Starting phenix.real_space_refine on Thu Feb 5 18:48:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dd6_46758/02_2026/9dd6_46758.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dd6_46758/02_2026/9dd6_46758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dd6_46758/02_2026/9dd6_46758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dd6_46758/02_2026/9dd6_46758.map" model { file = "/net/cci-nas-00/data/ceres_data/9dd6_46758/02_2026/9dd6_46758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dd6_46758/02_2026/9dd6_46758.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 11880 2.51 5 N 3222 2.21 5 O 3726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18906 Number of models: 1 Model: "" Number of chains: 18 Chain: "E" Number of atoms: 4512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4512 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 27, 'TRANS': 532} Chain breaks: 3 Chain: "F" Number of atoms: 4512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4512 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 27, 'TRANS': 532} Chain breaks: 3 Chain: "G" Number of atoms: 4512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4512 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 27, 'TRANS': 532} Chain breaks: 3 Chain: "H" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "I" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "J" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "M" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "N" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "A" 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: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "G" 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 Time building chain proxies: 3.47, per 1000 atoms: 0.18 Number of scatterers: 18906 At special positions: 0 Unit cell: (159.36, 151.89, 114.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3726 8.00 N 3222 7.00 C 11880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS E 116 " - pdb=" SG CYS E 573 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 529 " distance=2.03 Simple disulfide: pdb=" SG CYS E 207 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS E 364 " - pdb=" SG CYS E 412 " distance=2.03 Simple disulfide: pdb=" SG CYS E 596 " - pdb=" SG CYS E 633 " distance=2.05 Simple disulfide: pdb=" SG CYS F 116 " - pdb=" SG CYS F 573 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 529 " distance=2.03 Simple disulfide: pdb=" SG CYS F 207 " - pdb=" SG CYS F 271 " distance=2.03 Simple disulfide: pdb=" SG CYS F 364 " - pdb=" SG CYS F 412 " distance=2.03 Simple disulfide: pdb=" SG CYS F 596 " - pdb=" SG CYS F 633 " distance=2.05 Simple disulfide: pdb=" SG CYS G 116 " - pdb=" SG CYS G 573 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 529 " distance=2.03 Simple disulfide: pdb=" SG CYS G 207 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 364 " - pdb=" SG CYS G 412 " distance=2.03 Simple disulfide: pdb=" SG CYS G 596 " - pdb=" SG CYS G 633 " distance=2.05 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 1 " - " ASN E 141 " " NAG B 1 " - " ASN E 398 " " NAG C 1 " - " ASN F 141 " " NAG D 1 " - " ASN F 398 " " NAG E 901 " - " ASN E 430 " " NAG E 902 " - " ASN E 674 " " NAG F 901 " - " ASN F 430 " " NAG F 902 " - " ASN F 674 " " NAG G 901 " - " ASN G 430 " " NAG G 902 " - " ASN G 674 " " NAG K 1 " - " ASN G 141 " " NAG O 1 " - " ASN G 398 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 707.6 milliseconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4398 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 48 sheets defined 20.2% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'E' and resid 193 through 200 removed outlier: 3.559A pdb=" N VAL E 197 " --> pdb=" O PRO E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 205 Processing helix chain 'E' and resid 223 through 227 Processing helix chain 'E' and resid 306 through 310 removed outlier: 4.364A pdb=" N THR E 309 " --> pdb=" O GLY E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 317 No H-bonds generated for 'chain 'E' and resid 315 through 317' Processing helix chain 'E' and resid 403 through 408 removed outlier: 4.908A pdb=" N ASP E 408 " --> pdb=" O SER E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 429 removed outlier: 4.045A pdb=" N LYS E 415 " --> pdb=" O ASP E 411 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP E 416 " --> pdb=" O CYS E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 473 removed outlier: 3.584A pdb=" N SER E 473 " --> pdb=" O LEU E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 546 Proline residue: E 516 - end of helix removed outlier: 3.625A pdb=" N VAL E 524 " --> pdb=" O MET E 520 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 538 " --> pdb=" O HIS E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 577 through 579 No H-bonds generated for 'chain 'E' and resid 577 through 579' Processing helix chain 'E' and resid 660 through 664 removed outlier: 3.513A pdb=" N ASP E 663 " --> pdb=" O SER E 660 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE E 664 " --> pdb=" O ARG E 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 660 through 664' Processing helix chain 'E' and resid 686 through 691 Processing helix chain 'E' and resid 701 through 721 removed outlier: 3.984A pdb=" N GLN E 710 " --> pdb=" O GLN E 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 200 removed outlier: 3.560A pdb=" N VAL F 197 " --> pdb=" O PRO F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 205 Processing helix chain 'F' and resid 223 through 227 Processing helix chain 'F' and resid 306 through 310 removed outlier: 4.363A pdb=" N THR F 309 " --> pdb=" O GLY F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 317 No H-bonds generated for 'chain 'F' and resid 315 through 317' Processing helix chain 'F' and resid 403 through 408 removed outlier: 4.909A pdb=" N ASP F 408 " --> pdb=" O SER F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 429 removed outlier: 4.046A pdb=" N LYS F 415 " --> pdb=" O ASP F 411 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP F 416 " --> pdb=" O CYS F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 473 removed outlier: 3.584A pdb=" N SER F 473 " --> pdb=" O LEU F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 546 Proline residue: F 516 - end of helix removed outlier: 3.625A pdb=" N VAL F 524 " --> pdb=" O MET F 520 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU F 538 " --> pdb=" O HIS F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 577 through 579 No H-bonds generated for 'chain 'F' and resid 577 through 579' Processing helix chain 'F' and resid 660 through 664 removed outlier: 3.513A pdb=" N ASP F 663 " --> pdb=" O SER F 660 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE F 664 " --> pdb=" O ARG F 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 660 through 664' Processing helix chain 'F' and resid 686 through 691 Processing helix chain 'F' and resid 701 through 721 removed outlier: 3.984A pdb=" N GLN F 710 " --> pdb=" O GLN F 706 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 200 removed outlier: 3.559A pdb=" N VAL G 197 " --> pdb=" O PRO G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 205 Processing helix chain 'G' and resid 223 through 227 Processing helix chain 'G' and resid 306 through 310 removed outlier: 4.363A pdb=" N THR G 309 " --> pdb=" O GLY G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 317 No H-bonds generated for 'chain 'G' and resid 315 through 317' Processing helix chain 'G' and resid 403 through 408 removed outlier: 4.908A pdb=" N ASP G 408 " --> pdb=" O SER G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 429 removed outlier: 4.045A pdb=" N LYS G 415 " --> pdb=" O ASP G 411 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP G 416 " --> pdb=" O CYS G 412 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 473 removed outlier: 3.585A pdb=" N SER G 473 " --> pdb=" O LEU G 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 546 Proline residue: G 516 - end of helix removed outlier: 3.625A pdb=" N VAL G 524 " --> pdb=" O MET G 520 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU G 538 " --> pdb=" O HIS G 534 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 556 Processing helix chain 'G' and resid 577 through 579 No H-bonds generated for 'chain 'G' and resid 577 through 579' Processing helix chain 'G' and resid 660 through 664 removed outlier: 3.513A pdb=" N ASP G 663 " --> pdb=" O SER G 660 