Starting phenix.real_space_refine on Thu Feb 5 01:33:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dda_46762/02_2026/9dda_46762.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dda_46762/02_2026/9dda_46762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dda_46762/02_2026/9dda_46762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dda_46762/02_2026/9dda_46762.map" model { file = "/net/cci-nas-00/data/ceres_data/9dda_46762/02_2026/9dda_46762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dda_46762/02_2026/9dda_46762.cif" } resolution = 2.99 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= 0.001 sd= 0.011 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 69 5.16 5 C 8676 2.51 5 N 2388 2.21 5 O 2682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s 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: 13815 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4510 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 27, 'TRANS': 532} Chain breaks: 3 Chain: "B" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4510 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 27, 'TRANS': 532} Chain breaks: 3 Chain: "C" Number of atoms: 4510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4510 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 27, 'TRANS': 532} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "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: 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: "H" 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: "I" 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: "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: 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: "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 Time building chain proxies: 3.37, per 1000 atoms: 0.24 Number of scatterers: 13815 At special positions: 0 Unit cell: (115.37, 123.67, 112.05, 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 69 16.00 O 2682 8.00 N 2388 7.00 C 8676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 607 " distance=1.85 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 607 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.04 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 240 " - pdb=" SG CYS C 607 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A 901 " - " ASN A 430 " " NAG A 902 " - " ASN A 674 " " NAG B 901 " - " ASN B 430 " " NAG B 902 " - " ASN B 674 " " NAG C 901 " - " ASN C 430 " " NAG C 902 " - " ASN C 674 " " NAG D 1 " - " ASN A 141 " " NAG E 1 " - " ASN A 398 " " NAG F 1 " - " ASN B 141 " " NAG G 1 " - " ASN B 398 " " NAG H 1 " - " ASN C 141 " " NAG I 1 " - " ASN C 398 " Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 473.8 milliseconds 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 30 sheets defined 26.1% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 193 through 199 Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.890A pdb=" N ASP A 226 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 408 through 429 removed outlier: 3.796A pdb=" N CYS A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 473 removed outlier: 3.722A pdb=" N LEU A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 510 through 546 Proline residue: A 516 - end of helix removed outlier: 3.543A pdb=" N VAL A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 686 through 691 removed outlier: 3.727A pdb=" N THR A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 721 removed outlier: 3.543A pdb=" N ASN A 709 " --> pdb=" O VAL A 705 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN A 710 " --> pdb=" O GLN A 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'B' and resid 223 through 227 removed outlier: 4.097A pdb=" N ASP B 226 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 408 through 428 removed outlier: 3.636A pdb=" N CYS B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG B 418 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 473 removed outlier: 3.635A pdb=" N LEU B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 510 through 546 Proline residue: B 516 - end of helix Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 686 through 691 removed outlier: 3.755A pdb=" N THR B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 721 removed outlier: 4.477A pdb=" N GLN B 710 " --> pdb=" O GLN B 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.752A pdb=" N ASP C 226 " --> pdb=" O PHE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 408 through 429 removed outlier: 3.801A pdb=" N CYS C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG C 418 " --> pdb=" O GLY C 414 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C 420 " --> pdb=" O ASP C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 473 removed outlier: 3.723A pdb=" N LEU C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 507 Processing helix chain 'C' and resid 510 through 546 Proline residue: C 516 - end of helix removed outlier: 3.613A pdb=" N VAL C 524 " --> pdb=" O MET C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 581 Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 686 through 