Starting phenix.real_space_refine on Mon Apr 6 10:19:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e0l_47361/04_2026/9e0l_47361.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e0l_47361/04_2026/9e0l_47361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e0l_47361/04_2026/9e0l_47361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e0l_47361/04_2026/9e0l_47361.map" model { file = "/net/cci-nas-00/data/ceres_data/9e0l_47361/04_2026/9e0l_47361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e0l_47361/04_2026/9e0l_47361.cif" } resolution = 2.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.057 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 93 5.16 5 C 10803 2.51 5 N 3003 2.21 5 O 3575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17474 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5670 Classifications: {'peptide': 714} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 684} Chain breaks: 4 Chain: "B" Number of atoms: 5670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5670 Classifications: {'peptide': 714} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 684} Chain breaks: 4 Chain: "C" Number of atoms: 5670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 5670 Classifications: {'peptide': 714} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 684} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Time building chain proxies: 4.03, per 1000 atoms: 0.23 Number of scatterers: 17474 At special positions: 0 Unit cell: (117.48, 123.42, 196.02, 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 93 16.00 O 3575 8.00 N 3003 7.00 C 10803 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.04 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.06 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.04 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.04 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.04 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.04 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.07 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 F 1 " - " NAG F 2 " NAG-ASN " NAG D 1 " - " ASN A 398 " " NAG E 1 " - " ASN B 398 " " NAG F 1 " - " ASN C 398 " Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 787.2 milliseconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4014 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 27 sheets defined 39.6% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 87 through 106 Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.807A pdb=" N GLY A 184 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 260 through 265 removed outlier: 4.222A pdb=" N TYR A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 removed outlier: 4.175A pdb=" N GLY A 306 " --> pdb=" O TYR A 303 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N HIS A 308 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR A 309 " --> pdb=" O GLY A 306 " (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 411 through 429 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 501 through 546 removed outlier: 3.539A pdb=" N GLU A 530 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 545 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 660 through 664 Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 701 through 724 Processing helix chain 'A' and resid 726 through 741 removed outlier: 3.615A pdb=" N ALA A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 772 removed outlier: 3.573A pdb=" N VAL A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 803 Processing helix chain 'A' and resid 804 through 810 Processing helix chain 'A' and resid 838 through 862 Processing helix chain 'B' and resid 88 through 106 Processing helix chain 'B' and resid 172 through 176 removed outlier: 4.171A pdb=" N PHE B 175 " --> pdb=" O GLN B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 260 through 265 removed outlier: 4.194A pdb=" N TYR B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 310 removed outlier: 4.178A pdb=" N GLY B 306 " --> pdb=" O TYR B 303 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N HIS B 308 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR B 309 " --> pdb=" O GLY B 306 " (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 411 through 429 removed outlier: 3.537A pdb=" N ASP B 416 " --> pdb=" O CYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 501 through 546 removed outlier: 3.586A pdb=" N ARG B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 530 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 545 " --> pdb=" O GLU B 541 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 701 through 724 Processing helix chain 'B' and resid 726 through 742 removed outlier: 3.577A pdb=" N ALA B 730 " --> pdb=" O ASP B 726 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 738 " --> pdb=" O GLY B 734 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 739 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 741 " --> pdb=" O ALA B 737 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET B 742 " --> pdb=" O PHE B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 772 Processing helix chain 'B' and resid 773 through 803 Processing helix chain 'B' and resid 804 through 810 Processing helix chain 'B' and resid 838 through 862 removed outlier: 3.579A pdb=" N ARG B 848 " --> pdb=" O ARG B 844 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 862 " --> pdb=" O ARG B 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 106 removed outlier: 3.647A pdb=" N ALA C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 176 removed outlier: 4.146A pdb=" N PHE C 175 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 184 removed outlier: 3.824A pdb=" N GLY C 184 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 260 through 265 removed outlier: 4.214A pdb=" N TYR C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 310 removed outlier: 4.162A pdb=" N GLY C 306 " --> pdb=" O TYR C 303 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N HIS C 308 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR C 309 " --> pdb=" O GLY C 306 " (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 