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE G 664 " --> pdb=" O ARG G 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 660 through 664' Processing helix chain 'G' and resid 686 through 691 Processing helix chain 'G' and resid 701 through 721 removed outlier: 3.984A pdb=" N GLN G 710 " --> pdb=" O GLN G 706 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.629A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.629A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.629A pdb=" N THR J 91 " --> pdb=" O ALA J 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 113 through 115 removed outlier: 3.638A pdb=" N VAL E 574 " --> pdb=" O VAL E 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 559 through 563 removed outlier: 3.803A pdb=" N MET E 568 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR E 123 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR F 665 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 395 through 397 removed outlier: 3.519A pdb=" N THR E 397 " --> pdb=" O PHE E 384 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N THR E 367 " --> pdb=" O GLU E 152 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU E 152 " --> pdb=" O THR E 367 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TRP E 369 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE E 150 " --> pdb=" O TRP E 369 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLU E 371 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL E 148 " --> pdb=" O GLU E 371 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ASP E 373 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE E 146 " --> pdb=" O ASP E 373 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET E 375 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU E 144 " --> pdb=" O MET E 375 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG E 377 " --> pdb=" O TYR E 142 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR E 142 " --> pdb=" O ARG E 377 " (cutoff:3.500A) removed outlier: 13.897A pdb=" N TYR E 142 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N SER E 457 " --> pdb=" O TYR E 142 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU E 144 " --> pdb=" O LEU E 455 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU E 456 " --> pdb=" O ILE E 434 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 395 through 397 removed outlier: 3.519A pdb=" N THR E 397 " --> pdb=" O PHE E 384 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N THR E 367 " --> pdb=" O GLU E 152 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU E 152 " --> pdb=" O THR E 367 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TRP E 369 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE E 150 " --> pdb=" O TRP E 369 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLU E 371 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL E 148 " --> pdb=" O GLU E 371 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ASP E 373 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE E 146 " --> pdb=" O ASP E 373 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET E 375 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU E 144 " --> pdb=" O MET E 375 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG E 377 " --> pdb=" O TYR E 142 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR E 142 " --> pdb=" O ARG E 377 " (cutoff:3.500A) removed outlier: 13.897A pdb=" N TYR E 142 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N SER E 457 " --> pdb=" O TYR E 142 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU E 144 " --> pdb=" O LEU E 455 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E 448 " --> pdb=" O ALA E 444 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 188 through 190 Processing sheet with id=AA6, first strand: chain 'E' and resid 235 through 236 removed outlier: 7.576A pdb=" N LYS E 160 " --> pdb=" O ASP E 355 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP E 355 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 206 through 208 Processing sheet with id=AA8, first strand: chain 'E' and resid 211 through 214 Processing sheet with id=AA9, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AB1, first strand: chain 'E' and resid 595 through 597 Processing sheet with id=AB2, first strand: chain 'E' and resid 638 through 643 removed outlier: 3.532A pdb=" N HIS E 657 " --> pdb=" O TYR E 649 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU E 651 " --> pdb=" O TYR E 655 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR E 655 " --> pdb=" O GLU E 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 665 through 666 removed outlier: 5.718A pdb=" N THR E 665 " --> pdb=" O GLN G 126 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR G 123 " --> pdb=" O VAL G 570 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET G 568 " --> pdb=" O VAL G 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 113 through 115 removed outlier: 3.638A pdb=" N VAL F 574 " --> pdb=" O VAL F 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 559 through 563 removed outlier: 3.804A pdb=" N MET F 568 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR F 123 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR G 665 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 395 through 397 removed outlier: 3.520A pdb=" N THR F 397 " --> pdb=" O PHE F 384 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N THR F 367 " --> pdb=" O GLU F 152 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU F 152 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TRP F 369 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE F 150 " --> pdb=" O TRP F 369 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLU F 371 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL F 148 " --> pdb=" O GLU F 371 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ASP F 373 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE F 146 " --> pdb=" O ASP F 373 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET F 375 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU F 144 " --> pdb=" O MET F 375 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG F 377 " --> pdb=" O TYR F 142 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR F 142 " --> pdb=" O ARG F 377 " (cutoff:3.500A) removed outlier: 13.896A pdb=" N TYR F 142 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N SER F 457 " --> pdb=" O TYR F 142 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU F 144 " --> pdb=" O LEU F 455 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU F 456 " --> pdb=" O ILE F 434 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 395 through 397 removed outlier: 3.520A pdb=" N THR F 397 " --> pdb=" O PHE F 384 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N THR F 367 " --> pdb=" O GLU F 152 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU F 152 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TRP F 369 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE F 150 " --> pdb=" O TRP F 369 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLU F 371 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL F 148 " --> pdb=" O GLU F 371 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ASP F 373 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE F 146 " --> pdb=" O ASP F 373 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET F 375 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU F 144 " --> pdb=" O MET F 375 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG F 377 " --> pdb=" O TYR F 142 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR F 142 " --> pdb=" O ARG F 377 " (cutoff:3.500A) removed outlier: 13.896A pdb=" N TYR F 142 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N SER F 457 " --> pdb=" O TYR F 142 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU F 144 " --> pdb=" O LEU F 455 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE F 448 " --> pdb=" O ALA F 444 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 188 through 190 Processing sheet with id=AB9, first strand: chain 'F' and resid 235 through 236 removed outlier: 7.576A pdb=" N LYS F 160 " --> pdb=" O ASP F 355 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP F 355 " --> pdb=" O LYS F 160 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 206 through 208 Processing sheet with id=AC2, first strand: chain 'F' and resid 211 through 214 Processing sheet with id=AC3, first strand: chain 'F' and resid 581 through 583 Processing sheet with id=AC4, first strand: chain 