691 removed outlier: 3.759A pdb=" N THR C 690 " --> pdb=" O LEU C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 721 removed outlier: 4.387A pdb=" N GLN C 710 " --> pdb=" O GLN C 706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 6.460A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 563 removed outlier: 3.551A pdb=" N MET A 568 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL C 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLN A 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 395 through 396 removed outlier: 5.403A pdb=" N THR A 367 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU A 152 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TRP A 369 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHE A 150 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU A 371 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 148 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP A 373 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE A 146 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N MET A 375 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU A 144 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG A 377 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR A 142 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 13.717A pdb=" N TYR A 142 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N SER A 457 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 456 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396 removed outlier: 5.403A pdb=" N THR A 367 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLU A 152 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TRP A 369 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHE A 150 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU A 371 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 148 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP A 373 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE A 146 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N MET A 375 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU A 144 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG A 377 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR A 142 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 13.717A pdb=" N TYR A 142 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N SER A 457 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 157 through 160 Processing sheet with id=AA6, first strand: chain 'A' and resid 187 through 191 Processing sheet with id=AA7, first strand: chain 'A' and resid 187 through 191 Processing sheet with id=AA8, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA9, first strand: chain 'A' and resid 211 through 215 Processing sheet with id=AB1, first strand: chain 'A' and resid 638 through 643 removed outlier: 6.017A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 665 through 667 removed outlier: 5.970A pdb=" N THR A 665 " --> pdb=" O GLN B 126 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET B 568 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.470A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 395 through 396 removed outlier: 6.094A pdb=" N TRP B 369 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS B 151 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLU B 371 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL B 149 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASP B 373 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA B 147 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU B 379 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASN B 141 " --> pdb=" O GLU B 379 " (cutoff:3.500A) removed outlier: 13.814A pdb=" N TYR B 142 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N SER B 457 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 456 " --> pdb=" O ILE B 434 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 395 through 396 removed outlier: 6.094A pdb=" N TRP B 369 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS B 151 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLU B 371 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL B 149 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASP B 373 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA B 147 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU B 379 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASN B 141 " --> pdb=" O GLU B 379 " (cutoff:3.500A) removed outlier: 13.814A pdb=" N TYR B 142 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N SER B 457 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 157 through 160 Processing sheet with id=AB7, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.508A pdb=" N THR B 268 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 187 through 191 Processing sheet with id=AB9, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC1, first strand: chain 'B' and resid 211 through 215 Processing sheet with id=AC2, first strand: chain 'B' and resid 638 through 643 removed outlier: 6.126A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 665 through 667 removed outlier: 