Starting phenix.real_space_refine on Mon Aug 25 02:09:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gc2_29926/08_2025/8gc2_29926.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gc2_29926/08_2025/8gc2_29926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gc2_29926/08_2025/8gc2_29926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gc2_29926/08_2025/8gc2_29926.map" model { file = "/net/cci-nas-00/data/ceres_data/8gc2_29926/08_2025/8gc2_29926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gc2_29926/08_2025/8gc2_29926.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 121 5.16 5 C 15613 2.51 5 N 3980 2.21 5 O 4628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24342 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5916 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain breaks: 2 Chain: "B" Number of atoms: 5906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5906 Classifications: {'peptide': 744} Link IDs: {'PTRANS': 27, 'TRANS': 716} Chain breaks: 2 Chain: "C" Number of atoms: 5906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5906 Classifications: {'peptide': 744} Link IDs: {'PTRANS': 27, 'TRANS': 716} Chain breaks: 2 Chain: "D" Number of atoms: 6014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6014 Classifications: {'peptide': 760} Link IDs: {'PTRANS': 28, 'TRANS': 731} Chain breaks: 1 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" 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: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.73, per 1000 atoms: 0.24 Number of scatterers: 24342 At special positions: 0 Unit cell: (126.14, 149.46, 186.56, 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 121 16.00 O 4628 8.00 N 3980 7.00 C 15613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " MAN L 3 " - " MAN L 4 " ALPHA1-4 " NAG E 2 " - " MAN E 3 " " NAG G 2 " - " MAN G 3 " " NAG L 2 " - " MAN L 3 " ALPHA1-6 " MAN E 3 " - " MAN E 5 " " MAN G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 5 " " MAN L 3 " - " MAN L 5 " BETA1-3 " MAN G 3 " - " BMA G 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1001 " - " ASN A 412 " " NAG A1002 " - " ASN A 423 " " NAG B1001 " - " ASN B 412 " " NAG B1002 " - " ASN B 275 " " NAG C1001 " - " ASN C 412 " " NAG C1002 " - " ASN C 423 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " " NAG E 1 " - " ASN A 378 " " NAG F 1 " - " ASN A 430 " " NAG G 1 " - " ASN A 275 " " NAG H 1 " - " ASN B 378 " " NAG I 1 " - " ASN C 378 " " NAG J 1 " - " ASN C 430 " " NAG K 1 " - " ASN C 275 " " NAG L 1 " - " ASN D 378 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 989.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5594 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 31 sheets defined 47.4% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.625A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.511A pdb=" N ARG A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.201A pdb=" N ARG A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 removed outlier: 4.123A pdb=" N LEU A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 286 through 299 Processing helix chain 'A' and resid 317 through 335 removed outlier: 3.809A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.538A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 removed outlier: 3.916A pdb=" N LEU A 428 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.532A pdb=" N ASP A 457 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG A 458 " --> pdb=" O GLY A 455 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 459 " --> pdb=" O ASN A 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 454 through 459' Processing helix chain 'A' and resid 461 through 475 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.644A pdb=" N ARG A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 527 Processing helix chain 'A' and resid 560 through 584 Processing helix chain 'A' and resid 631 through 664 removed outlier: 3.573A pdb=" N GLU A 662 " --> pdb=" O PHE A 658 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 699 through 712 Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 739 through 749 removed outlier: 4.459A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 789 Processing helix chain 'A' and resid 789 through 799 Processing helix chain 'A' and resid 818 through 839 removed outlier: 4.181A pdb=" N ILE A 823 " --> pdb=" O ASN A 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.922A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.766A pdb=" N LYS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 removed outlier: 3.766A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 removed outlier: 4.588A pdb=" N LEU B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.511A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 335 removed outlier: 3.633A pdb=" N ALA B 321 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 424 through 429 removed outlier: 3.694A pdb=" N LEU B 428 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 429 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.628A pdb=" N ASP B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 508 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 551 through 556 Processing helix chain 'B' and resid 560 through 584 Processing helix chain 'B' and resid 631 through 665 Processing helix chain 'B' and resid 688 through 696 removed outlier: 3.668A pdb=" N THR B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 Processing helix chain 'B' and resid 712 through 717 removed outlier: 3.949A pdb=" N LEU B 717 " --> pdb=" O ARG B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.834A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 