'F' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'F' and resid 638 through 643 removed outlier: 3.531A pdb=" N HIS F 657 " --> pdb=" O TYR F 649 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU F 651 " --> pdb=" O TYR F 655 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR F 655 " --> pdb=" O GLU F 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 113 through 115 removed outlier: 3.638A pdb=" N VAL G 574 " --> pdb=" O VAL G 115 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 395 through 397 removed outlier: 3.519A pdb=" N THR G 397 " --> pdb=" O PHE G 384 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N THR G 367 " --> pdb=" O GLU G 152 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU G 152 " --> pdb=" O THR G 367 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TRP G 369 " --> pdb=" O PHE G 150 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE G 150 " --> pdb=" O TRP G 369 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU G 371 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL G 148 " --> pdb=" O GLU G 371 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ASP G 373 " --> pdb=" O ILE G 146 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE G 146 " --> pdb=" O ASP G 373 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET G 375 " --> pdb=" O GLU G 144 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU G 144 " --> pdb=" O MET G 375 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG G 377 " --> pdb=" O TYR G 142 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR G 142 " --> pdb=" O ARG G 377 " (cutoff:3.500A) removed outlier: 13.897A pdb=" N TYR G 142 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N SER G 457 " --> pdb=" O TYR G 142 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU G 144 " --> pdb=" O LEU G 455 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU G 456 " --> pdb=" O ILE G 434 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 395 through 397 removed outlier: 3.519A pdb=" N THR G 397 " --> pdb=" O PHE G 384 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N THR G 367 " --> pdb=" O GLU G 152 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU G 152 " --> pdb=" O THR G 367 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TRP G 369 " --> pdb=" O PHE G 150 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N PHE G 150 " --> pdb=" O TRP G 369 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU G 371 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL G 148 " --> pdb=" O GLU G 371 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ASP G 373 " --> pdb=" O ILE G 146 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE G 146 " --> pdb=" O ASP G 373 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET G 375 " --> pdb=" O GLU G 144 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU G 144 " --> pdb=" O MET G 375 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG G 377 " --> pdb=" O TYR G 142 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR G 142 " --> pdb=" O ARG G 377 " (cutoff:3.500A) removed outlier: 13.897A pdb=" N TYR G 142 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N SER G 457 " --> pdb=" O TYR G 142 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU G 144 " --> pdb=" O LEU G 455 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE G 448 " --> pdb=" O ALA G 444 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 188 through 190 Processing sheet with id=AD1, first strand: chain 'G' and resid 235 through 236 removed outlier: 7.576A pdb=" N LYS G 160 " --> pdb=" O ASP G 355 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP G 355 " --> pdb=" O LYS G 160 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 206 through 208 Processing sheet with id=AD3, first strand: chain 'G' and resid 211 through 214 Processing sheet with id=AD4, first strand: chain 'G' and resid 581 through 583 Processing sheet with id=AD5, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AD6, first strand: chain 'G' and resid 638 through 643 removed outlier: 3.532A pdb=" N HIS G 657 " --> pdb=" O TYR G 649 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU G 651 " --> pdb=" O TYR G 655 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR G 655 " --> pdb=" O GLU G 651 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'H' and resid 12 through 13 removed outlier: 6.649A pdb=" N VAL H 35 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL H 51 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP H 37 " --> pdb=" O LEU H 49 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'I' and resid 12 through 13 removed outlier: 6.650A pdb=" N VAL I 35 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL I 51 " --> pdb=" O VAL I 35 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP I 37 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'J' and resid 12 through 13 removed outlier: 6.649A pdb=" N VAL J 35 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL J 51 " --> pdb=" O VAL J 35 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP J 37 " --> pdb=" O LEU J 49 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.537A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.275A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.275A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.536A pdb=" N VAL M 19 " --> pdb=" O ILE M 75 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.274A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP M 85 " --> pdb=" O GLN M 38 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.274A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.537A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.275A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP N 85 " --> pdb=" O GLN N 38 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.275A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 1.86 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: 6138 1.34 - 1.46: 4485 1.46 - 1.58: 8595 1.58 - 1.70: 3 1.70 - 1.82: 114 Bond restraints: 19335 Sorted by residual: bond pdb=" N GLN G 129 " pdb=" CA GLN G 129 " ideal model delta sigma weight residual 1.455 1.489 -0.034 7.00e-03 2.04e+04 2.32e+01 bond pdb=" N GLN F 129 " pdb=" CA GLN F 129 " ideal model delta sigma weight residual 1.455 1.489 -0.034 7.00e-03 2.04e+04 2.31e+01 bond pdb=" N GLN E 129 " pdb=" CA GLN E 129 " ideal model delta sigma weight residual 1.455 1.489 -0.033 7.00e-03 2.04e+04 2.29e+01 bond pdb=" N TYR I 99 " pdb=" CA TYR I 99 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.16e-02 7.43e+03 1.26e+01 bond pdb=" N VAL J 97 " pdb=" CA VAL J 97 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.27e-02 6.20e+03 1.23e+01 ... (remaining 19330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 26076 3.70 - 7.39: 177 7.39 - 11.09: 12 11.09 - 14.79: 0 14.79 - 18.48: 6 Bond angle restraints: 26271 Sorted by residual: angle pdb=" N PHE F 127 " pdb=" CA PHE F 127 " pdb=" CB PHE F 127 " ideal model delta sigma weight residual 111.13 93.63 17.50 1.79e+00 3.12e-01 9.55e+01 angle pdb=" N PHE E 127 " pdb=" CA PHE E 127 " pdb=" CB PHE E 127 " ideal model delta sigma weight residual 111.13 93.64 17.49 1.79e+00 3.12e-01 9.54e+01 angle pdb=" N PHE G 127 " pdb=" CA PHE G 127 " pdb=" CB PHE G 127 " ideal model delta sigma weight residual 111.13 93.67 17.46 1.79e+00 3.12e-01 9.51e+01 angle pdb=" C PHE E 127 " pdb=" CA PHE E 127 " pdb=" CB PHE E 127 " ideal model delta sigma weight residual 109.38 127.86 -18.48 2.03e+00 2.43e-01 8.29e+01 angle pdb=" C PHE G 127 " pdb=" CA PHE G 127 " pdb=" CB PHE G 127 " ideal model delta sigma weight residual 109.38 127.85 -18.47 2.03e+00 2.43e-01 8.28e+01 ... (remaining 26266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 10811 16.93 - 33.86: 784 33.86 - 50.79: 135 50.79 - 67.72: 48 67.72 - 84.65: 45 Dihedral angle restraints: 11823 sinusoidal: 4971 harmonic: 6852 Sorted by residual: dihedral pdb=" CB CYS E 596 " pdb=" SG CYS E 596 " pdb=" SG CYS E 633 " pdb=" CB CYS E 633 " ideal model delta sinusoidal sigma weight residual -86.00 -154.72 68.72 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CB CYS G 596 " pdb=" SG CYS G 596 " pdb=" SG CYS G 633 " pdb=" CB CYS G 633 " ideal model delta sinusoidal sigma weight residual -86.00 -154.70 68.70 1 1.00e+01 1.00e-02 6.11e+01 dihedral pdb=" CB CYS F 596 " pdb=" SG CYS F 596 " pdb=" SG CYS F 633 " pdb=" CB CYS F 633 " ideal model delta sinusoidal sigma weight residual -86.00 -154.68 68.68 1 1.00e+01 1.00e-02 6.11e+01 ... (remaining 11820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2350 