5.860A pdb=" N THR B 665 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.507A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 395 through 396 removed outlier: 5.700A pdb=" N THR C 367 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLU C 152 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TRP C 369 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE C 150 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU C 371 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 148 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ASP C 373 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE C 146 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N MET C 375 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU C 144 " --> pdb=" O MET C 375 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG C 377 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR C 142 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 13.807A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 456 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 395 through 396 removed outlier: 5.700A pdb=" N THR C 367 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLU C 152 " --> pdb=" O THR C 367 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TRP C 369 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE C 150 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU C 371 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 148 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ASP C 373 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE C 146 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N MET C 375 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU C 144 " --> pdb=" O MET C 375 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG C 377 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR C 142 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 13.807A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 157 through 160 Processing sheet with id=AC8, first strand: chain 'C' and resid 187 through 191 removed outlier: 3.513A pdb=" N THR C 268 " --> pdb=" O THR C 169 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 187 through 191 Processing sheet with id=AD1, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AD2, first strand: chain 'C' and resid 211 through 215 Processing sheet with id=AD3, first strand: chain 'C' and resid 638 through 642 removed outlier: 6.156A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1563 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: 2.46 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2410 1.32 - 1.45: 4009 1.45 - 1.58: 7612 1.58 - 1.70: 0 1.70 - 1.83: 102 Bond restraints: 14133 Sorted by residual: bond pdb=" N TYR B 142 " pdb=" CA TYR B 142 " ideal model delta sigma weight residual 1.456 1.516 -0.060 1.25e-02 6.40e+03 2.33e+01 bond pdb=" N GLN C 129 " pdb=" CA GLN C 129 " ideal model delta sigma weight residual 1.455 1.488 -0.033 7.00e-03 2.04e+04 2.20e+01 bond pdb=" N GLN A 129 " pdb=" CA GLN A 129 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.71e+01 bond pdb=" N VAL C 635 " pdb=" CA VAL C 635 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.14e-02 7.69e+03 1.14e+01 bond pdb=" N CYS C 573 " pdb=" CA CYS C 573 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.19e-02 7.06e+03 1.12e+01 ... (remaining 14128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.89: 19141 4.89 - 9.77: 56 9.77 - 14.66: 8 14.66 - 19.54: 0 19.54 - 24.43: 1 Bond angle restraints: 19206 Sorted by residual: angle pdb=" N TYR B 142 " pdb=" CA TYR B 142 " pdb=" CB TYR B 142 " ideal model delta sigma weight residual 109.95 134.38 -24.43 1.55e+00 4.16e-01 2.48e+02 angle pdb=" C TYR B 142 " pdb=" CA TYR B 142 " pdb=" CB TYR B 142 " ideal model delta sigma weight residual 109.84 96.84 13.00 1.63e+00 3.76e-01 6.36e+01 angle pdb=" C CYS C 633 " pdb=" CA CYS C 633 " pdb=" CB CYS C 633 " ideal model delta sigma weight residual 109.53 122.04 -12.51 1.69e+00 3.50e-01 5.48e+01 angle pdb=" C PHE C 127 " pdb=" CA PHE C 127 " pdb=" CB PHE C 127 " ideal model delta sigma weight residual 109.35 123.98 -14.63 1.98e+00 2.55e-01 5.46e+01 angle pdb=" C PHE A 127 " pdb=" CA PHE A 127 " pdb=" CB PHE A 127 " ideal model delta sigma weight residual 109.38 124.02 -14.64 2.03e+00 2.43e-01 5.20e+01 ... (remaining 19201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.22: 7861 16.22 - 32.44: 650 32.44 - 48.66: 166 48.66 - 64.89: 60 64.89 - 81.11: 20 Dihedral angle restraints: 8757 sinusoidal: 3807 harmonic: 4950 Sorted by residual: dihedral pdb=" CB CYS B 240 " pdb=" SG CYS B 240 " pdb=" SG CYS B 607 " pdb=" CB CYS B 607 " ideal model delta sinusoidal sigma weight residual 93.00 166.60 -73.60 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS C 240 " pdb=" SG CYS C 240 " pdb=" SG CYS C 607 " pdb=" CB CYS C 607 " ideal model delta sinusoidal sigma weight residual 93.00 164.81 -71.81 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" N TYR B 142 " pdb=" C TYR B 142 " pdb=" CA TYR B 142 " pdb=" CB TYR B 142 " ideal model delta harmonic sigma weight residual 122.80 139.02 -16.22 0 2.50e+00 