411 through 429 Processing helix chain 'C' and resid 459 through 467 removed outlier: 3.627A pdb=" N GLU C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 546 removed outlier: 3.908A pdb=" N ALA C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 545 " --> pdb=" O GLU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 removed outlier: 4.784A pdb=" N SER C 552 " --> pdb=" O ASN C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 685 through 691 removed outlier: 4.223A pdb=" N TYR C 689 " --> pdb=" O PRO C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 724 Processing helix chain 'C' and resid 726 through 742 removed outlier: 3.583A pdb=" N ALA C 730 " --> pdb=" O ASP C 726 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE C 738 " --> pdb=" O GLY C 734 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET C 742 " --> pdb=" O PHE C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 772 removed outlier: 3.530A pdb=" N VAL C 752 " --> pdb=" O ALA C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 803 Processing helix chain 'C' and resid 804 through 810 Processing helix chain 'C' and resid 810 through 815 removed outlier: 4.411A pdb=" N THR C 814 " --> pdb=" O TYR C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 838 through 862 removed outlier: 3.710A pdb=" N ARG C 848 " --> pdb=" O ARG C 844 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 6.525A 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: 6.604A pdb=" N VAL A 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL C 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN A 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 433 through 435 removed outlier: 3.523A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 443 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN A 398 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASP A 373 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLY A 145 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET A 375 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR A 143 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 191 Processing sheet with id=AA5, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.223A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG A 342 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASP A 323 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU A 344 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLN A 321 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR A 346 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE A 319 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA7, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA8, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AA9, first strand: chain 'A' and resid 638 through 643 removed outlier: 5.914A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 665 through 667 removed outlier: 3.546A pdb=" N THR A 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.564A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 433 through 435 removed outlier: 3.530A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B 443 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN B 398 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ASP B 373 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLY B 145 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET B 375 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR B 143 " --> pdb=" O MET B 375 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG B 377 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASN B 141 " --> pdb=" O ARG B 377 " (cutoff:3.500A) removed outlier: 14.018A pdb=" N TYR B 142 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N SER B 457 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 186 through 191 Processing sheet with id=AB5, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.238A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N THR B 340 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 324 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AB7, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AB8, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AB9, first strand: chain 'B' and resid 638 through 642 removed outlier: 3.577A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 665 through 667 removed outlier: 3.541A pdb=" N THR B 665 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.545A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 433 through 435 removed outlier: 3.507A pdb=" N PHE C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU C 443 " --> pdb=" O ASN C 398 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN C 398 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASP C 373 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLY C 145 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N MET C 375 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR C 143 " --> pdb=" O MET C 375 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 186 through 191 Processing sheet with id=AC5, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.240A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AC7, first strand: chain 'C' and resid 210 through 214 Processing sheet with id=AC8, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AC9, first strand: chain 'C' and resid 638 through 642 removed outlier: 3.600A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2790 1.29 - 1.43: 4808 1.43 - 1.56: 9733 1.56 - 1.69: 0 1.69 - 1.82: 156 Bond restraints: 17487 Sorted by residual: bond pdb=" C SER C 598 " pdb=" O SER C 598 " ideal model delta sigma weight residual 1.236 1.163 0.072 1.29e-02 6.01e+03 3.15e+01 bond pdb=" C SER B 598 " pdb=" O SER B 598 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.29e-02 6.01e+03 2.59e+01 bond pdb=" N VAL C 635 " pdb=" CA VAL C 635 " ideal model delta sigma weight residual 1.456 1.508 -0.052 1.08e-02 8.57e+03 2.30e+01 bond pdb=" N ILE A 391 " pdb=" CA ILE A 391 " ideal model delta sigma weight residual 1.454 1.499 -0.045 1.19e-02 7.06e+03 1.42e+01 bond pdb=" N THR B 634 " pdb=" CA THR B 634 " ideal