Processing helix chain 'B' and resid 772 through 789 removed outlier: 3.957A pdb=" N ASP B 776 " --> pdb=" O SER B 772 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 798 Processing helix chain 'B' and resid 823 through 836 Processing helix chain 'C' and resid 52 through 65 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 126 Processing helix chain 'C' and resid 152 through 167 Processing helix chain 'C' and resid 179 through 185 removed outlier: 4.282A pdb=" N ILE C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 removed outlier: 3.985A pdb=" N ARG C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 removed outlier: 4.293A pdb=" N LEU C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 246 Processing helix chain 'C' and resid 286 through 301 removed outlier: 3.734A pdb=" N ILE C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 removed outlier: 3.710A pdb=" N GLY C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.799A pdb=" N GLN C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.543A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 462 through 475 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.956A pdb=" N VAL C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 555 removed outlier: 3.597A pdb=" N SER C 554 " --> pdb=" O PRO C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 583 Processing helix chain 'C' and resid 631 through 664 removed outlier: 3.557A pdb=" N MET C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 677 Processing helix chain 'C' and resid 688 through 693 Processing helix chain 'C' and resid 699 through 712 Processing helix chain 'C' and resid 712 through 716 Processing helix chain 'C' and resid 721 through 731 Processing helix chain 'C' and resid 739 through 748 Processing helix chain 'C' and resid 773 through 789 removed outlier: 4.299A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 799 Processing helix chain 'C' and resid 822 through 838 removed outlier: 3.883A pdb=" N VAL C 826 " --> pdb=" O GLY C 822 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 838 " --> pdb=" O SER C 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 152 through 168 Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.891A pdb=" N ARG D 184 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 246 Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.714A pdb=" N GLY D 273 " --> pdb=" O ARG D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.829A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 310 removed outlier: 3.850A pdb=" N GLY D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.542A pdb=" N GLN D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 560 through 582 removed outlier: 3.724A pdb=" N TRP D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 663 removed outlier: 3.646A pdb=" N ARG D 663 " --> pdb=" O LEU D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 677 Processing helix chain 'D' and resid 688 through 696 removed outlier: 4.191A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 removed outlier: 3.705A pdb=" N ARG D 712 " --> pdb=" O PHE D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 739 through 747 Processing helix chain 'D' and resid 772 through 789 removed outlier: 4.306A pdb=" N ASP D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU D 783 " --> pdb=" O THR D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 798 Processing helix chain 'D' and resid 822 through 839 removed outlier: 3.543A pdb=" N VAL D 826 " --> pdb=" O GLY D 822 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 43 removed outlier: 3.637A pdb=" N GLN A 81 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 107 removed outlier: 6.586A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 203 removed outlier: 6.634A pdb=" N VAL A 172 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ILE A 227 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 279 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU A 389 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N THR A 404 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 Processing sheet with id=AA5, first strand: chain 'A' and resid 432 through 436 Processing sheet with id=AA6, first strand: chain 'A' and resid 513 through 518 removed outlier: 4.892A pdb=" N ALA A 515 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLY A 765 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU A 517 " --> pdb=" O GLY A 763 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLY A 763 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 683 removed outlier: 6.510A pdb=" N GLU A 681 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LEU A 736 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N TYR A 733 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG A 543 " --> pdb=" O TYR A 733 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A 737 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 38 removed outlier: 6.117A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 41 through 43 removed outlier: 6.295A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.222A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ARG B 384 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N SER B 148 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 203 removed outlier: 6.762A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N HIS B 225 " --> pdb=" O THR B 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.942A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 389 through 394 removed outlier: 6.900A pdb=" N LEU B 389 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR B 404 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 