1.60e-01 4.21e+01 ... (remaining 8754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1585 0.045 - 0.090: 404 0.090 - 0.134: 136 0.134 - 0.179: 34 0.179 - 0.224: 7 Chirality restraints: 2166 Sorted by residual: chirality pdb=" CA CYS C 633 " pdb=" N CYS C 633 " pdb=" C CYS C 633 " pdb=" CB CYS C 633 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ARG A 131 " pdb=" N ARG A 131 " pdb=" C ARG A 131 " pdb=" CB ARG A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA TYR B 142 " pdb=" N TYR B 142 " pdb=" C TYR B 142 " pdb=" CB TYR B 142 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2163 not shown) Planarity restraints: 2496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 123 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C THR C 123 " 0.040 2.00e-02 2.50e+03 pdb=" O THR C 123 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL C 124 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 330 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C LEU A 330 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU A 330 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A 331 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 186 " -0.011 2.00e-02 2.50e+03 1.69e-02 5.00e+00 pdb=" CG PHE A 186 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 186 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 186 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 186 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 186 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 186 " 0.006 2.00e-02 2.50e+03 ... (remaining 2493 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 133 2.62 - 3.19: 12484 3.19 - 3.76: 20767 3.76 - 4.33: 29441 4.33 - 4.90: 49801 Nonbonded interactions: 112626 Sorted by model distance: nonbonded pdb=" OD1 ASP A 293 " pdb=" NH2 ARG C 638 " model vdw 2.053 3.120 nonbonded pdb=" OE1 GLU A 187 " pdb=" OG1 THR C 690 " model vdw 2.192 3.040 nonbonded pdb=" OG1 THR B 347 " pdb=" O PHE B 350 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR B 690 " pdb=" OE1 GLU C 187 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASP B 720 " pdb=" NH2 ARG C 715 " model vdw 2.271 3.120 ... (remaining 112621 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 4.060 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.430 Find NCS groups from input model: 0.200 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 14172 Z= 0.294 Angle : 0.972 24.429 19305 Z= 0.579 Chirality : 0.049 0.224 2166 Planarity : 0.005 0.044 2484 Dihedral : 13.478 81.108 5511 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.20), residues: 1656 helix: -0.50 (0.28), residues: 360 sheet: -0.45 (0.25), residues: 426 loop : -0.79 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 131 TYR 0.022 0.001 TYR C 282 PHE 0.038 0.001 PHE A 186 TRP 0.007 0.001 TRP C 539 HIS 0.003 0.001 HIS B 512 Details of bonding type rmsd covalent geometry : bond 0.00473 (14133) covalent geometry : angle 0.95119 (19206) SS BOND : bond 0.04240 ( 18) SS BOND : angle 3.73904 ( 36) hydrogen bonds : bond 0.22756 ( 536) hydrogen bonds : angle 10.25320 ( 1563) link_BETA1-4 : bond 0.00460 ( 9) link_BETA1-4 : angle 2.47647 ( 27) link_NAG-ASN : bond 0.04116 ( 12) link_NAG-ASN : angle 2.36864 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 212 LYS cc_start: 0.8731 (mptt) cc_final: 0.7823 (pmtt) REVERT: A 653 TYR cc_start: 0.8311 (m-80) cc_final: 0.7858 (m-10) REVERT: A 704 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7131 (tm-30) REVERT: B 232 MET cc_start: 0.8100 (mmt) cc_final: 0.7889 (mtm) REVERT: B 631 GLU cc_start: 0.8290 (pt0) cc_final: 0.7999 (pp20) REVERT: B 704 GLU cc_start: 0.7689 (mm-30) cc_final: 0.6788 (tm-30) REVERT: C 232 MET cc_start: 0.8116 (mmm) cc_final: 0.7875 (mtm) REVERT: C 585 ASN cc_start: 0.8170 (p0) cc_final: 0.7607 (m-40) REVERT: C 704 GLU cc_start: 0.7674 (mm-30) cc_final: 0.6888 (tm-30) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.6861 time to fit residues: 58.8475 Evaluate side-chains 66 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.096156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.072145 restraints weight = 34823.761| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.66 r_work: 0.3219 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14172 Z= 0.184 Angle : 0.621 8.246 19305 Z= 0.322 Chirality : 0.044 0.182 2166 Planarity : 0.005 0.039 2484 Dihedral : 5.049 58.966 2328 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.64 % Allowed : 12.13 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.20), residues: 1656 helix: 0.09 (0.26), residues: 357 sheet: -0.59 (0.23), residues: 474 loop : -0.37 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 131 TYR 0.014 0.001 TYR A 164 PHE 0.017 0.002 PHE B 127 TRP 0.012 0.002 TRP B 528 HIS 0.004 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00405 (14133) covalent geometry : angle 0.60876 (19206) SS BOND : bond 0.00359 ( 18) SS BOND : angle 1.96979 ( 36) hydrogen bonds : bond 0.04787 ( 536) hydrogen bonds : angle 5.97805 ( 1563) link_BETA1-4 : bond 0.00610 ( 9) link_BETA1-4 : angle 2.10850 ( 27) link_NAG-ASN : bond 0.00221 ( 12) link_NAG-ASN : angle 1.31368 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.571 Fit side-chains REVERT: A 232 MET cc_start: 0.7976 (mtm) cc_final: 0.7304 (mpp) REVERT: A 421 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.6655 (mpp) REVERT: A 653 TYR cc_start: 0.8340 (m-80) cc_final: 0.7907 (m-10) REVERT: A 704 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7127 (tm-30) REVERT: B 212 LYS cc_start: 0.8575 (mptt) cc_final: 0.7707 (pmtt) REVERT: B 421 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7072 (mpp) REVERT: B 704 GLU cc_start: 0.7830 (mm-30) cc_final: 0.6810 (tm-30) REVERT: C 585 ASN cc_start: 0.8198 (p0) cc_final: 0.7646 (m-40) REVERT: C 704 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6835 (tm-30) outliers start: 24 outliers final: 7 residues processed: 85 average time/residue: 0.5380 time to fit residues: 51.0837 Evaluate side-chains 73 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 705 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.096460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.072579 restraints weight = 35407.821| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.55 r_work: 0.3223 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14172 Z= 0.151 Angle : 0.569 8.279 19305 Z= 0.293 Chirality : 0.043 0.180 2166 Planarity : 0.004 0.040 2484 Dihedral : 5.001 56.718 2328 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.57 % Allowed : 14.38 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.21), residues: 1656 helix: 0.24 (0.27), residues: 357 sheet: -0.46 (0.24), residues: 477 loop : -0.19 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 691 TYR 0.018 0.001 TYR B 597 PHE 0.012 0.001 PHE B 127 TRP 0.007 0.001 TRP C 354 HIS 0.004 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00335 (14133) covalent geometry : angle 0.55909 (19206) SS BOND : bond 0.00225 ( 18) SS BOND : angle 1.67520 ( 36) hydrogen bonds : bond 0.04236 ( 536) hydrogen bonds : angle 5.45981 ( 1563) link_BETA1-4 : bond 0.00545 ( 9) link_BETA1-4 : angle 1.74463 ( 27) link_NAG-ASN : bond 0.00219 ( 12) link_NAG-ASN : angle 1.22300 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.549 Fit side-chains REVERT: A 232 MET cc_start: 0.8070 (mtm) cc_final: 0.7507 (mpp) REVERT: A 704 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7092 (tm-30) REVERT: B 232 MET cc_start: 0.7982 (mtm) cc_final: 0.7714 (mpp) REVERT: B 704 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7007 (tm-30) REVERT: C 232 MET cc_start: 0.7814 (mtm) cc_final: 0.7370 (mpp) REVERT: C 421 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.6518 (mpp) REVERT: C 585 ASN cc_start: 0.8135 (p0) cc_final: 0.7782 (m-40) REVERT: C 704 GLU cc_start: 0.7943 (mm-30) cc_final: 0.6999 (tm-30) outliers start: 23 outliers final: 5 residues processed: 79 average time/residue: 0.4855 time to fit residues: 43.0486 Evaluate side-chains 67 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 421 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 45 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 136 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.096098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.072268 restraints weight = 35390.159| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.54 r_work: 0.3226 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14172 Z= 0.138 Angle : 0.544 8.969 19305 Z= 0.280 Chirality : 0.042 0.177 2166 Planarity : 0.004 0.042 2484 Dihedral : 4.998 55.178 2328 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.04 % Allowed : 15.27 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.21), residues: 1656 helix: 0.51 (0.28), residues: 339 sheet: -0.41 (0.24), residues: 483 loop : -0.14 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 691 TYR 0.017 0.001 TYR A 597 PHE 0.011 0.001 PHE B 127 TRP 0.006 0.001 TRP C 354 HIS 0.003 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00306 (14133) covalent geometry : angle 0.53548 (19206) SS BOND : bond 0.00236 ( 18) SS BOND : angle 1.56663 ( 36) hydrogen bonds : bond 0.03864 ( 536) hydrogen bonds : angle 5.18832 ( 1563) link_BETA1-4 : bond 0.00470 ( 9) link_BETA1-4 : angle 1.57906 ( 27) link_NAG-ASN : bond 0.00222 ( 12) link_NAG-ASN : angle 1.22868 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.518 Fit side-chains REVERT: A 232 MET cc_start: 0.8051 (mtm) cc_final: 0.7545 (mpp) REVERT: A 704 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7124 (tm-30) REVERT: B 232 MET cc_start: 0.8126 (mtm) cc_final: 0.7774 (mpp) REVERT: B 704 GLU cc_start: 0.7923 (mm-30) cc_final: 0.6964 (tm-30) REVERT: C 232 MET cc_start: 0.7939 (mtm) cc_final: 0.7393 (mpp) REVERT: C 585 ASN cc_start: 0.8120 (p0) cc_final: 0.7790 (m-40) REVERT: C 704 GLU cc_start: 0.7838 (mm-30) cc_final: 0.6922 (tm-30) outliers start: 30 outliers final: 9 residues processed: 85 average time/residue: 0.4800 time to fit residues: 45.9943 Evaluate side-chains 67 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 583 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 116 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.0470 chunk 103 