Starting phenix.real_space_refine on Thu Sep 26 12:32:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/09_2024/7sim_25144.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/09_2024/7sim_25144.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/7sim_25144/09_2024/7sim_25144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/09_2024/7sim_25144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/09_2024/7sim_25144.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sim_25144/09_2024/7sim_25144.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= 0.052 sd= 0.225 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 2 5.49 5 S 70 5.16 5 C 8386 2.51 5 N 2030 2.21 5 O 2330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 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: 12826 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'TCR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 149 Unusual residues: {' CA': 4, 'CLR': 5, 'PO4': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'TCR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 93 Unusual residues: {' CA': 4, 'CLR': 3, 'PO4': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 7.71, per 1000 atoms: 0.60 Number of scatterers: 12826 At special positions: 0 Unit cell: (100.43, 97.11, 173.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 70 16.00 P 2 15.00 O 2330 8.00 N 2030 7.00 C 8386 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=2.03 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=2.04 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 468 " " NAG B 901 " - " 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: 3.22 Conformation dependent library (CDL) restraints added in 1.8 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 14 sheets defined 51.7% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 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: 3.789A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.664A 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 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: 3.742A pdb=" N VAL A 455 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 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: 3.554A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 669 removed outlier: 3.759A pdb=" N PHE A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 4.062A 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 Processing helix chain 'A' and resid 723 through 746 Processing helix chain 'A' and resid 769 through 794 removed outlier: 3.659A pdb=" N SER A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 removed outlier: 3.553A pdb=" N PHE A 806 " --> pdb=" O ASN A 802 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE A 821 " --> pdb=" O VAL A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 826 removed outlier: 3.958A pdb=" N ALA A 826 " --> pdb=" O PRO A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 861 removed outlier: 3.967A pdb=" N SER A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.841A 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: 3.789A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.664A 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 232 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: 3.819A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 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: 3.595A pdb=" N THR B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 669 removed outlier: 3.803A pdb=" N PHE B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) removed outlier: 4.076A 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 Processing helix chain 'B' and resid 723 through 746 Processing helix chain 'B' and resid 769 through 794 removed outlier: 3.786A pdb=" N SER B 794 " --> pdb=" O PHE B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 821 removed outlier: 3.731A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 826 removed outlier: 3.892A pdb=" N ALA B 826 " --> pdb=" O PRO B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 861 removed outlier: 3.958A pdb=" N SER B 834 " --> pdb=" O GLY B 830 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 4.786A 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: 6.911A pdb=" N ILE A 33 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL A 165 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.189A 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: 7.935A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR A 489 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR A 510 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 491 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 554 Processing sheet with id=AA5, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AA6, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AA7, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.124A pdb=" N GLU A 602 " --> pdb=" O ILE A 761 