0.053 - 0.107: 471 0.107 - 0.160: 122 0.160 - 0.213: 15 0.213 - 0.267: 3 Chirality restraints: 2961 Sorted by residual: chirality pdb=" CA VAL J 97 " pdb=" N VAL J 97 " pdb=" C VAL J 97 " pdb=" CB VAL J 97 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA VAL H 97 " pdb=" N VAL H 97 " pdb=" C VAL H 97 " pdb=" CB VAL H 97 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA VAL I 97 " pdb=" N VAL I 97 " pdb=" C VAL I 97 " pdb=" CB VAL I 97 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 2958 not shown) Planarity restraints: 3387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL J 97 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C VAL J 97 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL J 97 " -0.020 2.00e-02 2.50e+03 pdb=" N SER J 98 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 97 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C VAL I 97 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL I 97 " 0.020 2.00e-02 2.50e+03 pdb=" N SER I 98 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 97 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C VAL H 97 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL H 97 " -0.020 2.00e-02 2.50e+03 pdb=" N SER H 98 " -0.019 2.00e-02 2.50e+03 ... (remaining 3384 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3265 2.77 - 3.30: 17989 3.30 - 3.84: 29795 3.84 - 4.37: 35729 4.37 - 4.90: 64147 Nonbonded interactions: 150925 Sorted by model distance: nonbonded pdb=" OG1 THR F 241 " pdb=" OG SER F 244 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR G 241 " pdb=" OG SER G 244 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR E 241 " pdb=" OG SER E 244 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP G 701 " pdb=" N TYR G 702 " model vdw 2.290 3.120 nonbonded pdb=" OD1 ASP E 701 " pdb=" N TYR E 702 " model vdw 2.290 3.120 ... (remaining 150920 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: 0.03 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.760 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 0.085 19377 Z= 0.253 Angle : 0.889 18.483 26376 Z= 0.526 Chirality : 0.048 0.267 2961 Planarity : 0.005 0.045 3375 Dihedral : 13.214 84.651 7362 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.17), residues: 2310 helix: 0.13 (0.30), residues: 312 sheet: -0.57 (0.18), residues: 762 loop : -0.62 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 304 TYR 0.009 0.001 TYR E 640 PHE 0.015 0.001 PHE F 287 TRP 0.006 0.001 TRP J 106 HIS 0.007 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00435 (19335) covalent geometry : angle 0.87761 (26271) SS BOND : bond 0.00620 ( 21) SS BOND : angle 2.65066 ( 42) hydrogen bonds : bond 0.22973 ( 746) hydrogen bonds : angle 9.68118 ( 2220) link_BETA1-4 : bond 0.00452 ( 9) link_BETA1-4 : angle 2.48956 ( 27) link_NAG-ASN : bond 0.00420 ( 12) link_NAG-ASN : angle 1.89094 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 242 ARG cc_start: 0.7330 (ptp-170) cc_final: 0.6944 (ptp-170) REVERT: G 242 ARG cc_start: 0.7300 (ptp-170) cc_final: 0.6974 (ptp-170) REVERT: H 5 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8421 (mmtm) REVERT: H 82 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8200 (tppt) REVERT: I 5 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8575 (mmtm) REVERT: I 60 TYR cc_start: 0.8168 (m-80) cc_final: 0.7568 (m-80) REVERT: I 82 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8183 (tppt) REVERT: J 5 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8615 (mmmt) REVERT: J 60 TYR cc_start: 0.8144 (m-80) cc_final: 0.7731 (m-80) REVERT: J 82 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8192 (tppt) REVERT: L 4 MET cc_start: 0.9007 (mmm) cc_final: 0.8312 (mmm) REVERT: L 18 ARG cc_start: 0.8712 (ttt90) cc_final: 0.7675 (tpt-90) REVERT: L 24 ARG cc_start: 0.8453 (mtp-110) cc_final: 0.8185 (mtp-110) REVERT: L 85 ASP cc_start: 0.8854 (m-30) cc_final: 0.8309 (m-30) REVERT: L 103 LYS cc_start: 0.8789 (tttt) cc_final: 0.8584 (tppt) REVERT: M 4 MET cc_start: 0.9043 (mmm) cc_final: 0.8765 (mmm) REVERT: M 18 ARG cc_start: 0.8763 (ttt90) cc_final: 0.8172 (tpt-90) REVERT: M 79 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8261 (mp0) REVERT: M 85 ASP cc_start: 0.8839 (m-30) cc_final: 0.8234 (m-30) REVERT: M 103 LYS cc_start: 0.8816 (tttt) cc_final: 0.8557 (tppt) REVERT: N 4 MET cc_start: 0.9015 (mmm) cc_final: 0.8044 (mmm) REVERT: N 18 ARG cc_start: 0.8650 (ttt90) cc_final: 0.7648 (tpt-90) REVERT: N 24 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.8008 (mtp-110) REVERT: N 85 ASP cc_start: 0.8844 (m-30) cc_final: 0.8307 (m-30) REVERT: N 87 TYR cc_start: 0.7013 (m-80) cc_final: 0.6681 (m-80) REVERT: N 103 LYS cc_start: 0.8752 (tttt) cc_final: 0.8470 (tppt) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1783 time to fit residues: 56.7092 Evaluate side-chains 184 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.083316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.059052 restraints weight = 52330.095| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.44 r_work: 0.2919 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19377 Z= 0.192 Angle : 0.601 6.742 26376 Z= 0.321 Chirality : 0.044 0.181 2961 Planarity : 0.005 0.042 3375 Dihedral : 4.621 54.017 3045 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.42 % Allowed : 9.63 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.18), residues: 2310 helix: 1.16 (0.30), residues: 333 sheet: -0.01 (0.19), residues: 723 loop : -0.43 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 61 TYR 0.016 0.001 TYR G 640 PHE 0.018 0.002 PHE G 287 TRP 0.011 0.001 TRP F 528 HIS 0.004 0.001 HIS E 637 Details of bonding type rmsd covalent geometry : bond 0.00442 (19335) covalent geometry : angle 0.59543 (26271) SS BOND : bond 0.00423 ( 21) SS BOND : angle 0.77552 ( 42) hydrogen bonds : bond 0.04625 ( 746) hydrogen bonds : angle 6.29978 ( 2220) link_BETA1-4 : bond 0.00368 ( 9) link_BETA1-4 : angle 1.98756 ( 27) link_NAG-ASN : bond 0.00292 ( 12) link_NAG-ASN : angle 1.38430 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 718 ASP cc_start: 0.8254 (t0) cc_final: 0.8051 (t70) REVERT: F 242 ARG cc_start: 0.7538 (ptp-170) cc_final: 0.7117 (ptp-170) REVERT: F 718 ASP cc_start: 0.8200 (t0) cc_final: 0.7973 (t70) REVERT: G 242 ARG cc_start: 0.7468 (ptp-170) cc_final: 0.7121 (ptp-170) REVERT: G 614 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8090 (mm-30) REVERT: G 718 ASP cc_start: 0.8262 (t0) cc_final: 0.8006 (t70) REVERT: H 17 GLN cc_start: 0.7921 (mp10) cc_final: 0.7656 (pm20) REVERT: H 82 LYS cc_start: 0.8531 (ttmm) cc_final: 0.7996 (tptt) REVERT: H 99 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: I 3 GLN cc_start: 0.7606 (pp30) cc_final: 0.7213 (pp30) REVERT: I 5 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8647 (mmtt) REVERT: I 17 GLN cc_start: 0.7956 (mp10) cc_final: 0.7697 (pm20) REVERT: I 60 TYR cc_start: 0.8363 (m-80) cc_final: 0.7891 (m-80) REVERT: I 82 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8061 (tptt) REVERT: I 99 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: J 3 GLN cc_start: 0.7634 (pp30) cc_final: 0.7277 (pp30) REVERT: J 17 GLN cc_start: 0.7984 (mp10) cc_final: 0.7669 (pm20) REVERT: J 60 TYR cc_start: 0.8383 (m-80) cc_final: 0.8086 (m-80) REVERT: J 82 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8063 (tptt) REVERT: J 99 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: L 4 MET cc_start: 0.9073 (mmm) cc_final: 0.8357 (mmm) REVERT: L 18 ARG cc_start: 0.8390 (ttt90) cc_final: 0.8158 (tpt-90) REVERT: L 24 ARG cc_start: 0.8630 (mtp-110) cc_final: 0.8160 (mtp-110) REVERT: L 39 LYS cc_start: 0.9124 (mmtt) cc_final: 0.8751 (mmmt) REVERT: L 79 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8166 (mp0) REVERT: L 81 GLU cc_start: 0.9055 (tp30) cc_final: 0.8608 (tp30) REVERT: L 85 ASP cc_start: 0.8682 (m-30) cc_final: 0.8043 (m-30) REVERT: L 103 LYS cc_start: 0.8906 (tttt) cc_final: 0.8629 (tppt) REVERT: M 4 MET cc_start: 0.9107 (mmm) cc_final: 0.8828 (mmm) REVERT: M 39 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8933 (mmmt) REVERT: M 79 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8302 (mp0) REVERT: M 81 GLU cc_start: 0.9070 (tp30) cc_final: 0.8780 (tp30) REVERT: M 85 ASP cc_start: 0.8699 (m-30) cc_final: 0.7978 (m-30) REVERT: M 103 LYS cc_start: 0.8931 (tttt) cc_final: 0.8563 (tppt) REVERT: N 4 MET cc_start: 0.9059 (mmm) cc_final: 0.8416 (mmm) REVERT: N 18 ARG cc_start: 0.8340 (ttt90) cc_final: 0.7964 (tpt-90) REVERT: N 24 ARG