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.096708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.072892 restraints weight = 35313.838| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.52 r_work: 0.3231 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14172 Z= 0.120 Angle : 0.528 9.216 19305 Z= 0.269 Chirality : 0.041 0.174 2166 Planarity : 0.004 0.042 2484 Dihedral : 4.918 54.178 2328 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.04 % Allowed : 15.68 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.21), residues: 1656 helix: 0.58 (0.29), residues: 339 sheet: -0.20 (0.25), residues: 468 loop : -0.16 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 592 TYR 0.014 0.001 TYR C 597 PHE 0.010 0.001 PHE B 127 TRP 0.006 0.001 TRP A 356 HIS 0.003 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00265 (14133) covalent geometry : angle 0.52072 (19206) SS BOND : bond 0.00216 ( 18) SS BOND : angle 1.44981 ( 36) hydrogen bonds : bond 0.03593 ( 536) hydrogen bonds : angle 4.99170 ( 1563) link_BETA1-4 : bond 0.00455 ( 9) link_BETA1-4 : angle 1.43170 ( 27) link_NAG-ASN : bond 0.00201 ( 12) link_NAG-ASN : angle 1.21753 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.409 Fit side-chains REVERT: A 212 LYS cc_start: 0.8708 (mptt) cc_final: 0.7777 (pmtt) REVERT: A 232 MET cc_start: 0.8014 (mtm) cc_final: 0.7699 (mpp) REVERT: A 409 LEU cc_start: 0.5944 (mm) cc_final: 0.5703 (mm) REVERT: A 704 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7104 (tm-30) REVERT: B 212 LYS cc_start: 0.8584 (mptt) cc_final: 0.7716 (pmtt) REVERT: B 232 MET cc_start: 0.8097 (mtm) cc_final: 0.7807 (mpp) REVERT: B 421 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7187 (mpp) REVERT: B 704 GLU cc_start: 0.7887 (mm-30) cc_final: 0.6963 (tm-30) REVERT: C 232 MET cc_start: 0.7941 (mtm) cc_final: 0.7458 (mpp) REVERT: C 421 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.6422 (mpp) REVERT: C 585 ASN cc_start: 0.8101 (p0) cc_final: 0.7802 (m-40) REVERT: C 704 GLU cc_start: 0.7816 (mm-30) cc_final: 0.6877 (tm-30) outliers start: 30 outliers final: 12 residues processed: 88 average time/residue: 0.4210 time to fit residues: 42.1260 Evaluate side-chains 78 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 673 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 89 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.095994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.072186 restraints weight = 35203.792| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.49 r_work: 0.3214 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14172 Z= 0.149 Angle : 0.539 8.910 19305 Z= 0.274 Chirality : 0.042 0.167 2166 Planarity : 0.004 0.043 2484 Dihedral : 5.010 55.218 2328 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.70 % Allowed : 16.77 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.21), residues: 1656 helix: 0.67 (0.29), residues: 339 sheet: -0.17 (0.25), residues: 468 loop : -0.14 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 131 TYR 0.013 0.001 TYR C 597 PHE 0.011 0.001 PHE C 325 TRP 0.005 0.001 TRP C 354 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00333 (14133) covalent geometry : angle 0.53185 (19206) SS BOND : bond 0.00189 ( 18) SS BOND : angle 1.45722 ( 36) hydrogen bonds : bond 0.03572 ( 536) hydrogen bonds : angle 4.95445 ( 1563) link_BETA1-4 : bond 0.00460 ( 9) link_BETA1-4 : angle 1.41685 ( 27) link_NAG-ASN : bond 0.00262 ( 12) link_NAG-ASN : angle 1.23462 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.544 Fit side-chains REVERT: A 212 LYS cc_start: 0.8722 (mptt) cc_final: 0.7737 (pmtt) REVERT: A 232 MET cc_start: 0.8025 (mtm) cc_final: 0.7622 (mpp) REVERT: A 409 LEU cc_start: 0.6005 (mm) cc_final: 0.5752 (mm) REVERT: A 704 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7112 (tm-30) REVERT: B 212 LYS cc_start: 0.8593 (mptt) cc_final: 0.7706 (pmtt) REVERT: B 232 MET cc_start: 0.8075 (mtm) cc_final: 0.7692 (mpp) REVERT: B 704 GLU cc_start: 0.7893 (mm-30) cc_final: 0.6982 (tm-30) REVERT: C 232 MET cc_start: 0.7914 (mtm) cc_final: 0.7448 (mpp) REVERT: C 421 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.6560 (mpp) REVERT: C 585 ASN cc_start: 0.8104 (p0) cc_final: 0.7795 (m-40) REVERT: C 704 GLU cc_start: 0.7810 (mm-30) cc_final: 0.6884 (tm-30) outliers start: 25 outliers final: 11 residues processed: 85 average time/residue: 0.4627 time to fit residues: 44.2678 Evaluate side-chains 77 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 583 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 36 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.095695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.071717 restraints weight = 35518.143| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.53 r_work: 0.3202 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14172 Z= 0.164 Angle : 0.544 9.033 19305 Z= 0.277 Chirality : 0.042 0.167 2166 Planarity : 0.004 0.044 2484 Dihedral : 5.049 55.203 2328 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.84 % Allowed : 17.31 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1656 helix: 0.76 (0.29), residues: 339 sheet: -0.15 (0.25), residues: 468 loop : -0.13 