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A 763 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU A 604 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N CYS A 765 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.980A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.920A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TRP B 208 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N VAL B 268 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY B 210 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N PHE B 270 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE B 212 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 468 through 470 Processing sheet with id=AB2, first strand: chain 'B' and resid 550 through 554 Processing sheet with id=AB3, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AB4, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AB5, first strand: chain 'B' and resid 602 through 604 648 hydrogen bonds defined for protein. 1854 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: 4.33 Time building geometry restraints manager: 3.69 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: 3944 1.34 - 1.46: 2632 1.46 - 1.58: 6496 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 13156 Sorted by residual: bond pdb=" CG TCR B 902 " pdb=" CD1 TCR B 902 " ideal model delta sigma weight residual 1.364 1.473 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" CG TCR A 902 " pdb=" CD1 TCR A 902 " ideal model delta sigma weight residual 1.364 1.472 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" O2 PO4 A 903 " pdb=" P PO4 A 903 " ideal model delta sigma weight residual 1.567 1.502 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O4 PO4 B 903 " pdb=" P PO4 B 903 " ideal model delta sigma weight residual 1.568 1.504 0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" O2 PO4 B 903 " pdb=" P PO4 B 903 " ideal model delta sigma weight residual 1.567 1.503 0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 13151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 17719 2.81 - 5.61: 160 5.61 - 8.42: 16 8.42 - 11.22: 4 11.22 - 14.03: 1 Bond angle restraints: 17900 Sorted by residual: angle pdb=" CA CYS B 598 " pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " ideal model delta sigma weight residual 114.40 124.06 -9.66 2.30e+00 1.89e-01 1.76e+01 angle pdb=" CA LEU A 690 " pdb=" CB LEU A 690 " pdb=" CG LEU A 690 " ideal model delta sigma weight residual 116.30 130.33 -14.03 3.50e+00 8.16e-02 1.61e+01 angle pdb=" CA CYS A 598 " pdb=" CB CYS A 598 " pdb=" SG CYS A 598 " ideal model delta sigma weight residual 114.40 123.22 -8.82 2.30e+00 1.89e-01 1.47e+01 angle pdb=" N GLY B 219 " pdb=" CA GLY B 219 " pdb=" C GLY B 219 " ideal model delta sigma weight residual 112.49 116.76 -4.27 1.21e+00 6.83e-01 1.25e+01 angle pdb=" N GLY A 219 " pdb=" CA GLY A 219 " pdb=" C GLY A 219 " ideal model delta sigma weight residual 112.49 116.76 -4.27 1.21e+00 6.83e-01 1.24e+01 ... (remaining 17895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 7481 17.52 - 35.03: 601 35.03 - 52.55: 136 52.55 - 70.06: 22 70.06 - 87.58: 12 Dihedral angle restraints: 8252 sinusoidal: 3706 harmonic: 4546 Sorted by residual: dihedral pdb=" CB CYS B 358 " pdb=" SG CYS B 358 " pdb=" SG CYS B 395 " pdb=" CB CYS B 395 " ideal model delta sinusoidal sigma weight residual 93.00 34.39 58.61 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CB CYS A 358 " pdb=" SG CYS A 358 " pdb=" SG CYS A 395 " pdb=" CB CYS A 395 " ideal model delta sinusoidal sigma weight residual 93.00 46.44 46.56 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CB CYS B 585 " pdb=" SG CYS B 585 " pdb=" SG CYS B 598 " pdb=" CB CYS B 598 " ideal model delta sinusoidal sigma weight residual -86.00 -126.15 40.15 1 1.00e+01 1.00e-02 2.26e+01 ... (remaining 8249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1805 0.071 - 0.142: 208 0.142 - 0.213: 14 0.213 - 0.284: 9 0.284 - 0.355: 8 Chirality restraints: 2044 Sorted by residual: chirality pdb=" C14 CLR B 910 " pdb=" C13 CLR B 910 " pdb=" C15 CLR B 910 " pdb=" C8 CLR B 910 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C14 CLR A 911 " pdb=" C13 CLR A 911 " pdb=" C15 CLR A 911 " pdb=" C8 CLR A 911 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C14 CLR B 908 " pdb=" C13 CLR B 908 " pdb=" C15 CLR B 908 " pdb=" C8 CLR B 908 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 2041 not shown) Planarity restraints: 2210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 818 " 0.010 2.00e-02 2.50e+03 1.11e-02 3.07e+00 pdb=" CG TRP A 818 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 818 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 818 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 818 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 818 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 818 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 818 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 