cc_start: 0.8669 (mtp-110) cc_final: 0.8290 (mtp-110) REVERT: N 39 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8762 (mmmt) REVERT: N 85 ASP cc_start: 0.8678 (m-30) cc_final: 0.7991 (m-30) REVERT: N 103 LYS cc_start: 0.8882 (tttt) cc_final: 0.8554 (tppt) outliers start: 29 outliers final: 13 residues processed: 199 average time/residue: 0.1637 time to fit residues: 46.4719 Evaluate side-chains 192 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 694 ILE Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain J residue 99 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 145 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 137 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 106 optimal weight: 0.0770 chunk 228 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN I 87 GLN J 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.084024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.059656 restraints weight = 52455.329| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.50 r_work: 0.2936 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19377 Z= 0.109 Angle : 0.511 5.896 26376 Z= 0.271 Chirality : 0.042 0.188 2961 Planarity : 0.004 0.044 3375 Dihedral : 4.566 52.677 3045 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.12 % Allowed : 11.05 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2310 helix: 1.49 (0.29), residues: 333 sheet: 0.22 (0.19), residues: 741 loop : -0.24 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 61 TYR 0.016 0.001 TYR M 49 PHE 0.012 0.001 PHE G 287 TRP 0.007 0.001 TRP H 48 HIS 0.002 0.000 HIS E 228 Details of bonding type rmsd covalent geometry : bond 0.00233 (19335) covalent geometry : angle 0.50682 (26271) SS BOND : bond 0.00305 ( 21) SS BOND : angle 0.45307 ( 42) hydrogen bonds : bond 0.03799 ( 746) hydrogen bonds : angle 5.71097 ( 2220) link_BETA1-4 : bond 0.00475 ( 9) link_BETA1-4 : angle 1.64261 ( 27) link_NAG-ASN : bond 0.00293 ( 12) link_NAG-ASN : angle 1.29708 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 132 ARG cc_start: 0.8127 (tmt170) cc_final: 0.7896 (ttp80) REVERT: F 242 ARG cc_start: 0.7470 (ptp-170) cc_final: 0.7017 (ptp-170) REVERT: G 242 ARG cc_start: 0.7432 (ptp-170) cc_final: 0.7062 (ptp-170) REVERT: G 718 ASP cc_start: 0.8268 (t0) cc_final: 0.8023 (t70) REVERT: H 82 LYS cc_start: 0.8515 (ttmm) cc_final: 0.7990 (tptt) REVERT: H 99 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: I 3 GLN cc_start: 0.7643 (pp30) cc_final: 0.7200 (pp30) REVERT: I 5 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8656 (mmtt) REVERT: I 60 TYR cc_start: 0.8353 (m-80) cc_final: 0.7853 (m-80) REVERT: I 82 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8068 (tptt) REVERT: I 99 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: J 3 GLN cc_start: 0.7547 (pp30) cc_final: 0.7218 (pp30) REVERT: J 60 TYR cc_start: 0.8344 (m-80) cc_final: 0.8028 (m-80) REVERT: J 82 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8017 (tptt) REVERT: J 99 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7508 (m-80) REVERT: L 17 GLU cc_start: 0.8797 (tp30) cc_final: 0.8500 (tp30) REVERT: L 18 ARG cc_start: 0.8382 (ttt90) cc_final: 0.7845 (tpt-90) REVERT: L 81 GLU cc_start: 0.9056 (tp30) cc_final: 0.8784 (tp30) REVERT: L 85 ASP cc_start: 0.8635 (m-30) cc_final: 0.7792 (m-30) REVERT: L 103 LYS cc_start: 0.8892 (tttt) cc_final: 0.8594 (tppt) REVERT: M 39 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8734 (mmmt) REVERT: M 79 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8363 (mp0) REVERT: M 81 GLU cc_start: 0.9096 (tp30) cc_final: 0.8599 (tp30) REVERT: M 85 ASP cc_start: 0.8652 (m-30) cc_final: 0.7787 (m-30) REVERT: M 103 LYS cc_start: 0.8931 (tttt) cc_final: 0.8543 (tppt) REVERT: N 4 MET cc_start: 0.9053 (mmm) cc_final: 0.8345 (mmm) REVERT: N 24 ARG cc_start: 0.8701 (mtp-110) cc_final: 0.8296 (mtp-110) REVERT: N 81 GLU cc_start: 0.9024 (tp30) cc_final: 0.8796 (tp30) REVERT: N 85 ASP cc_start: 0.8604 (m-30) cc_final: 0.7671 (m-30) REVERT: N 103 LYS cc_start: 0.8872 (tttt) cc_final: 0.8522 (tppt) outliers start: 23 outliers final: 11 residues processed: 198 average time/residue: 0.1597 time to fit residues: 45.3667 Evaluate side-chains 183 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 694 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 99 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 217 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 114 optimal weight: 0.0670 chunk 125 optimal weight: 7.9990 overall best weight: 1.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS ** G 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** J 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.082915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.058637 restraints weight = 52572.730| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.44 r_work: 0.2902 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19377 Z= 0.163 Angle : 0.525 5.730 26376 Z= 0.276 Chirality : 0.042 0.180 2961 Planarity : 0.004 0.040 3375 Dihedral : 4.719 53.125 3045 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.81 % Allowed : 11.93 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 2310 helix: 1.64 (0.29), residues: 333 sheet: 0.34 (0.19), residues: 756 loop : -0.25 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 18 TYR 0.015 0.001 TYR L 49 PHE 0.013 0.001 PHE G 287 TRP 0.009 0.001 TRP H 48 HIS 0.004 0.001 HIS E 637 Details of bonding type rmsd covalent geometry : bond 0.00377 (19335) covalent geometry : angle 0.52038 (26271) SS BOND : bond 0.00316 ( 21) SS BOND : angle 0.55621 ( 42) hydrogen bonds : bond 0.03620 ( 746) hydrogen bonds : angle 5.47292 ( 2220) link_BETA1-4 : bond 0.00425 ( 9) link_BETA1-4 : angle 1.53484 ( 27) link_NAG-ASN : bond 0.00284 ( 12) link_NAG-ASN : angle 1.36018 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 242 ARG cc_start: 0.7565 (ptp-170) cc_final: 0.6971 (ptp-170) REVERT: G 242 ARG cc_start: 0.7487 (ptp-170) cc_final: 0.7126 (ptp-170) REVERT: G 718 ASP cc_start: 0.8317 (t0) cc_final: 0.8080 (t70) REVERT: H 3 GLN cc_start: 0.7322 (pp30) cc_final: 0.7094 (pp30) REVERT: H 82 LYS cc_start: 0.8487 (ttmm) cc_final: 0.7980 (tptp) REVERT: H 99 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: I 3 GLN cc_start: 0.7703 (pp30) cc_final: 0.7340 (pp30) REVERT: I 60 TYR cc_start: 0.8444 (m-80) cc_final: 0.7937 (m-80) REVERT: I 82 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8077 (tptp) REVERT: I 99 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: J 60 TYR cc_start: 0.8446 (m-80) cc_final: 0.8099 (m-80) REVERT: J 99 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: L 4 MET cc_start: 0.9071 (mmm) cc_final: 0.8332 (mmm) REVERT: L 18 ARG cc_start: 0.8400 (ttt90) cc_final: 0.7771 (ttp80) REVERT: L 39 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8770 (mmmt) REVERT: L 81 GLU cc_start: 0.9040 (tp30) cc_final: 0.8536 (tp30) REVERT: L 85 ASP cc_start: 0.8618 (m-30) cc_final: 0.7642 (m-30) REVERT: L 103 LYS cc_start: 0.8921 (tttt) cc_final: 0.8595 (tppt) REVERT: M 4 MET cc_start: 0.9124 (mmm) cc_final: 0.8847 (mmm) REVERT: M 17 GLU cc_start: 0.9174 (tp30) cc_final: 0.8751 (tp30) REVERT: M 39 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8755 (mmmt) REVERT: M 79 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8400 (mp0) REVERT: M 81 GLU cc_start: 0.9121 (tp30) cc_final: 0.8584 (tp30) REVERT: M 85 ASP cc_start: 0.8623 (m-30) cc_final: 0.7793 (m-30) REVERT: M 103 LYS cc_start: 0.8964 (tttt) cc_final: 0.8585 (tppt) REVERT: N 4 MET cc_start: 0.9074 (mmm) cc_final: 0.8423 (mmm) REVERT: N 17 GLU cc_start: 0.9002 (tp30) cc_final: 0.8744 (tp30) REVERT: N 18 ARG cc_start: 0.8477 (ttt90) cc_final: 0.8098 (ttt90) REVERT: N 24 ARG cc_start: 0.8712 (mtp-110) cc_final: 0.8284 (mtp-110) REVERT: N 39 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8692 (mmmt) REVERT: N 81 GLU cc_start: 0.8997 (tp30) cc_final: 0.8553 (tp30) REVERT: N 85 ASP cc_start: 0.8626 (m-30) cc_final: 0.7762 (m-30) REVERT: N 103 LYS cc_start: 0.8901 (tttt) cc_final: 0.8558 (tppt) outliers start: 37 outliers final: 25 residues processed: 196 average time/residue: 0.1556 time to fit residues: 44.0274 Evaluate side-chains 194 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 596 CYS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 694 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 596 CYS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 694 ILE Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 99 TYR Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 