model delta sigma weight residual 1.454 1.500 -0.046 1.31e-02 5.83e+03 1.22e+01 ... (remaining 17482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 23195 2.07 - 4.13: 463 4.13 - 6.20: 47 6.20 - 8.27: 4 8.27 - 10.33: 3 Bond angle restraints: 23712 Sorted by residual: angle pdb=" O GLY A 410 " pdb=" C GLY A 410 " pdb=" N ASP A 411 " ideal model delta sigma weight residual 122.64 116.16 6.48 1.16e+00 7.43e-01 3.12e+01 angle pdb=" C ILE A 413 " pdb=" N GLY A 414 " pdb=" CA GLY A 414 " ideal model delta sigma weight residual 119.94 126.00 -6.06 1.11e+00 8.12e-01 2.98e+01 angle pdb=" C GLY A 410 " pdb=" N ASP A 411 " pdb=" CA ASP A 411 " ideal model delta sigma weight residual 123.13 113.78 9.35 1.89e+00 2.80e-01 2.45e+01 angle pdb=" CA ILE C 413 " pdb=" C ILE C 413 " pdb=" O ILE C 413 " ideal model delta sigma weight residual 120.96 115.30 5.66 1.19e+00 7.06e-01 2.26e+01 angle pdb=" CA THR B 634 " pdb=" C THR B 634 " pdb=" O THR B 634 " ideal model delta sigma weight residual 121.68 116.08 5.60 1.18e+00 7.18e-01 2.25e+01 ... (remaining 23707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 9125 17.68 - 35.35: 964 35.35 - 53.03: 310 53.03 - 70.70: 63 70.70 - 88.38: 26 Dihedral angle restraints: 10488 sinusoidal: 4242 harmonic: 6246 Sorted by residual: dihedral pdb=" CB CYS A 364 " pdb=" SG CYS A 364 " pdb=" SG CYS A 412 " pdb=" CB CYS A 412 " ideal model delta sinusoidal sigma weight residual -86.00 -129.48 43.48 1 1.00e+01 1.00e-02 2.63e+01 dihedral pdb=" CA ASN C 548 " pdb=" C ASN C 548 " pdb=" N ALA C 549 " pdb=" CA ALA C 549 " ideal model delta harmonic sigma weight residual 180.00 158.00 22.00 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CB CYS C 364 " pdb=" SG CYS C 364 " pdb=" SG CYS C 412 " pdb=" CB CYS C 412 " ideal model delta sinusoidal sigma weight residual -86.00 -122.50 36.50 1 1.00e+01 1.00e-02 1.88e+01 ... (remaining 10485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2220 0.059 - 0.119: 344 0.119 - 0.178: 35 0.178 - 0.237: 9 0.237 - 0.296: 2 Chirality restraints: 2610 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.77e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.59e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 398 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 2607 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.084 2.00e-02 2.50e+03 6.99e-02 6.10e+01 pdb=" C7 NAG F 2 " 0.021 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.063 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.113 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.082 2.00e-02 2.50e+03 6.77e-02 5.73e+01 pdb=" C7 NAG E 2 " 0.021 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.061 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.109 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.064 2.00e-02 2.50e+03 5.29e-02 3.50e+01 pdb=" C7 NAG D 2 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.048 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.085 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.011 2.00e-02 2.50e+03 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1166 2.74 - 3.28: 16438 3.28 - 3.82: 30242 3.82 - 4.36: 36566 4.36 - 4.90: 60328 Nonbonded interactions: 144740 Sorted by model distance: nonbonded pdb=" O GLY C 645 " pdb=" O HOH C1001 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR B 669 " pdb=" O HOH B1001 " model vdw 2.198 3.040 nonbonded pdb=" O CYS A 573 " pdb=" O HOH A1001 " model vdw 2.208 3.040 nonbonded pdb=" O GLY B 645 " pdb=" O HOH B1002 " model vdw 2.211 3.040 nonbonded pdb=" O CYS C 573 " pdb=" O HOH C1002 " model vdw 2.215 3.040 ... (remaining 144735 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 9.160 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: 0.500 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.350 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17505 Z= 0.265 Angle : 0.656 10.333 23754 Z= 0.395 Chirality : 0.045 0.296 2610 Planarity : 0.005 0.070 3081 Dihedral : 16.772 88.375 6438 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Rotamer: Outliers : 4.02 % Allowed : 16.81 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.69 (0.18), residues: 2112 helix: 2.80 (0.19), residues: 720 sheet: 1.26 (0.23), residues: 480 loop : -0.34 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 661 TYR 0.015 0.001 TYR B 849 PHE 0.017 0.002 PHE C 287 TRP 0.016 0.001 TRP A 539 HIS 0.003 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00407 (17487) covalent geometry : angle 0.64753 (23712) SS BOND : bond 0.01578 ( 12) SS BOND : angle 2.67619 ( 24) hydrogen bonds : bond 0.13690 ( 883) hydrogen bonds : angle 5.99958 ( 2607) link_BETA1-4 : bond 0.00035 ( 3) link_BETA1-4 : angle 1.41400 ( 9) link_NAG-ASN : bond 0.00778 ( 3) link_NAG-ASN : angle 2.87580 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 189 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: A 304 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.7005 (mtp85) REVERT: A 462 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6474 (pt0) REVERT: A 531 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8849 (tt) REVERT: A 579 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7809 (p0) REVERT: A 658 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8327 (tt0) REVERT: B 183 MET cc_start: 0.6318 (OUTLIER) cc_final: 0.4129 (ppp) REVERT: B 195 GLU cc_start: 0.7162 (pp20) cc_final: 0.6820 (tm-30) REVERT: B 235 LYS cc_start: 0.7701 (mtmm) cc_final: 0.7394 (mtmm) REVERT: B 349 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7620 (ptpt) REVERT: B 531 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8966 (tt) REVERT: B 579 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7733 (p0) REVERT: B 587 MET cc_start: 0.9034 (mtp) cc_final: 0.8805 (mtp) REVERT: B 742 MET cc_start: 0.4539 (mpp) cc_final: 0.4052 (tpp) REVERT: B 850 MET cc_start: 0.4899 (mpp) cc_final: 0.4483 (mpp) REVERT: C 183 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.4092 (ppp) REVERT: C 195 GLU cc_start: 0.7263 (pp20) cc_final: 0.7000 (tm-30) REVERT: C 415 LYS cc_start: 0.8042 (ttmm) cc_final: 0.7822 (mttt) REVERT: C 423 ARG cc_start: 0.7610 (ttp-110) cc_final: 0.7287 (mtm110) REVERT: C 503 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.4771 (t80) REVERT: C 531 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8881 (tt) REVERT: C 674 ASN cc_start: 0.6020 (t0) cc_final: 0.5792 (t0) REVERT: C 742 MET cc_start: 0.3524 (tmt) cc_final: 0.2457 (mmm) REVERT: C 850 MET cc_start: 0.5473 (OUTLIER) cc_final: 0.5175 (mpp) outliers start: 72 outliers final: 50 residues processed: 238 average time/residue: 0.6024 time to fit residues: 160.4036 Evaluate side-chains 248 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 184 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 503 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 845 GLU Chi-restraints excluded: chain C residue 850 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 534 HIS B 248 HIS B 516 HIS C 126 GLN C 248 HIS C 534 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.193387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.134237 restraints weight = 14461.852| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.74 r_work: 0.3277 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 17505 Z= 0.118 Angle : 0.523 11.871 23754 Z= 0.284 Chirality : 0.040 0.146 2610 Planarity : 0.004 0.049 3081 Dihedral : 8.637 66.045 2649 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.52 % Allowed : 17.03 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.74 (0.18), residues: 2112 helix: 2.80 (0.19), residues: 729 sheet: 0.98 (0.22), residues: 543 loop : -0.20 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 428 TYR 0.011 0.001 TYR B 849 PHE 0.017 0.001 PHE C 287 TRP 0.013 0.001 TRP A 539 HIS 0.002 0.000 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00230 (17487) covalent geometry : angle 0.51864 (23712) SS BOND : bond 0.00603 ( 12) SS BOND : angle 1.70347 ( 24) hydrogen bonds : bond 0.05151 ( 883) hydrogen bonds : angle 4.87022 ( 2607) link_BETA1-4 : bond 0.00503 ( 3) link_BETA1-4 : angle 1.72446 ( 9) link_NAG-ASN : bond 0.00208 ( 3) link_NAG-ASN : angle 1.53672 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.7148 (pp20) cc_final: 0.6646 (tm-30) REVERT: A 360 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6098 (mtp180) REVERT: A 658 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: B 183 MET cc_start: 0.6328 (OUTLIER) cc_final: 0.4040 (ppp) REVERT: B 195 GLU cc_start: 0.7072 (pp20) cc_final: 0.6637 (tm-30) REVERT: B 235 LYS cc_start: 0.7653 (mtmm) cc_final: 0.7264 (mtmm) REVERT: B 416 ASP cc_start: 0.7690 (m-30) cc_final: 0.7447 (m-30) REVERT: B 584 GLN cc_start: 0.8259 (mt0) cc_final: 0.8018 (mm110) REVERT: B 614 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8084 (mm-30) REVERT: B 699 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8754 (mp) REVERT: B 742 MET cc_start: 0.4564 (mpp) cc_final: 0.4063 (tpp) REVERT: B 850 MET cc_start: 0.4745 (OUTLIER) cc_final: 0.4090 (mpp) REVERT: C 182 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.6662 (m-80) REVERT: C 195 GLU cc_start: 0.7107 (pp20) cc_final: 0.6725 (tm-30) REVERT: C 415 LYS cc_start: 0.7876 (ttmm) cc_final: 0.7653 (mttt) REVERT: C 423 ARG cc_start: 0.7520 (ttp-110) cc_final: 0.7152 (mtm110) REVERT: C 674 ASN cc_start: 0.5816 (t0) cc_final: 0.5612 (t0) REVERT: C 742 MET cc_start: 0.3462 (OUTLIER) cc_final: 0.2431 (mmm) REVERT: C 850 MET cc_start: 0.5068 (OUTLIER) cc_final: 0.4593 (mpp) outliers start: 63 outliers final: 26 residues processed: 236 average time/residue: 0.5941 time to fit residues: 156.3631 Evaluate side-chains 222 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain C residue 182 PHE Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 742 MET Chi-restraints excluded: chain C residue 850 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 180 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 445 ASN B 445 ASN B 458 ASN C 126 GLN C 445 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.187706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133243 restraints weight = 14253.220| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.01 r_work: 0.3250 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 17505 Z= 0.292 Angle : 0.759 15.002 23754 Z= 0.416 Chirality : 0.050 0.263 2610 Planarity : 0.006 0.066 3081 Dihedral : 8.230 64.692 2571 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.86 % Allowed : 15.13 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.45 (0.18), residues: 2112 helix: 2.46 (0.19), residues: 702 sheet: 1.10 (0.22), residues: 516 loop : -0.33 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 661 TYR 0.021 0.002 TYR A 702 PHE 0.030 0.003 PHE C 287 TRP 0.021 0.003 TRP C 539 HIS 0.007 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00655 (17487) covalent geometry : angle 0.75064 (23712) SS BOND : bond 0.01761 ( 12) SS BOND : angle 3.10456 ( 24) hydrogen bonds : bond 0.07056 ( 883) hydrogen bonds : angle 5.10963 ( 2607) link_BETA1-4 : bond 0.00696 ( 3) link_BETA1-4 : angle 2.31244 ( 9) link_NAG-ASN : bond 0.00142 ( 3) link_NAG-ASN : angle 2.19195 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 185 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6733 (mp10) REVERT: A 195 GLU cc_start: 0.7237 (pp20) cc_final: 0.6801 (tm-30) REVERT: A 218 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6759 (pp) REVERT: A 349 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7196 (ptmt) REVERT: A 360 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.5976 (mtp180) REVERT: A 502 GLU cc_start: 0.5046 (OUTLIER) cc_final: 0.4580 (mt-10) REVERT: A 521 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8105 (mp) REVERT: A 531 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8856 (tt) REVERT: A 579 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7898 (p0) REVERT: A 771 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7433 (mtp) REVERT: A 850 MET cc_start: 0.5393 (mmm) cc_final: 0.5148 (mmm) REVERT: B 181 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6751 (mp10) REVERT: B 183 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.4131 (ppp) REVERT: B 195 GLU cc_start: 0.7103 (pp20) cc_final: 0.6747 (tm-30) REVERT: B 235 