818 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 818 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 187 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A 188 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 187 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO B 188 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 188 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 188 " 0.024 5.00e-02 4.00e+02 ... (remaining 2207 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3837 2.82 - 3.34: 12227 3.34 - 3.86: 22254 3.86 - 4.38: 26262 4.38 - 4.90: 43675 Nonbonded interactions: 108255 Sorted by model distance: nonbonded pdb=" OG SER A 657 " pdb=" O SER A 687 " model vdw 2.302 3.040 nonbonded pdb=" OG SER B 657 " pdb=" O SER B 687 " model vdw 2.313 3.040 nonbonded pdb=" O PHE A 351 " pdb=" OG1 THR A 355 " model vdw 2.317 3.040 nonbonded pdb=" OD2 ASP A 238 " pdb=" OG SER A 262 " model vdw 2.328 3.040 nonbonded pdb=" OG SER A 175 " pdb=" NH2 ARG A 185 " model vdw 2.338 3.120 ... (remaining 108250 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 21 through 861 or resid 901 through 902 or resid 903 throu \ gh 910)) 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: 0.300 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: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.070 Find NCS groups from input model: 0.560 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: 0.010 Load rotamer database and sin/cos tables:10.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 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 : 0.005 0.109 13156 Z= 0.349 Angle : 0.705 14.030 17900 Z= 0.360 Chirality : 0.052 0.355 2044 Planarity : 0.004 0.043 2204 Dihedral : 13.376 87.577 5258 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.07 % Allowed : 0.07 % Favored : 99.85 % 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: 0.36 (0.20), residues: 1546 helix: 1.10 (0.18), residues: 728 sheet: -0.65 (0.36), residues: 212 loop : -0.37 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 818 HIS 0.006 0.001 HIS B 312 PHE 0.017 0.002 PHE B 788 TYR 0.024 0.002 TYR A 425 ARG 0.008 0.001 ARG B 795 *********************** 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 218 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 1.472 Fit side-chains REVERT: B 257 GLU cc_start: 0.6822 (tp30) cc_final: 0.6602 (mm-30) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 1.2203 time to fit residues: 290.2401 Evaluate side-chains 204 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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: 0.3980 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 74 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 595 HIS A 722 ASN B 312 HIS B 357 ASN B 466 HIS B 722 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13156 Z= 0.173 Angle : 0.529 7.927 17900 Z= 0.280 Chirality : 0.042 0.159 2044 Planarity : 0.004 0.042 2204 Dihedral : 6.719 59.162 2404 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.74 % Allowed : 7.30 % Favored : 91.96 % 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: 1.34 (0.18), residues: 728 sheet: -0.51 (0.36), residues: 210 loop : -0.36 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 742 HIS 0.005 0.001 HIS A 312 PHE 0.012 0.001 PHE B 226 TYR 0.015 0.001 TYR B 435 ARG 0.005 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 217 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 207 time to evaluate : 1.388 Fit side-chains REVERT: A 227 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7822 (ttp80) REVERT: A 516 LYS cc_start: 0.7486 (ttpp) cc_final: 0.7190 (ttpp) REVERT: B 771 MET cc_start: 0.4695 (OUTLIER) cc_final: 0.4464 (mmm) outliers start: 10 outliers final: 6 residues processed: 209 average time/residue: 1.1894 time to fit residues: 272.3690 Evaluate side-chains 205 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 198 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 771 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 117 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 312 HIS ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN B 357 ASN B 722 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13156 Z= 0.190 Angle : 0.517 8.354 17900 Z= 0.273 Chirality : 0.041 0.166 2044 Planarity : 0.004 0.041 2204 Dihedral : 6.343 57.732 2404 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.18 % Allowed : 9.66 % Favored : 89.16 % 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: 0.62 (0.21), residues: 1546 helix: 1.45 (0.18), residues: 728 sheet: -0.60 (0.36), residues: 210 loop : -0.40 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 742 HIS 0.004 0.001 HIS A 312 PHE 0.012 0.001 PHE B 832 TYR 0.017 0.002 TYR A 435 ARG 0.008 0.001 ARG B 25 *********************** 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 215 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 1.376 