73 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 35 optimal weight: 0.0170 chunk 143 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 248 HIS G 248 HIS H 87 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** J 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.083257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.059102 restraints weight = 51839.157| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.43 r_work: 0.2917 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19377 Z= 0.118 Angle : 0.502 5.901 26376 Z= 0.264 Chirality : 0.041 0.178 2961 Planarity : 0.004 0.039 3375 Dihedral : 4.688 52.652 3045 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.91 % Allowed : 13.20 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 2310 helix: 1.68 (0.29), residues: 333 sheet: 0.42 (0.19), residues: 756 loop : -0.23 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 18 TYR 0.017 0.001 TYR M 49 PHE 0.013 0.001 PHE E 287 TRP 0.009 0.001 TRP H 48 HIS 0.003 0.001 HIS E 637 Details of bonding type rmsd covalent geometry : bond 0.00266 (19335) covalent geometry : angle 0.49830 (26271) SS BOND : bond 0.00265 ( 21) SS BOND : angle 0.45264 ( 42) hydrogen bonds : bond 0.03347 ( 746) hydrogen bonds : angle 5.28916 ( 2220) link_BETA1-4 : bond 0.00374 ( 9) link_BETA1-4 : angle 1.40914 ( 27) link_NAG-ASN : bond 0.00282 ( 12) link_NAG-ASN : angle 1.30365 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 242 ARG cc_start: 0.7573 (ptp-170) cc_final: 0.6946 (ptp-170) REVERT: F 456 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8268 (pp) REVERT: G 242 ARG cc_start: 0.7495 (ptp-170) cc_final: 0.7117 (ptp-170) REVERT: G 456 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8312 (pp) REVERT: H 82 LYS cc_start: 0.8497 (ttmm) cc_final: 0.7921 (tptt) REVERT: H 99 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: I 60 TYR cc_start: 0.8427 (m-80) cc_final: 0.7886 (m-80) REVERT: I 82 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8053 (tptt) REVERT: J 60 TYR cc_start: 0.8424 (m-80) cc_final: 0.8104 (m-80) REVERT: J 82 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8057 (tptt) REVERT: J 99 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: L 4 MET cc_start: 0.9087 (mmm) cc_final: 0.8411 (mmm) REVERT: L 18 ARG cc_start: 0.8566 (ttt90) cc_final: 0.8066 (ttp80) REVERT: L 39 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8758 (mmmt) REVERT: L 81 GLU cc_start: 0.9040 (tp30) cc_final: 0.8554 (tp30) REVERT: L 85 ASP cc_start: 0.8596 (m-30) cc_final: 0.7514 (m-30) REVERT: L 103 LYS cc_start: 0.8931 (tttt) cc_final: 0.8602 (tppt) REVERT: M 4 MET cc_start: 0.9128 (mmm) cc_final: 0.8831 (mmm) REVERT: M 17 GLU cc_start: 0.9253 (tp30) cc_final: 0.8875 (tp30) REVERT: M 18 ARG cc_start: 0.8616 (ttp80) cc_final: 0.7680 (ttp80) REVERT: M 39 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8703 (mmmt) REVERT: M 79 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8431 (mp0) REVERT: M 81 GLU cc_start: 0.9118 (tp30) cc_final: 0.8680 (tp30) REVERT: M 85 ASP cc_start: 0.8622 (m-30) cc_final: 0.7720 (m-30) REVERT: M 103 LYS cc_start: 0.8966 (tttt) cc_final: 0.8569 (tppt) REVERT: N 3 GLN cc_start: 0.8422 (tp-100) cc_final: 0.8222 (tp40) REVERT: N 4 MET cc_start: 0.9098 (mmm) cc_final: 0.8397 (mmm) REVERT: N 17 GLU cc_start: 0.9115 (tp30) cc_final: 0.8809 (tp30) REVERT: N 24 ARG cc_start: 0.8720 (mtp-110) cc_final: 0.8276 (mtp-110) REVERT: N 39 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8641 (mmmt) REVERT: N 85 ASP cc_start: 0.8608 (m-30) cc_final: 0.7702 (m-30) REVERT: N 103 LYS cc_start: 0.8918 (tttt) cc_final: 0.8553 (tppt) outliers start: 39 outliers final: 21 residues processed: 201 average time/residue: 0.1538 time to fit residues: 45.0147 Evaluate side-chains 183 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 596 CYS Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 596 CYS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 694 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 596 CYS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 694 ILE Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 99 TYR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 43 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 113 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 217 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 133 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN H 108 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN I 108 GLN ** J 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.082300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.058069 restraints weight = 52132.470| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.43 r_work: 0.2882 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19377 Z= 0.170 Angle : 0.530 7.478 26376 Z= 0.277 Chirality : 0.042 0.184 2961 Planarity : 0.004 0.039 3375 Dihedral : 4.807 52.942 3045 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.35 % Allowed : 13.20 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.18), residues: 2310 helix: 1.73 (0.29), residues: 333 sheet: 0.36 (0.19), residues: 762 loop : -0.24 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 18 TYR 0.012 0.001 TYR G 640 PHE 0.013 0.001 PHE E 287 TRP 0.009 0.001 TRP H 48 HIS 0.004 0.001 HIS E 637 Details of bonding type rmsd covalent geometry : bond 0.00400 (19335) covalent geometry : angle 0.52581 (26271) SS BOND : bond 0.00284 ( 21) SS BOND : angle 0.52356 ( 42) hydrogen bonds : bond 0.03441 ( 746) hydrogen bonds : angle 5.26686 ( 2220) link_BETA1-4 : bond 0.00412 ( 9) link_BETA1-4 : angle 1.42103 ( 27) link_NAG-ASN : bond 0.00302 ( 12) link_NAG-ASN : angle 1.35320 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 132 ARG cc_start: 0.7730 (tmm160) cc_final: 0.7367 (tmt170) REVERT: F 242 ARG cc_start: 0.7632 (ptp-170) cc_final: 0.7321 (ptp-170) REVERT: F 456 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8309 (pp) REVERT: G 242 ARG cc_start: 0.7526 (ptp-170) cc_final: 0.7144 (ptp-170) REVERT: G 456 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8391 (pp) REVERT: H 82 LYS cc_start: 0.8505 (ttmm) cc_final: 0.7929 (tptp) REVERT: H 99 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: I 60 TYR cc_start: 0.8452 (m-80) cc_final: 0.7886 (m-80) REVERT: I 82 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8029 (tptt) REVERT: J 60 TYR cc_start: 0.8464 (m-80) cc_final: 0.8131 (m-80) REVERT: J 82 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8035 (tptt) REVERT: L 4 MET cc_start: 0.9106 (mmm) cc_final: 0.8370 (mmm) REVERT: L 17 GLU cc_start: 0.9091 (tp30) cc_final: 0.8888 (tp30) REVERT: L 39 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8700 (mmmt) REVERT: L 81 GLU cc_start: 0.9037 (tp30) cc_final: 0.8538 (tp30) REVERT: L 85 ASP cc_start: 0.8591 (m-30) cc_final: 0.7589 (m-30) REVERT: L 103 LYS cc_start: 0.8947 (tttt) cc_final: 0.8631 (tppt) REVERT: M 4 MET cc_start: 0.9115 (mmm) cc_final: 0.8808 (mmm) REVERT: M 17 GLU cc_start: 0.9237 (tp30) cc_final: 0.8886 (tp30) REVERT: M 39 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8731 (mmmt) REVERT: M 79 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8464 (mp0) REVERT: M 81 GLU cc_start: 0.9103 (tp30) cc_final: 0.8559 (tp30) REVERT: M 85 ASP cc_start: 0.8612 (m-30) cc_final: 0.7705 (m-30) REVERT: M 103 LYS cc_start: 0.8986 (tttt) cc_final: 0.8575 (tppt) REVERT: N 3 GLN cc_start: 0.8457 (tp-100) cc_final: 0.8253 (tp40) REVERT: N 4 MET cc_start: 0.9115 (mmm) cc_final: 0.8401 (mmm) REVERT: N 24 ARG cc_start: 0.8734 (mtp-110) cc_final: 0.8299 (mtp-110) REVERT: N 39 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8603 (mmmt) REVERT: N 85 ASP cc_start: 0.8606 (m-30) cc_final: 0.7716 (m-30) REVERT: N 103 LYS cc_start: 0.8931 (tttt) cc_final: 0.8561 (tppt) outliers start: 48 outliers final: 36 residues processed: 188 average time/residue: 0.1658 time to fit residues: 45.1143 Evaluate side-chains 191 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 596 CYS Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 596 CYS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 694 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 589 ILE Chi-restraints excluded: chain G residue 596 CYS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 694 ILE Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 133 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN H 108 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** J 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.082298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.057931 