14.68 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1546 helix: 1.53 (0.19), residues: 710 sheet: -1.30 (0.32), residues: 228 loop : -0.15 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 742 HIS 0.008 0.001 HIS B 766 PHE 0.026 0.001 PHE B 789 TYR 0.011 0.001 TYR A 421 ARG 0.002 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 197 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: A 285 ARG cc_start: 0.7732 (ttp80) cc_final: 0.7419 (ttp80) REVERT: A 536 GLU cc_start: 0.7013 (pm20) cc_final: 0.6806 (pm20) REVERT: B 270 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: B 285 ARG cc_start: 0.7737 (ttp80) cc_final: 0.7485 (ttp80) REVERT: B 743 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6425 (mp) outliers start: 33 outliers final: 14 residues processed: 212 average time/residue: 1.1461 time to fit residues: 268.1842 Evaluate side-chains 208 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 743 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 150 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS A 594 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13256 Z= 0.297 Angle : 0.598 9.858 18032 Z= 0.314 Chirality : 0.045 0.446 2066 Planarity : 0.004 0.044 2212 Dihedral : 7.726 60.389 2514 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.73 % Allowed : 15.49 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1546 helix: 1.53 (0.19), residues: 708 sheet: -1.34 (0.32), residues: 228 loop : -0.22 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 742 HIS 0.004 0.001 HIS B 463 PHE 0.021 0.002 PHE A 789 TYR 0.014 0.002 TYR B 425 ARG 0.003 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 199 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: A 285 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7410 (ttp80) REVERT: B 270 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: B 285 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7461 (ttp80) REVERT: B 743 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6432 (mp) outliers start: 37 outliers final: 22 residues processed: 217 average time/residue: 1.0345 time to fit residues: 248.3947 Evaluate side-chains 220 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 195 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 743 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 110 optimal weight: 0.0980 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS A 802 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13256 Z= 0.165 Angle : 0.545 8.973 18032 Z= 0.285 Chirality : 0.042 0.271 2066 Planarity : 0.004 0.041 2212 Dihedral : 7.444 62.290 2514 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.29 % Allowed : 16.45 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1546 helix: 1.57 (0.19), residues: 722 sheet: -1.45 (0.31), residues: 240 loop : -0.06 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 742 HIS 0.005 0.001 HIS B 463 PHE 0.012 0.001 PHE B 469 TYR 0.019 0.001 TYR A 573 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 196 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: A 285 ARG cc_start: 0.7658 (ttp80) cc_final: 0.7430 (ttp80) REVERT: B 270 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: B 605 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6740 (p90) REVERT: B 738 ILE cc_start: 0.6805 (pp) cc_final: 0.6600 (pt) REVERT: B 743 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6508 (mp) outliers start: 31 outliers final: 13 residues processed: 211 average time/residue: 1.0202 time to fit residues: 238.3556 Evaluate side-chains 204 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 743 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 0.0030 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS A 594 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13256 Z= 0.276 Angle : 0.599 9.660 18032 Z= 0.315 Chirality : 0.044 0.255 2066 Planarity : 0.004 0.042 2212 Dihedral : 7.556 62.376 2514 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.21 % Allowed : 16.74 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1546 helix: 1.66 (0.19), residues: 710 sheet: -1.36 (0.32), residues: 228 loop : -0.10 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 742 HIS 0.003 0.001 HIS B 463 PHE 0.018 0.002 PHE B 469 TYR 0.015 0.002 TYR A 573 ARG 0.008 0.000 ARG B 285 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: A 285 ARG cc_start: 0.7636 (ttp80) cc_final: 0.7379 (ttp80) REVERT: B 270 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: B 743 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6522 (mp) outliers start: 30 outliers final: 16 residues processed: 207 average time/residue: 1.0825 time to fit residues: 247.3954 Evaluate side-chains 203 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 743 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 126 optimal weight: 0.4980 chunk 132 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13256 Z= 0.202 Angle : 0.593 11.891 18032 Z= 0.308 Chirality : 0.043 0.268 2066 Planarity : 0.004 0.041 2212 Dihedral : 7.711 62.925 2514 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.99 % Allowed : 17.33 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1546 helix: 1.55 (0.19), residues: 722 sheet: -1.50 (0.31), residues: 240 loop : -0.10 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 742 HIS 0.005 0.001 HIS A 312 PHE 0.039 0.001 PHE A 789 TYR 0.015 0.001 TYR A 573 ARG 0.006 0.000 ARG B 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 195 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: B 270 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: B 605 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.6822 (p90) REVERT: B 743 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6501 (mp) outliers start: 27 outliers final: 14 residues processed: 211 average time/residue: 1.0502 time to fit residues: 245.1292 Evaluate side-chains 206 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 188 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 667 PHE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 743 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 338 HIS A 466 HIS ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 13256 Z= 0.368 Angle : 0.662 11.592 18032 Z= 0.346 Chirality : 0.046 0.216 2066 Planarity : 0.004 0.043 2212 Dihedral : 7.794 62.348 2514 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.70 % Allowed : 18.07 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1546 helix: 1.50 (0.19), residues: 710 sheet: -1.44 (0.31), residues: 228 loop : -0.25 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 742 HIS 0.005 0.001 HIS A 312 PHE 0.021 0.002 PHE B 469 TYR 0.020 0.002 TYR A 573 ARG 0.006 0.001 ARG B 285 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3092 Ramachandran restraints generated. 1546 Oldfield, 0 Emsley, 1546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: A 409 ILE cc_start: 0.8181 (mm) cc_final: 0.7920 (tp) REVERT: B 270 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7715 (m-80) REVERT: B 409 ILE cc_start: 0.8155 (mm) cc_final: 0.7902 (tp) REVERT: B 743 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6540 (mp) outliers start: 23 outliers final: 18 residues processed: 208 average time/residue: 1.1015 time to fit residues: 252.7520 Evaluate side-chains 208 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 60 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 775 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN A 253 GLN A 338 HIS A 466 HIS A 594 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 466 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.175607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153162 restraints weight = 17453.888| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.49 r_work: 0.3597 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13256 Z= 0.210 Angle : 0.590 10.772 18032 Z= 0.307 Chirality : 0.042 0.199 2066 Planarity : 0.004 0.042 2212 Dihedral : 7.551 63.154 2514 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.47 % Allowed : 18.58 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1546 helix: 1.59 (0.19), residues: 710 sheet: -1.54 (0.30), residues: 242 loop : -0.14 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 742 HIS 0.005 0.001 HIS B 463 PHE 0.030 0.001 PHE A 789 TYR 0.024 0.002 TYR A 573 ARG 0.007 0.000 ARG B 285 =============================================================================== Job complete usr+sys time: 4608.68 seconds wall clock time: 81 minutes 27.39 seconds (4887.39 seconds total)