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 131 TYR 0.012 0.001 TYR A 164 PHE 0.015 0.001 PHE B 127 TRP 0.006 0.001 TRP A 354 HIS 0.006 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00367 (14133) covalent geometry : angle 0.53617 (19206) SS BOND : bond 0.00192 ( 18) SS BOND : angle 1.45304 ( 36) hydrogen bonds : bond 0.03587 ( 536) hydrogen bonds : angle 4.93401 ( 1563) link_BETA1-4 : bond 0.00442 ( 9) link_BETA1-4 : angle 1.39135 ( 27) link_NAG-ASN : bond 0.00274 ( 12) link_NAG-ASN : angle 1.24637 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.514 Fit side-chains REVERT: A 212 LYS cc_start: 0.8735 (mptt) cc_final: 0.7692 (pmtt) REVERT: A 232 MET cc_start: 0.8031 (mtm) cc_final: 0.7660 (mpp) REVERT: A 409 LEU cc_start: 0.6010 (mm) cc_final: 0.5757 (mm) REVERT: A 704 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: B 212 LYS cc_start: 0.8590 (mptt) cc_final: 0.7675 (pmtt) REVERT: B 232 MET cc_start: 0.8120 (mtm) cc_final: 0.7708 (mpp) REVERT: B 704 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: C 232 MET cc_start: 0.7935 (mtm) cc_final: 0.7520 (mpp) REVERT: C 421 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.6583 (mpp) REVERT: C 585 ASN cc_start: 0.8102 (p0) cc_final: 0.7806 (m-40) REVERT: C 704 GLU cc_start: 0.7826 (mm-30) cc_final: 0.6901 (tm-30) outliers start: 27 outliers final: 17 residues processed: 86 average time/residue: 0.4760 time to fit residues: 46.0587 Evaluate side-chains 86 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 673 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 10 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN A 534 HIS ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.095664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.071831 restraints weight = 35398.080| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.48 r_work: 0.3203 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14172 Z= 0.159 Angle : 0.543 9.392 19305 Z= 0.277 Chirality : 0.042 0.165 2166 Planarity : 0.004 0.045 2484 Dihedral : 5.064 55.057 2328 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.04 % Allowed : 17.45 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1656 helix: 0.78 (0.29), residues: 339 sheet: -0.16 (0.25), residues: 468 loop : -0.14 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 131 TYR 0.013 0.001 TYR C 282 PHE 0.011 0.001 PHE C 325 TRP 0.006 0.001 TRP A 354 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00356 (14133) covalent geometry : angle 0.53615 (19206) SS BOND : bond 0.00182 ( 18) SS BOND : angle 1.40766 ( 36) hydrogen bonds : bond 0.03567 ( 536) hydrogen bonds : angle 4.91947 ( 1563) link_BETA1-4 : bond 0.00415 ( 9) link_BETA1-4 : angle 1.36296 ( 27) link_NAG-ASN : bond 0.00273 ( 12) link_NAG-ASN : angle 1.25332 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.599 Fit side-chains REVERT: A 212 LYS cc_start: 0.8755 (mptt) cc_final: 0.7705 (pmtt) REVERT: A 232 MET cc_start: 0.8032 (mtm) cc_final: 0.7707 (mpp) REVERT: A 409 LEU cc_start: 0.6023 (mm) cc_final: 0.5779 (mm) REVERT: A 506 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8438 (mp) REVERT: A 704 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7137 (tm-30) REVERT: B 212 LYS cc_start: 0.8602 (mptt) cc_final: 0.7685 (pmtt) REVERT: B 232 MET cc_start: 0.8154 (mtm) cc_final: 0.7827 (mpp) REVERT: B 704 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: C 232 MET cc_start: 0.7941 (mtm) cc_final: 0.7448 (mpp) REVERT: C 409 LEU cc_start: 0.6179 (mm) cc_final: 0.5974 (mm) REVERT: C 421 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.6605 (mpp) REVERT: C 585 ASN cc_start: 0.8110 (p0) cc_final: 0.7810 (m-40) REVERT: C 704 GLU cc_start: 0.7829 (mm-30) cc_final: 0.6890 (tm-30) outliers start: 30 outliers final: 14 residues processed: 89 average time/residue: 0.4862 time to fit residues: 48.8871 Evaluate side-chains 82 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 589 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 6 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.096332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.072432 restraints weight = 35543.585| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.52 r_work: 0.3219 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14172 Z= 0.121 Angle : 0.522 9.369 19305 Z= 0.265 Chirality : 0.041 0.166 2166 Planarity : 0.004 0.044 2484 Dihedral : 4.949 53.868 2328 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.70 % Allowed : 17.93 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1656 helix: 0.80 (0.29), residues: 339 sheet: -0.13 (0.25), residues: 468 loop : -0.17 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 131 TYR 0.012 0.001 TYR A 164 PHE 0.009 0.001 PHE C 325 TRP 0.008 0.001 TRP B 528 HIS 0.007 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00265 (14133) covalent geometry : angle 0.51497 (19206) SS BOND : bond 0.00175 ( 18) SS BOND : angle 1.33293 ( 36) hydrogen bonds : bond 0.03420 ( 536) hydrogen bonds : angle 4.82010 ( 1563) link_BETA1-4 : bond 0.00431 ( 9) link_BETA1-4 : angle 1.30300 ( 27) link_NAG-ASN : bond 0.00221 ( 12) link_NAG-ASN : angle 1.21271 