restraints weight = 52761.089| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.47 r_work: 0.2867 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19377 Z= 0.198 Angle : 0.547 6.541 26376 Z= 0.287 Chirality : 0.042 0.181 2961 Planarity : 0.004 0.075 3375 Dihedral : 4.939 52.888 3045 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.44 % Allowed : 13.83 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.18), residues: 2310 helix: 1.75 (0.29), residues: 333 sheet: 0.36 (0.19), residues: 762 loop : -0.28 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 242 TYR 0.016 0.001 TYR M 49 PHE 0.014 0.001 PHE G 287 TRP 0.010 0.001 TRP J 48 HIS 0.005 0.001 HIS E 637 Details of bonding type rmsd covalent geometry : bond 0.00465 (19335) covalent geometry : angle 0.54330 (26271) SS BOND : bond 0.00290 ( 21) SS BOND : angle 0.56055 ( 42) hydrogen bonds : bond 0.03525 ( 746) hydrogen bonds : angle 5.25410 ( 2220) link_BETA1-4 : bond 0.00336 ( 9) link_BETA1-4 : angle 1.37328 ( 27) link_NAG-ASN : bond 0.00367 ( 12) link_NAG-ASN : angle 1.37581 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 132 ARG cc_start: 0.7743 (tmm160) cc_final: 0.7359 (tmt170) REVERT: F 242 ARG cc_start: 0.7719 (ptp-170) cc_final: 0.7407 (ptp-170) REVERT: F 456 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8342 (pp) REVERT: G 242 ARG cc_start: 0.7592 (ptp-170) cc_final: 0.7279 (ptp-170) REVERT: H 82 LYS cc_start: 0.8492 (ttmm) cc_final: 0.7924 (tptp) REVERT: I 60 TYR cc_start: 0.8476 (m-80) cc_final: 0.7936 (m-80) REVERT: I 82 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8022 (tptp) REVERT: J 60 TYR cc_start: 0.8480 (m-80) cc_final: 0.8115 (m-80) REVERT: J 82 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8025 (tptt) REVERT: L 4 MET cc_start: 0.9113 (mmm) cc_final: 0.8335 (mmm) REVERT: L 39 LYS cc_start: 0.9058 (mmtt) cc_final: 0.8658 (mmmt) REVERT: L 81 GLU cc_start: 0.9043 (tp30) cc_final: 0.8528 (tp30) REVERT: L 85 ASP cc_start: 0.8535 (m-30) cc_final: 0.7588 (m-30) REVERT: L 103 LYS cc_start: 0.8948 (tttt) cc_final: 0.8595 (tppt) REVERT: M 4 MET cc_start: 0.9123 (mmm) cc_final: 0.8786 (mmm) REVERT: M 17 GLU cc_start: 0.9256 (tp30) cc_final: 0.8907 (tp30) REVERT: M 39 LYS cc_start: 0.9076 (mmtt) cc_final: 0.8683 (mmmt) REVERT: M 79 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8510 (mp0) REVERT: M 81 GLU cc_start: 0.9081 (tp30) cc_final: 0.8612 (tp30) REVERT: M 85 ASP cc_start: 0.8628 (m-30) cc_final: 0.7782 (m-30) REVERT: M 103 LYS cc_start: 0.8966 (tttt) cc_final: 0.8553 (tppt) REVERT: N 4 MET cc_start: 0.9070 (mmm) cc_final: 0.8382 (mmm) REVERT: N 18 ARG cc_start: 0.8489 (ttt90) cc_final: 0.8161 (ttt90) REVERT: N 24 ARG cc_start: 0.8760 (mtp-110) cc_final: 0.8383 (mtp-110) REVERT: N 39 LYS cc_start: 0.8994 (mmtt) cc_final: 0.8626 (mmmt) REVERT: N 85 ASP cc_start: 0.8596 (m-30) cc_final: 0.7717 (m-30) REVERT: N 103 LYS cc_start: 0.8929 (tttt) cc_final: 0.8528 (tppt) outliers start: 50 outliers final: 37 residues processed: 184 average time/residue: 0.1562 time to fit residues: 41.8302 Evaluate side-chains 182 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 596 CYS Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 596 CYS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 694 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 589 ILE Chi-restraints excluded: chain G residue 596 CYS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 694 ILE Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 163 optimal weight: 4.9990 chunk 50 optimal weight: 0.0670 chunk 35 optimal weight: 0.5980 chunk 129 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 chunk 130 optimal weight: 0.8980 chunk 190 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN I 105 HIS I 108 GLN ** J 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.083077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.059195 restraints weight = 52154.468| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.39 r_work: 0.2916 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19377 Z= 0.099 Angle : 0.509 7.206 26376 Z= 0.266 Chirality : 0.041 0.173 2961 Planarity : 0.004 0.045 3375 Dihedral : 4.766 52.165 3045 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.71 % Allowed : 14.61 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.18), residues: 2310 helix: 1.82 (0.29), residues: 333 sheet: 0.39 (0.19), residues: 777 loop : -0.31 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 18 TYR 0.017 0.001 TYR M 49 PHE 0.012 0.001 PHE E 287 TRP 0.009 0.001 TRP J 48 HIS 0.002 0.000 HIS E 637 Details of bonding type rmsd covalent geometry : bond 0.00216 (19335) covalent geometry : angle 0.50611 (26271) SS BOND : bond 0.00233 ( 21) SS BOND : angle 0.38053 ( 42) hydrogen bonds : bond 0.03117 ( 746) hydrogen bonds : angle 5.11657 ( 2220) link_BETA1-4 : bond 0.00418 ( 9) link_BETA1-4 : angle 1.30005 ( 27) link_NAG-ASN : bond 0.00290 ( 12) link_NAG-ASN : angle 1.27930 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 132 ARG cc_start: 0.7727 (tmm160) cc_final: 0.7358 (tmt170) REVERT: E 242 ARG cc_start: 0.7677 (ptp-170) cc_final: 0.7466 (ptp-170) REVERT: F 242 ARG cc_start: 0.7651 (ptp-170) cc_final: 0.7448 (ptp-170) REVERT: F 456 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8325 (pp) REVERT: G 242 ARG cc_start: 0.7513 (ptp-170) cc_final: 0.7241 (ptp-170) REVERT: H 82 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8005 (tptp) REVERT: I 60 TYR cc_start: 0.8465 (m-80) cc_final: 0.7902 (m-80) REVERT: I 82 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8071 (tptp) REVERT: J 60 TYR cc_start: 0.8494 (m-80) cc_final: 0.8146 (m-80) REVERT: J 82 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8080 (tptt) REVERT: L 3 GLN cc_start: 0.8445 (tp-100) cc_final: 0.8167 (mm110) REVERT: L 4 MET cc_start: 0.9088 (mmm) cc_final: 0.8358 (mmm) REVERT: L 17 GLU cc_start: 0.9089 (tp30) cc_final: 0.8880 (tp30) REVERT: L 39 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8684 (mmmt) REVERT: L 81 GLU cc_start: 0.9009 (tp30) cc_final: 0.8516 (tp30) REVERT: L 85 ASP cc_start: 0.8586 (m-30) cc_final: 0.7556 (m-30) REVERT: L 103 LYS cc_start: 0.8974 (tttt) cc_final: 0.8619 (tppt) REVERT: M 4 MET cc_start: 0.9114 (mmm) cc_final: 0.8834 (mmm) REVERT: M 17 GLU cc_start: 0.9204 (tp30) cc_final: 0.8885 (tp30) REVERT: M 18 ARG cc_start: 0.8357 (ttp80) cc_final: 0.8017 (ttt90) REVERT: M 39 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8684 (mmmt) REVERT: M 79 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8562 (mp0) REVERT: M 81 GLU cc_start: 0.9040 (tp30) cc_final: 0.8579 (tp30) REVERT: M 85 ASP cc_start: 0.8593 (m-30) cc_final: 0.7707 (m-30) REVERT: M 103 LYS cc_start: 0.9017 (tttt) cc_final: 0.8631 (tppt) REVERT: N 4 MET cc_start: 0.9050 (mmm) cc_final: 0.8394 (mmm) REVERT: N 18 ARG cc_start: 0.8472 (ttt90) cc_final: 0.8190 (ttt90) REVERT: N 24 ARG cc_start: 0.8749 (mtp-110) cc_final: 0.8302 (mtp-110) REVERT: N 39 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8662 (mmmt) REVERT: N 85 ASP cc_start: 0.8581 (m-30) cc_final: 0.7659 (m-30) REVERT: N 103 LYS cc_start: 0.8952 (tttt) cc_final: 0.8554 (tppt) outliers start: 35 outliers final: 27 residues processed: 181 average time/residue: 0.1571 time to fit residues: 41.0801 Evaluate side-chains 179 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 596 CYS Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 596 CYS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 694 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 596 CYS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 43 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 122 optimal weight: 20.0000 chunk 170 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 chunk 209 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 155 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN H 108 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** J 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.083160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.059358 restraints weight = 51797.001| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.38 r_work: 0.2923 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19377 Z= 0.103 Angle : 0.502 7.240 26376 Z= 0.262 Chirality : 0.041 0.176 2961 Planarity : 0.004 0.039 3375 Dihedral : 4.716 52.363 3045 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.71 % Allowed : 15.00 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2310 helix: 1.87 (0.29), residues: 333 