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7415 (mtmm) REVERT: B 416 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7528 (t0) REVERT: B 505 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7639 (mtm-85) REVERT: B 521 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8304 (mp) REVERT: B 531 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8964 (tm) REVERT: B 579 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7816 (p0) REVERT: B 847 ILE cc_start: 0.4750 (OUTLIER) cc_final: 0.4407 (pp) REVERT: B 850 MET cc_start: 0.5054 (OUTLIER) cc_final: 0.4526 (mpp) REVERT: C 181 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6773 (mp10) REVERT: C 195 GLU cc_start: 0.7188 (pp20) cc_final: 0.6882 (tm-30) REVERT: C 415 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7871 (mttt) REVERT: C 521 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8062 (mp) REVERT: C 531 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8873 (tt) REVERT: C 674 ASN cc_start: 0.6077 (t0) cc_final: 0.5722 (t0) REVERT: C 701 ASP cc_start: 0.8669 (p0) cc_final: 0.8391 (p0) REVERT: C 742 MET cc_start: 0.3426 (tmt) cc_final: 0.2328 (mmm) outliers start: 105 outliers final: 60 residues processed: 252 average time/residue: 0.5955 time to fit residues: 167.7574 Evaluate side-chains 256 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 176 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 579 ASP Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 847 ILE Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 850 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 110 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 117 optimal weight: 0.0970 chunk 60 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 516 HIS B 248 HIS B 458 ASN B 516 HIS C 248 HIS C 516 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.192545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133590 restraints weight = 14553.261| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.77 r_work: 0.3252 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 17505 Z= 0.120 Angle : 0.517 9.541 23754 Z= 0.283 Chirality : 0.039 0.149 2610 Planarity : 0.004 0.055 3081 Dihedral : 7.456 62.811 2571 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.91 % Allowed : 17.36 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.64 (0.18), residues: 2112 helix: 2.68 (0.19), residues: 732 sheet: 0.93 (0.22), residues: 543 loop : -0.23 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 505 TYR 0.010 0.001 TYR B 849 PHE 0.017 0.001 PHE C 287 TRP 0.013 0.001 TRP A 539 HIS 0.003 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00236 (17487) covalent geometry : angle 0.51185 (23712) SS BOND : bond 0.00589 ( 12) SS BOND : angle 1.87020 ( 24) hydrogen bonds : bond 0.05123 ( 883) hydrogen bonds : angle 4.77172 ( 2607) link_BETA1-4 : bond 0.00580 ( 3) link_BETA1-4 : angle 1.80913 ( 9) link_NAG-ASN : bond 0.00228 ( 3) link_NAG-ASN : angle 1.54303 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 192 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLN cc_start: 0.6977 (OUTLIER) cc_final: 0.6750 (mp10) REVERT: A 195 GLU cc_start: 0.7132 (pp20) cc_final: 0.6652 (tm-30) REVERT: A 349 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7049 (ptmt) REVERT: A 360 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.5697 (mtp180) REVERT: A 502 GLU cc_start: 0.4978 (OUTLIER) cc_final: 0.4387 (mt-10) REVERT: A 531 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8847 (tt) REVERT: A 850 MET cc_start: 0.5401 (mmm) cc_final: 0.5195 (mmm) REVERT: B 183 MET cc_start: 0.6331 (OUTLIER) cc_final: 0.3990 (ppp) REVERT: B 195 GLU cc_start: 0.7078 (pp20) cc_final: 0.6635 (tm-30) REVERT: B 235 LYS cc_start: 0.7661 (mtmm) cc_final: 0.7259 (mtmm) REVERT: B 349 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7745 (ptmt) REVERT: B 416 ASP cc_start: 0.7642 (m-30) cc_final: 0.7400 (m-30) REVERT: B 584 GLN cc_start: 0.8274 (mt0) cc_final: 0.8004 (mm110) REVERT: B 699 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8758 (mp) REVERT: B 742 MET cc_start: 0.4550 (mpp) cc_final: 0.4063 (tpp) REVERT: B 850 MET cc_start: 0.4756 (OUTLIER) cc_final: 0.4266 (mpp) REVERT: C 195 GLU cc_start: 0.7116 (pp20) cc_final: 0.6728 (tm-30) REVERT: C 305 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: C 415 LYS cc_start: 0.7840 (ttmm) cc_final: 0.7636 (mttt) REVERT: C 423 ARG cc_start: 0.7484 (ttp-110) cc_final: 0.7094 (mtm110) REVERT: C 531 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8850 (tt) REVERT: C 742 MET cc_start: 0.3414 (OUTLIER) cc_final: 0.2337 (mmm) outliers start: 70 outliers final: 33 residues processed: 235 average time/residue: 0.6105 time to fit residues: 160.1191 Evaluate side-chains 231 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 742 MET Chi-restraints excluded: chain C residue 812 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 200 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 210 optimal weight: 7.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 516 HIS B 248 HIS B 516 HIS C 248 HIS C 516 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.191694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.137583 restraints weight = 14402.418| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.04 r_work: 0.3313 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17505 Z= 0.132 Angle : 0.530 9.075 23754 Z= 0.289 Chirality : 0.040 0.154 2610 Planarity : 0.004 0.055 3081 Dihedral : 7.184 61.102 2565 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.02 % Allowed : 17.14 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.69 (0.18), residues: 2112 helix: 2.77 (0.19), residues: 732 sheet: 0.89 (0.22), residues: 546 loop : -0.20 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 132 TYR 0.011 0.001 TYR B 849 PHE 0.018 0.002 PHE C 287 TRP 0.015 0.001 TRP A 539 HIS 0.003 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00269 (17487) covalent geometry : angle 0.52547 (23712) SS BOND : bond 0.00776 ( 12) SS BOND : angle 1.79970 ( 24) hydrogen bonds : bond 0.05249 ( 883) hydrogen bonds : angle 4.70140 ( 2607) link_BETA1-4 : bond 0.00516 ( 3) link_BETA1-4 : angle 1.72220 ( 9) link_NAG-ASN : bond 0.00190 ( 3) link_NAG-ASN : angle 1.56436 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 196 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6762 (mp10) REVERT: A 195 GLU cc_start: 0.7324 (pp20) cc_final: 0.6907 (tm-30) REVERT: A 360 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.5969 (mtp180) REVERT: A 502 GLU cc_start: 0.5092 (OUTLIER) cc_final: 0.4628 (mt-10) REVERT: A 531 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8882 (tt) REVERT: A 622 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7881 (tp30) REVERT: A 771 MET cc_start: 0.7593 (tpp) cc_final: 0.7224 (mtp) REVERT: A 850 MET cc_start: 0.5603 (mmm) cc_final: 0.5395 (mmm) REVERT: B 181 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6652 (mp10) REVERT: B 183 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.4115 (ppp) REVERT: B 195 GLU cc_start: 0.7230 (pp20) cc_final: 0.6884 (tm-30) REVERT: B 235 LYS cc_start: 0.7718 (mtmm) cc_final: 0.7374 (mtmm) REVERT: B 349 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7786 (ptmt) REVERT: B 416 ASP cc_start: 0.7699 (m-30) cc_final: 0.7342 (m-30) REVERT: B 699 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8806 (mp) REVERT: B 742 MET cc_start: 0.4510 (mpp) cc_final: 0.4074 (tpp) REVERT: B 850 MET cc_start: 0.5045 (OUTLIER) cc_final: 0.4542 (mpp) REVERT: C 195 GLU cc_start: 0.7313 (pp20) cc_final: 0.6977 (tm-30) REVERT: C 423 ARG cc_start: 0.7623 (ttp-110) cc_final: 0.7277 (mtm110) REVERT: C 742 MET cc_start: 0.3392 (tmt) cc_final: 0.2275 (mmm) outliers start: 72 outliers final: 36 residues processed: 244 average time/residue: 0.6203 time to fit residues: 168.4440 Evaluate side-chains 235 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 812 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 192 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 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 141 ASN A 248 HIS B 248 HIS B 458 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.189937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135952 restraints weight = 14158.573| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.03 r_work: 0.3285 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17505 Z= 0.176 Angle : 0.590 8.172 23754 Z= 0.323 Chirality : 0.043 0.173 2610 Planarity : 0.005 0.056 3081 Dihedral : 7.186 60.002 2558 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.08 % Allowed : 17.36 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.62 (0.18), residues: 2112 helix: 2.69 (0.19), residues: 732 sheet: 0.91 (0.22), residues: 543 loop : -0.27 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 661 TYR 0.012 0.001 TYR B 653 PHE 0.022 0.002 PHE C 287 TRP 0.017 0.002 TRP C 539 HIS 0.004 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00377 (17487) covalent geometry : angle 0.58533 (23712) SS BOND : bond 0.01041 ( 12) SS BOND : angle 2.03073 ( 24) hydrogen bonds : bond 0.05814 ( 883) hydrogen bonds : angle 4.79765 ( 2607) link_BETA1-4 : bond 0.00613 ( 3) link_BETA1-4 : angle 1.87437 ( 9) link_NAG-ASN : bond 0.00114 ( 3) link_NAG-ASN : angle 1.66942 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 187 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6785 (mp10) REVERT: A 195 GLU cc_start: 0.7166 (pp20) cc_final: 0.6710 (tm-30) REVERT: A 349 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7038 (ptmt) REVERT: A 360 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.5921 (mtp180) REVERT: A 502 GLU cc_start: 0.5048 (OUTLIER) cc_final: 0.4565 (mt-10) REVERT: A 531 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8887 (tt) REVERT: A 622 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7798 (tp30) REVERT: A 771 MET cc_start: 0.7735 (tpp) cc_final: 0.7381 (mtp) REVERT: B 181 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6602 (mp10) REVERT: B 183 MET cc_start: 0.6372 (OUTLIER) cc_final: 0.4040 (ppp) REVERT: B 195 GLU cc_start: 0.7131 (pp20) cc_final: 0.6745 (tm-30) REVERT: B 235 LYS cc_start: 0.7703 (mtmm) cc_final: 0.7360 (mtmm) REVERT: B 349 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7764 (ptmt) REVERT: B 465 VAL cc_start: 0.8040 (OUTLIER) cc_final: 0.7812 (t) REVERT: B 742 MET cc_start: 0.4614 (mpp) cc_final: 0.4138 (tpp) REVERT: C 195 GLU cc_start: 0.7183 (pp20) cc_final: 0.6872 (tm-30) REVERT: C 502 GLU cc_start: 0.4552 (OUTLIER) cc_final: 0.3578 (mt-10) REVERT: C 742 MET cc_start: 0.3403 (tmt) cc_final: 0.2306 (mmm) REVERT: C 771 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7389 (mtp) outliers start: 73 outliers final: 45 residues processed: 233 average time/residue: 0.6013 time to fit residues: 156.1209 Evaluate side-chains 240 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 183 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 771 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 209 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 49 optimal weight: 0.2980 chunk 155 optimal weight: 0.0030 chunk 1 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 248 HIS B 516 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.190616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3475 r_free = 0.3475 target = 0.132305 restraints weight = 14228.674| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.02 r_work: 0.3257 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17505 Z= 0.148 Angle : 0.554 7.723 23754 Z= 0.303 Chirality : 0.041 0.161 2610 Planarity : 0.004 0.056 3081 Dihedral : 7.035 57.924 2558 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.96 % Allowed : 17.64 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.63 (0.18), residues: 2112 helix: 2.71 (0.19), residues: 732 sheet: 0.92 (0.22), residues: 543 loop : -0.27 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 661 TYR 0.010 0.001 TYR B 849 PHE 0.020 0.002 PHE C 287 TRP 0.015 0.002 TRP A 539 HIS 0.003 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00308 (17487) covalent geometry : angle 0.54950 (23712) SS BOND : bond 0.00870 ( 12) SS BOND : angle 1.78623 ( 24) hydrogen bonds : bond 0.05494 ( 883) hydrogen bonds : angle 4.73878 ( 2607) link_BETA1-4 : bond 0.00568 ( 3) link_BETA1-4 : angle 1.83159 ( 9) link_NAG-ASN : bond 0.00168 ( 3) link_NAG-ASN : angle 1.60228 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 186 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: A 195 GLU cc_start: 0.7105 (pp20) cc_final: 0.6607 (tm-30) REVERT: A 241 THR cc_start: 0.7615 (p) cc_final: 0.7410 (p) REVERT: A 349 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7017 (ptmt) REVERT: A 360 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.5867 (mtp180) REVERT: A 502 GLU cc_start: 0.5031 (OUTLIER) cc_final: 0.4555 (mt-10) REVERT: A 531 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8816 (tt) REVERT: A 622 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7845 (tp30) REVERT: A 771 MET cc_start: 0.7557 (tpp) cc_final: 0.7213 (mtp) REVERT: B 181 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6623 (mp10) REVERT: B 183 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.4017 (ppp) REVERT: B 195 GLU cc_start: 0.7069 (pp20) cc_final: 0.6657 (tm-30) REVERT: B 235 LYS cc_start: 0.7692 (mtmm) cc_final: 0.7300 (mtmm) REVERT: B 349 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7742 (ptmt) REVERT: B 416 ASP cc_start: 0.7658 (m-30) cc_final: 0.7330 (m-30) REVERT: B 742 MET cc_start: 0.4679 (mpp) cc_final: 0.4180 (tpp) REVERT: C 195 GLU cc_start: 0.7133 (pp20) cc_final: 0.6775 (tm-30) REVERT: C 502 GLU cc_start: 0.4565 (OUTLIER) cc_final: 0.3641 (mt-10) REVERT: C 622 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7874 (tp30) REVERT: C 742 MET cc_start: 0.3433 (tmt) cc_final: 0.2331 (mmm) REVERT: C 771 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7208 (mtp) outliers start: 71 outliers final: 43 residues processed: 233 average time/residue: 0.5884 time to fit residues: 153.4985 Evaluate side-chains 238 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 771 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 248 HIS B 516 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.189955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135838 restraints weight = 14170.444| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.02 r_work: 0.3301 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17505 Z= 0.167 Angle : 0.581 8.053 23754 Z= 0.318 Chirality : 0.042 0.173 2610 Planarity : 0.004 0.056 3081 Dihedral : 7.112 59.158 2558 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.08 % Allowed : 17.64 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.59 (0.18), residues: 2112 helix: 2.66 (0.19), residues: 732 sheet: 0.90 (0.22), residues: 543 loop : -0.29 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 661 TYR 0.011 0.001 TYR B 653 PHE 0.022 0.002 PHE C 287 TRP 0.017 0.002 TRP A 539 HIS 0.004 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00355 (17487) covalent geometry : angle 0.57597 (23712) SS BOND : bond 0.00969 ( 12) SS BOND : angle 1.97159 ( 24) hydrogen bonds : bond 0.05717 ( 883) hydrogen bonds : angle 4.77930 ( 2607) link_BETA1-4 : bond 0.00615 ( 3) link_BETA1-4 : angle 1.88924 ( 9) link_NAG-ASN : bond 0.00132 ( 3) link_NAG-ASN : angle 1.65323 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 188 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6825 (mp10) REVERT: A 195 GLU cc_start: 0.7183 (pp20) cc_final: 0.6732 (tm-30) REVERT: A 349 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7042 (ptmt) REVERT: A 360 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.5917 (mtp180) REVERT: A 502 GLU cc_start: 0.5171 (OUTLIER) cc_final: 0.4763 (mt-10) REVERT: A 531 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8844 (tt) REVERT: A 622 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7785 (tp30) REVERT: A 771 MET cc_start: 0.7707 (tpp) cc_final: 0.7360 (mtp) REVERT: B 181 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6651 (mp10) REVERT: B 183 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.4123 (ppp) REVERT: B 195 GLU cc_start: 0.7151 (pp20) cc_final: 0.6769 (tm-30) REVERT: B 235 LYS cc_start: 0.7712 (mtmm) cc_final: 0.7369 (mtmm) REVERT: B 349 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7754 (ptmt) REVERT: B 505 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7352 (mtm-85) REVERT: B 850 MET cc_start: 0.5072 (OUTLIER) cc_final: 0.4569 (mpp) REVERT: C 195 GLU cc_start: 0.7205 (pp20) cc_final: 0.6897 (tm-30) REVERT: C 502 GLU cc_start: 0.4657 (OUTLIER) cc_final: 0.3777 (mt-10) REVERT: C 622 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7769 (tp30) REVERT: C 742 MET cc_start: 0.3476 (OUTLIER) cc_final: 0.2352 (mmm) REVERT: C 771 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7371 (mtp) outliers start: 73 outliers final: 44 residues processed: 235 average time/residue: 0.5875 time to fit residues: 154.6872 Evaluate side-chains 242 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 415 LYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 742 MET Chi-restraints excluded: chain C residue 771 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 165 optimal weight: 10.0000 chunk 49 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 199 optimal weight: 0.0040 chunk 83 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS A 516 HIS B 248 HIS B 516 HIS C 516 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.192062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138989 restraints weight = 14355.330| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.00 r_work: 0.3339 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 17505 Z= 0.118 Angle : 0.513 8.303 23754 Z= 0.279 Chirality : 0.039 0.142 2610 Planarity : 0.004 0.056 3081 Dihedral : 6.788 59.755 2558 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.63 % Allowed : 17.98 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.67 (0.18), residues: 2112 helix: 2.76 (0.19), residues: 732 sheet: 0.90 (0.22), residues: 546 loop : -0.23 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 691 TYR 0.010 0.001 TYR A 640 PHE 0.017 0.001 PHE B 287 TRP 0.014 0.001 TRP A 539 HIS 0.003 0.000 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00234 (17487) covalent geometry : angle 0.50854 (23712) SS