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.544 Fit side-chains REVERT: A 212 LYS cc_start: 0.8751 (mptt) cc_final: 0.7707 (pmtt) REVERT: A 232 MET cc_start: 0.8022 (mtm) cc_final: 0.7777 (mpp) REVERT: A 409 LEU cc_start: 0.5987 (mm) cc_final: 0.5715 (mm) REVERT: A 506 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8444 (mp) REVERT: A 704 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: B 212 LYS cc_start: 0.8573 (mptt) cc_final: 0.7678 (pmtt) REVERT: B 232 MET cc_start: 0.8092 (mtm) cc_final: 0.7865 (mpp) REVERT: B 421 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7247 (mpp) REVERT: B 704 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: C 232 MET cc_start: 0.7993 (mtm) cc_final: 0.7701 (mpp) REVERT: C 409 LEU cc_start: 0.6138 (mm) cc_final: 0.5922 (mm) REVERT: C 421 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.6584 (mpp) REVERT: C 585 ASN cc_start: 0.8107 (p0) cc_final: 0.7827 (m-40) REVERT: C 704 GLU cc_start: 0.7825 (mm-30) cc_final: 0.6879 (tm-30) outliers start: 25 outliers final: 12 residues processed: 84 average time/residue: 0.5029 time to fit residues: 47.3854 Evaluate side-chains 81 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 589 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 22 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.094961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.070923 restraints weight = 35480.958| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.49 r_work: 0.3183 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14172 Z= 0.203 Angle : 0.571 9.470 19305 Z= 0.290 Chirality : 0.042 0.161 2166 Planarity : 0.004 0.042 2484 Dihedral : 5.191 56.025 2328 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.43 % Allowed : 18.27 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.21), residues: 1656 helix: 0.87 (0.29), residues: 339 sheet: -0.18 (0.25), residues: 465 loop : -0.20 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 131 TYR 0.013 0.001 TYR C 282 PHE 0.013 0.001 PHE C 325 TRP 0.007 0.001 TRP A 354 HIS 0.007 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00459 (14133) covalent geometry : angle 0.56391 (19206) SS BOND : bond 0.00193 ( 18) SS BOND : angle 1.48969 ( 36) hydrogen bonds : bond 0.03675 ( 536) hydrogen bonds : angle 4.94312 ( 1563) link_BETA1-4 : bond 0.00492 ( 9) link_BETA1-4 : angle 1.43484 ( 27) link_NAG-ASN : bond 0.00392 ( 12) link_NAG-ASN : angle 1.31597 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.552 Fit side-chains REVERT: A 212 LYS cc_start: 0.8774 (mptt) cc_final: 0.7736 (pmtt) REVERT: A 232 MET cc_start: 0.8063 (mtm) cc_final: 0.7793 (mpp) REVERT: A 409 LEU cc_start: 0.6069 (mm) cc_final: 0.5805 (mm) REVERT: A 506 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 704 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: B 212 LYS cc_start: 0.8627 (mptt) cc_final: 0.7695 (pmtt) REVERT: B 232 MET cc_start: 0.8116 (mtm) cc_final: 0.7862 (mpp) REVERT: B 421 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7274 (mpp) REVERT: B 704 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7043 (tm-30) REVERT: C 232 MET cc_start: 0.8000 (mtm) cc_final: 0.7494 (mpp) REVERT: C 409 LEU cc_start: 0.6185 (mm) cc_final: 0.5977 (mm) REVERT: C 421 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.6600 (mpp) REVERT: C 585 ASN cc_start: 0.8127 (p0) cc_final: 0.7804 (m-40) REVERT: C 704 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6917 (tm-30) outliers start: 21 outliers final: 11 residues processed: 76 average time/residue: 0.5409 time to fit residues: 46.0783 Evaluate side-chains 78 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 690 THR Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 583 VAL Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 704 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 112 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.095980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.072210 restraints weight = 35456.090| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.48 r_work: 0.3211 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14172 Z= 0.130 Angle : 0.532 9.797 19305 Z= 0.269 Chirality : 0.041 0.165 2166 Planarity : 0.004 0.042 2484 Dihedral : 5.018 53.635 2328 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.57 % Allowed : 18.20 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.21), residues: 1656 helix: 0.87 (0.29), residues: 339 sheet: -0.18 (0.25), residues: 468 loop : -0.19 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 562 TYR 0.015 0.001 TYR A 164 PHE 0.010 0.001 PHE C 325 TRP 0.007 0.001 TRP B 528 HIS 0.006 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00287 (14133) covalent geometry : angle 0.52560 (19206) SS BOND : bond 0.00174 ( 18) SS BOND : angle 1.34385 ( 36) hydrogen bonds : bond 0.03456 ( 536) hydrogen bonds : angle 4.83417 ( 1563) link_BETA1-4 : bond 0.00426 ( 9) link_BETA1-4 : angle 1.29234 ( 27) link_NAG-ASN : bond 0.00259 ( 12) link_NAG-ASN : angle 1.22395 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3135.07 seconds wall clock time: 54 minutes 38.15 seconds (3278.15 seconds total)