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 200 average time/residue: 1.2428 time to fit residues: 271.1415 Evaluate side-chains 203 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 738 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 493 ASN A 595 HIS B 357 ASN B 493 ASN B 722 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.149 13156 Z= 0.585 Angle : 0.726 11.676 17900 Z= 0.386 Chirality : 0.053 0.224 2044 Planarity : 0.005 0.074 2204 Dihedral : 6.698 55.796 2404 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.84 % Allowed : 11.43 % Favored : 86.73 % 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: 0.10 (0.20), residues: 1546 helix: 1.08 (0.18), residues: 698 sheet: -0.99 (0.33), residues: 214 loop : -0.59 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 742 HIS 0.008 0.002 HIS B 429 PHE 0.029 0.003 PHE B 788 TYR 0.022 0.003 TYR A 425 ARG 0.007 0.001 ARG A 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 237 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 212 time to evaluate : 1.453 Fit side-chains REVERT: B 605 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7499 (p90) outliers start: 25 outliers final: 17 residues processed: 216 average time/residue: 1.1972 time to fit residues: 282.7094 Evaluate side-chains 228 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 210 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 822 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 179 GLN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 595 HIS A 722 ASN B 27 GLN B 179 GLN B 312 HIS B 357 ASN B 722 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13156 Z= 0.213 Angle : 0.548 11.135 17900 Z= 0.291 Chirality : 0.042 0.188 2044 Planarity : 0.004 0.047 2204 Dihedral : 6.308 57.317 2404 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.47 % Allowed : 13.79 % Favored : 84.73 % 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: 0.31 (0.21), residues: 1546 helix: 1.26 (0.18), residues: 714 sheet: -0.95 (0.33), residues: 224 loop : -0.49 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 742 HIS 0.005 0.001 HIS B 463 PHE 0.014 0.001 PHE A 762 TYR 0.022 0.002 TYR B 435 ARG 0.008 0.000 ARG B 227 *********************** 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 226 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 1.325 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 213 average time/residue: 1.2556 time to fit residues: 292.5774 Evaluate side-chains 211 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 201 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 828 THR 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: 0.9990 chunk 29 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 79 optimal weight: 0.0970 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 338 HIS A 722 ASN B 27 GLN B 359 HIS B 722 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13156 Z= 0.268 Angle : 0.564 12.233 17900 Z= 0.297 Chirality : 0.043 0.188 2044 Planarity : 0.004 0.047 2204 Dihedral : 6.355 59.803 2404 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.84 % Allowed : 14.38 % Favored : 83.78 % 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: 0.33 (0.21), residues: 1546 helix: 1.33 (0.18), residues: 712 sheet: -0.89 (0.33), residues: 222 loop : -0.59 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 742 HIS 0.006 0.001 HIS B 359 PHE 0.016 0.001 PHE A 762 TYR 0.021 0.002 TYR B 435 ARG 0.008 0.001 ARG A 25 *********************** 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 226 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 201 time to evaluate : 1.417 Fit side-chains REVERT: A 270 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8094 (t80) REVERT: B 270 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.8102 (t80) outliers start: 25 outliers final: 13 residues processed: 212 average time/residue: 1.1643 time to fit residues: 270.2480 Evaluate side-chains 211 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 771 MET Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 338 HIS A 722 ASN B 27 GLN B 722 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13156 Z= 0.226 Angle : 0.544 12.960 17900 Z= 0.285 Chirality : 0.042 0.199 2044 Planarity : 0.004 0.042 2204 Dihedral : 6.183 59.382 2404 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.99 % Allowed : 14.90 % Favored : 83.11 % 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: 0.37 (0.21), residues: 1546 helix: 1.37 (0.18), residues: 722 sheet: -0.88 (0.33), residues: 222 loop : -0.62 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 742 HIS 0.005 0.001 HIS B 463 PHE 0.014 0.001 PHE B 788 TYR 0.023 0.002 TYR B 435 ARG 0.010 0.001 ARG A 25 *********************** 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 221 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 1.443 Fit side-chains REVERT: A 257 GLU cc_start: 0.6422 (tm-30) cc_final: 0.5969 (tm-30) REVERT: A 270 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8075 (t80) REVERT: B 270 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8102 (t80) outliers start: 27 outliers final: 15 residues processed: 206 average time/residue: 1.2212 time to fit residues: 274.6916 Evaluate side-chains 210 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 144 optimal weight: 0.0270 overall best weight: 4.