sheet: 0.42 (0.19), residues: 777 loop : -0.33 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 18 TYR 0.016 0.001 TYR M 49 PHE 0.012 0.001 PHE G 287 TRP 0.010 0.001 TRP J 48 HIS 0.002 0.000 HIS E 637 Details of bonding type rmsd covalent geometry : bond 0.00231 (19335) covalent geometry : angle 0.49910 (26271) SS BOND : bond 0.00244 ( 21) SS BOND : angle 0.43538 ( 42) hydrogen bonds : bond 0.03034 ( 746) hydrogen bonds : angle 5.03533 ( 2220) link_BETA1-4 : bond 0.00421 ( 9) link_BETA1-4 : angle 1.30108 ( 27) link_NAG-ASN : bond 0.00283 ( 12) link_NAG-ASN : angle 1.26540 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 132 ARG cc_start: 0.7756 (tmm160) cc_final: 0.7374 (tmt170) REVERT: F 456 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8325 (pp) REVERT: G 242 ARG cc_start: 0.7531 (ptp-170) cc_final: 0.7278 (ptp-170) REVERT: H 82 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8025 (tptp) REVERT: I 60 TYR cc_start: 0.8471 (m-80) cc_final: 0.7912 (m-80) REVERT: I 82 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8078 (tptp) REVERT: J 60 TYR cc_start: 0.8495 (m-80) cc_final: 0.8158 (m-80) REVERT: L 3 GLN cc_start: 0.8471 (tp-100) cc_final: 0.8182 (mm110) REVERT: L 4 MET cc_start: 0.9096 (mmm) cc_final: 0.8369 (mmm) REVERT: L 17 GLU cc_start: 0.9120 (tp30) cc_final: 0.8898 (tp30) REVERT: L 39 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8666 (mmmt) REVERT: L 81 GLU cc_start: 0.9008 (tp30) cc_final: 0.8491 (tp30) REVERT: L 85 ASP cc_start: 0.8574 (m-30) cc_final: 0.7526 (m-30) REVERT: L 103 LYS cc_start: 0.8966 (tttt) cc_final: 0.8638 (tppt) REVERT: M 4 MET cc_start: 0.9127 (mmm) cc_final: 0.8803 (mmm) REVERT: M 17 GLU cc_start: 0.9208 (tp30) cc_final: 0.8890 (tp30) REVERT: M 18 ARG cc_start: 0.8342 (ttp80) cc_final: 0.8040 (ttt90) REVERT: M 39 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8681 (mmmt) REVERT: M 79 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8567 (mp0) REVERT: M 81 GLU cc_start: 0.9025 (tp30) cc_final: 0.8561 (tp30) REVERT: M 85 ASP cc_start: 0.8594 (m-30) cc_final: 0.7694 (m-30) REVERT: M 103 LYS cc_start: 0.9026 (tttt) cc_final: 0.8635 (tppt) REVERT: N 4 MET cc_start: 0.9029 (mmm) cc_final: 0.8411 (mmm) REVERT: N 18 ARG cc_start: 0.8422 (ttt90) cc_final: 0.8144 (ttt90) REVERT: N 24 ARG cc_start: 0.8753 (mtp-110) cc_final: 0.8310 (mtp-110) REVERT: N 39 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8823 (mmtm) REVERT: N 85 ASP cc_start: 0.8578 (m-30) cc_final: 0.7641 (m-30) REVERT: N 103 LYS cc_start: 0.8961 (tttt) cc_final: 0.8541 (tppt) outliers start: 35 outliers final: 29 residues processed: 180 average time/residue: 0.1633 time to fit residues: 42.5240 Evaluate side-chains 182 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 596 CYS Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 596 CYS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 694 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 596 CYS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain I residue 99 TYR Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 43 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 221 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 228 optimal weight: 20.0000 chunk 218 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 156 optimal weight: 0.0170 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN I 108 GLN ** J 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.082849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.058678 restraints weight = 52074.313| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.44 r_work: 0.2890 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19377 Z= 0.123 Angle : 0.510 7.583 26376 Z= 0.266 Chirality : 0.041 0.173 2961 Planarity : 0.004 0.045 3375 Dihedral : 4.737 52.534 3045 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.61 % Allowed : 15.20 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.18), residues: 2310 helix: 1.89 (0.29), residues: 333 sheet: 0.43 (0.19), residues: 777 loop : -0.35 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG F 242 TYR 0.015 0.001 TYR M 49 PHE 0.013 0.001 PHE F 287 TRP 0.010 0.001 TRP J 48 HIS 0.003 0.001 HIS E 637 Details of bonding type rmsd covalent geometry : bond 0.00282 (19335) covalent geometry : angle 0.50724 (26271) SS BOND : bond 0.00252 ( 21) SS BOND : angle 0.43785 ( 42) hydrogen bonds : bond 0.03068 ( 746) hydrogen bonds : angle 5.01633 ( 2220) link_BETA1-4 : bond 0.00416 ( 9) link_BETA1-4 : angle 1.30054 ( 27) link_NAG-ASN : bond 0.00286 ( 12) link_NAG-ASN : angle 1.28241 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 132 ARG cc_start: 0.7765 (tmm160) cc_final: 0.7369 (tmt170) REVERT: E 375 MET cc_start: 0.8942 (ptm) cc_final: 0.8721 (ptm) REVERT: F 456 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8273 (pp) REVERT: H 82 LYS cc_start: 0.8544 (ttmm) cc_final: 0.7990 (tptp) REVERT: I 60 TYR cc_start: 0.8472 (m-80) cc_final: 0.7883 (m-80) REVERT: I 82 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8049 (tptp) REVERT: J 60 TYR cc_start: 0.8489 (m-80) cc_final: 0.8139 (m-80) REVERT: L 3 GLN cc_start: 0.8490 (tp-100) cc_final: 0.8172 (mm110) REVERT: L 4 MET cc_start: 0.9112 (mmm) cc_final: 0.8395 (mmm) REVERT: L 17 GLU cc_start: 0.9160 (tp30) cc_final: 0.8739 (mp0) REVERT: L 39 LYS cc_start: 0.9055 (mmtt) cc_final: 0.8649 (mmmt) REVERT: L 81 GLU cc_start: 0.9015 (tp30) cc_final: 0.8497 (tp30) REVERT: L 85 ASP cc_start: 0.8525 (m-30) cc_final: 0.7470 (m-30) REVERT: L 103 LYS cc_start: 0.8960 (tttt) cc_final: 0.8620 (tppt) REVERT: M 4 MET cc_start: 0.9019 (mmm) cc_final: 0.8753 (mmm) REVERT: M 17 GLU cc_start: 0.9234 (tp30) cc_final: 0.8915 (tp30) REVERT: M 18 ARG cc_start: 0.8354 (ttp80) cc_final: 0.8059 (ttt90) REVERT: M 39 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8668 (mmmt) REVERT: M 79 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8552 (mp0) REVERT: M 81 GLU cc_start: 0.9035 (tp30) cc_final: 0.8555 (tp30) REVERT: M 85 ASP cc_start: 0.8586 (m-30) cc_final: 0.7711 (m-30) REVERT: M 103 LYS cc_start: 0.9011 (tttt) cc_final: 0.8607 (tppt) REVERT: N 4 MET cc_start: 0.9017 (mmm) cc_final: 0.8390 (mmm) REVERT: N 18 ARG cc_start: 0.8426 (ttt90) cc_final: 0.8178 (ttt90) REVERT: N 24 ARG cc_start: 0.8747 (mtp-110) cc_final: 0.8302 (mtp-110) REVERT: N 85 ASP cc_start: 0.8580 (m-30) cc_final: 0.7655 (m-30) REVERT: N 103 LYS cc_start: 0.8955 (tttt) cc_final: 0.8516 (tppt) outliers start: 33 outliers final: 29 residues processed: 176 average time/residue: 0.1618 time to fit residues: 41.2851 Evaluate side-chains 181 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 596 CYS Chi-restraints excluded: chain E residue 630 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 596 CYS Chi-restraints excluded: chain F residue 630 ILE Chi-restraints excluded: chain F residue 694 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 596 CYS Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 56 optimal weight: 5.9990 chunk 220 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 9 optimal weight: 0.0570 chunk 131 optimal weight: 0.0670 chunk 219 optimal weight: 10.0000 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN H 108 GLN ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN ** J 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.082947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.058915 restraints weight = 52231.868| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.44 r_work: 0.2916 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19377 Z= 0.105 Angle : 0.508 7.716 26376 Z= 0.265 Chirality : 0.041 0.166 2961 Planarity : 0.004 0.078 3375 Dihedral : 4.713 52.371 3045 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.76 % Allowed : 15.25 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2310 helix: 1.91 (0.29), residues: 333 sheet: 0.43 (0.19), residues: 762 loop : -0.33 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 18 TYR 0.015 0.001 TYR M 49 PHE 0.013 0.001 PHE F 287 TRP 0.010 0.001 TRP J 48 HIS 0.002 0.000 HIS E 637 Details of bonding type rmsd covalent geometry : bond 0.00234 (19335) covalent geometry : angle 0.50468 (26271) SS BOND : bond 0.00253 ( 21) SS BOND : angle 0.41297 ( 42) hydrogen bonds : bond 0.02988 ( 746) hydrogen bonds : angle 4.97891 ( 2220) link_BETA1-4 : bond 0.00441 ( 9) link_BETA1-4 : angle 1.28981 ( 27) link_NAG-ASN : bond 0.00285 ( 12) link_NAG-ASN : angle 1.26248 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3902.51 seconds wall clock time: 67 minutes 46.47 seconds (4066.47 seconds total)