BOND : bond 0.00612 ( 12) SS BOND : angle 1.71041 ( 24) hydrogen bonds : bond 0.04980 ( 883) hydrogen bonds : angle 4.64459 ( 2607) link_BETA1-4 : bond 0.00584 ( 3) link_BETA1-4 : angle 1.70831 ( 9) link_NAG-ASN : bond 0.00229 ( 3) link_NAG-ASN : angle 1.51828 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.7226 (pp20) cc_final: 0.6836 (tm-30) REVERT: A 349 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.6977 (ptmt) REVERT: A 360 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.5996 (mtp180) REVERT: A 502 GLU cc_start: 0.5263 (OUTLIER) cc_final: 0.4906 (mt-10) REVERT: A 531 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8868 (tt) REVERT: A 771 MET cc_start: 0.7535 (tpp) cc_final: 0.7184 (mtp) REVERT: B 181 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6664 (mp10) REVERT: B 183 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.4071 (ppp) REVERT: B 195 GLU cc_start: 0.7145 (pp20) cc_final: 0.6787 (tm-30) REVERT: B 235 LYS cc_start: 0.7669 (mtmm) cc_final: 0.7321 (mtmm) REVERT: B 349 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7698 (ptmt) REVERT: B 416 ASP cc_start: 0.7588 (m-30) cc_final: 0.7233 (m-30) REVERT: B 614 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8034 (mm-30) REVERT: B 742 MET cc_start: 0.4475 (mpp) cc_final: 0.4085 (tpp) REVERT: C 195 GLU cc_start: 0.7236 (pp20) cc_final: 0.6917 (tm-30) REVERT: C 423 ARG cc_start: 0.7572 (ttp-110) cc_final: 0.7225 (mtm110) REVERT: C 502 GLU cc_start: 0.4727 (OUTLIER) cc_final: 0.3931 (mm-30) REVERT: C 742 MET cc_start: 0.3462 (OUTLIER) cc_final: 0.2351 (mmm) outliers start: 65 outliers final: 40 residues processed: 229 average time/residue: 0.5943 time to fit residues: 152.0613 Evaluate side-chains 234 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 742 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 12 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 248 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.190120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135901 restraints weight = 14115.068| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.02 r_work: 0.3292 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17505 Z= 0.162 Angle : 0.577 8.978 23754 Z= 0.315 Chirality : 0.042 0.200 2610 Planarity : 0.004 0.056 3081 Dihedral : 6.718 57.691 2548 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.18 % Allowed : 18.54 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.57 (0.18), residues: 2112 helix: 2.67 (0.19), residues: 732 sheet: 0.73 (0.21), residues: 564 loop : -0.22 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 661 TYR 0.011 0.001 TYR A 702 PHE 0.021 0.002 PHE C 287 TRP 0.017 0.002 TRP A 539 HIS 0.004 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00345 (17487) covalent geometry : angle 0.57224 (23712) SS BOND : bond 0.00941 ( 12) SS BOND : angle 2.07819 ( 24) hydrogen bonds : bond 0.05607 ( 883) hydrogen bonds : angle 4.73320 ( 2607) link_BETA1-4 : bond 0.00589 ( 3) link_BETA1-4 : angle 1.82577 ( 9) link_NAG-ASN : bond 0.00121 ( 3) link_NAG-ASN : angle 1.62506 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.7236 (pp20) cc_final: 0.6795 (tm-30) REVERT: A 349 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7064 (ptmt) REVERT: A 360 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.5904 (mtp180) REVERT: A 502 GLU cc_start: 0.5340 (OUTLIER) cc_final: 0.4984 (mt-10) REVERT: A 531 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8859 (tt) REVERT: A 771 MET cc_start: 0.7664 (tpp) cc_final: 0.7315 (mtp) REVERT: A 850 MET cc_start: 0.5138 (mmt) cc_final: 0.4633 (mmm) REVERT: B 181 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6663 (mp10) REVERT: B 183 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.4129 (ppp) REVERT: B 195 GLU cc_start: 0.7180 (pp20) cc_final: 0.6818 (tm-30) REVERT: B 235 LYS cc_start: 0.7718 (mtmm) cc_final: 0.7374 (mtmm) REVERT: B 349 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7754 (ptmt) REVERT: B 614 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8057 (mm-30) REVERT: B 742 MET cc_start: 0.4530 (mpp) cc_final: 0.4135 (tpp) REVERT: B 850 MET cc_start: 0.5145 (OUTLIER) cc_final: 0.4586 (mpp) REVERT: C 195 GLU cc_start: 0.7238 (pp20) cc_final: 0.6919 (tm-30) REVERT: C 502 GLU cc_start: 0.4831 (OUTLIER) cc_final: 0.4052 (mm-30) REVERT: C 742 MET cc_start: 0.3488 (OUTLIER) cc_final: 0.2351 (mmm) outliers start: 57 outliers final: 42 residues processed: 221 average time/residue: 0.5859 time to fit residues: 145.1367 Evaluate side-chains 236 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 845 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 850 MET Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 415 LYS Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 742 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 248 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.191410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.137716 restraints weight = 14238.162| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.02 r_work: 0.3326 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17505 Z= 0.130 Angle : 0.533 8.616 23754 Z= 0.290 Chirality : 0.040 0.174 2610 Planarity : 0.004 0.056 3081 Dihedral : 6.551 57.188 2548 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.18 % Allowed : 18.54 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.62 (0.18), residues: 2112 helix: 2.71 (0.19), residues: 732 sheet: 0.76 (0.22), residues: 564 loop : -0.20 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 215 TYR 0.010 0.001 TYR B 849 PHE 0.018 0.001 PHE B 287 TRP 0.015 0.001 TRP A 539 HIS 0.003 0.000 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00266 (17487) covalent geometry : angle 0.52854 (23712) SS BOND : bond 0.00692 ( 12) SS BOND : angle 1.83429 ( 24) hydrogen bonds : bond 0.05175 ( 883) hydrogen bonds : angle 4.65759 ( 2607) link_BETA1-4 : bond 0.00579 ( 3) link_BETA1-4 : angle 1.74523 ( 9) link_NAG-ASN : bond 0.00199 ( 3) link_NAG-ASN : angle 1.53895 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10482.91 seconds wall clock time: 177 minutes 50.82 seconds (10670.82 seconds total)