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 ASN B 27 GLN B 722 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 13156 Z= 0.420 Angle : 0.649 16.322 17900 Z= 0.340 Chirality : 0.047 0.205 2044 Planarity : 0.005 0.054 2204 Dihedral : 6.340 56.746 2404 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.43 % Allowed : 15.04 % Favored : 82.52 % 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: 0.22 (0.20), residues: 1546 helix: 1.28 (0.18), residues: 696 sheet: -0.98 (0.33), residues: 222 loop : -0.64 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 742 HIS 0.006 0.001 HIS A 429 PHE 0.019 0.002 PHE B 788 TYR 0.022 0.002 TYR A 435 ARG 0.013 0.001 ARG A 25 *********************** 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 233 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 1.515 Fit side-chains REVERT: B 605 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7352 (p90) outliers start: 33 outliers final: 20 residues processed: 217 average time/residue: 1.2325 time to fit residues: 294.3077 Evaluate side-chains 220 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 738 ILE Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 84 optimal weight: 0.0370 chunk 61 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN B 27 GLN B 722 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13156 Z= 0.169 Angle : 0.540 11.709 17900 Z= 0.280 Chirality : 0.041 0.176 2044 Planarity : 0.004 0.042 2204 Dihedral : 5.946 56.597 2404 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.33 % Allowed : 16.45 % Favored : 82.23 % 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: 0.42 (0.21), residues: 1546 helix: 1.29 (0.18), residues: 734 sheet: -0.61 (0.37), residues: 186 loop : -0.59 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 818 HIS 0.006 0.001 HIS A 463 PHE 0.017 0.001 PHE A 788 TYR 0.022 0.001 TYR A 435 ARG 0.008 0.001 ARG A 25 *********************** 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 207 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 1.389 Fit side-chains REVERT: A 257 GLU cc_start: 0.6406 (tm-30) cc_final: 0.5958 (tm-30) outliers start: 18 outliers final: 8 residues processed: 197 average time/residue: 1.2093 time to fit residues: 260.4073 Evaluate side-chains 197 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 738 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 123 optimal weight: 0.2980 chunk 12 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 722 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 13156 Z= 0.364 Angle : 0.621 12.482 17900 Z= 0.327 Chirality : 0.045 0.192 2044 Planarity : 0.004 0.048 2204 Dihedral : 6.083 57.975 2404 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.40 % Allowed : 16.96 % Favored : 81.64 % 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: 0.34 (0.21), residues: 1546 helix: 1.33 (0.18), residues: 706 sheet: -0.84 (0.35), residues: 200 loop : -0.59 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 818 HIS 0.005 0.001 HIS B 429 PHE 0.016 0.002 PHE B 788 TYR 0.023 0.002 TYR A 435 ARG 0.012 0.001 ARG A 25 ********************** 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 217 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 1.401 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 208 average time/residue: 1.2131 time to fit residues: 275.7584 Evaluate side-chains 211 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 199 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 738 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 ASN B 722 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.182135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.158019 restraints weight = 17078.149| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.75 r_work: 0.3598 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13156 Z= 0.166 Angle : 0.535 9.917 17900 Z= 0.277 Chirality : 0.040 0.178 2044 Planarity : 0.004 0.040 2204 Dihedral : 5.740 55.520 2404 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.59 % Allowed : 18.07 % Favored : 81.34 % 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: 0.50 (0.21), residues: 1546 helix: 1.36 (0.19), residues: 734 sheet: -0.59 (0.37), residues: 186 loop : -0.53 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 818 HIS 0.005 0.001 HIS A 463 PHE 0.014 0.001 PHE B 688 TYR 0.022 0.001 TYR A 435 ARG 0.007 0.000 ARG A 25 =============================================================================== Job complete usr+sys time: 4758.95 seconds wall clock time: 83 minutes 42.76 seconds (5022.76 seconds total)