391 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 434 through 437 Processing sheet with id=AB6, first strand: chain 'B' and resid 681 through 683 removed outlier: 6.806A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LEU B 736 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N TYR B 733 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG B 543 " --> pdb=" O TYR B 733 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 76 through 80 removed outlier: 7.311A pdb=" N ARG C 37 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N PHE C 107 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY C 39 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N HIS C 129 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU C 149 " --> pdb=" O HIS C 129 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N GLN C 131 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG C 384 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TYR C 150 " --> pdb=" O ARG C 384 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 198 through 203 removed outlier: 6.093A pdb=" N VAL C 172 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR C 171 " --> pdb=" O HIS C 225 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE C 227 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.981A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 389 through 395 removed outlier: 7.068A pdb=" N LEU C 389 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N THR C 404 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 432 through 436 removed outlier: 7.123A pdb=" N LEU C 433 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ARG C 481 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 444 through 446 Processing sheet with id=AC4, first strand: chain 'C' and resid 528 through 532 removed outlier: 5.232A pdb=" N VAL C 766 " --> pdb=" O SER C 530 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 717 through 718 removed outlier: 7.027A pdb=" N ALA C 684 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N VAL C 685 " --> pdb=" O GLU C 738 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET C 737 " --> pdb=" O SER C 539 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER C 539 " --> pdb=" O MET C 737 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 79 through 83 removed outlier: 6.270A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY D 39 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 198 through 203 removed outlier: 3.531A pdb=" N LYS D 200 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N HIS D 225 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N PHE D 279 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE D 256 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER D 393 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LYS D 401 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 369 through 370 Processing sheet with id=AC9, first strand: chain 'D' and resid 477 through 482 removed outlier: 8.341A pdb=" N LEU D 512 " --> pdb=" O SER D 432 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE D 434 " --> pdb=" O LEU D 512 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 490 through 491 removed outlier: 3.817A pdb=" N ALA D 490 " --> pdb=" O ASN D 499 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AD3, first strand: chain 'D' and resid 681 through 683 removed outlier: 7.003A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N TYR D 733 " --> pdb=" O ARG D 543 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ARG D 543 " --> pdb=" O TYR D 733 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 681 through 683 removed outlier: 7.003A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N TYR D 733 " --> pdb=" O ARG D 543 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ARG D 543 " --> pdb=" O TYR D 733 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 3099 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: 5.02 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6814 1.34 - 1.46: 5638 1.46 - 1.58: 12192 1.58 - 1.70: 0 1.70 - 1.82: 217 Bond restraints: 24861 Sorted by residual: bond pdb=" C GLU D 267 " pdb=" N PRO D 268 " ideal model delta sigma weight residual 1.331 1.383 -0.052 7.90e-03 1.60e+04 4.31e+01 bond pdb=" N ASN B 378 " pdb=" CA ASN B 378 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.30e-02 5.92e+03 8.89e+00 bond pdb=" N ASN A 557 " pdb=" CA ASN A 557 " ideal model delta sigma weight residual 1.461 1.488 -0.027 9.20e-03 1.18e+04 8.57e+00 bond pdb=" N ASN A 549 " pdb=" CA ASN A 549 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.30e-02 5.92e+03 7.73e+00 bond pdb=" N VAL A 552 " pdb=" CA VAL A 552 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.27e-02 6.20e+03 7.28e+00 ... (remaining 24856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 32440 1.99 - 3.98: 1059 3.98 - 5.97: 118 5.97 - 7.96: 38 7.96 - 9.95: 9 Bond angle restraints: 33664 Sorted by residual: angle pdb=" N ILE B 281 " pdb=" CA ILE B 281 " pdb=" C ILE B 281 " ideal model delta sigma weight residual 113.71 107.73 5.98 9.50e-01 1.11e+00 3.96e+01 angle pdb=" C ALA A 657 " pdb=" N PHE A 658 " pdb=" CA PHE A 658 " ideal model delta sigma weight residual 122.06 113.86 8.20 1.86e+00 2.89e-01 1.95e+01 angle pdb=" N LEU A 556 " pdb=" CA LEU A 556 " pdb=" C LEU A 556 " ideal model delta sigma weight residual 113.28 107.97 5.31 1.22e+00 6.72e-01 1.89e+01 angle pdb=" C ILE A 581 " pdb=" N ALA A 582 " pdb=" CA ALA A 582 " ideal model delta sigma weight residual 122.11 115.13 6.98 1.64e+00 3.72e-01 1.81e+01 angle pdb=" C GLU D 440 " pdb=" N GLU D 441 " pdb=" CA GLU D 441 " ideal model delta sigma weight residual 121.80 131.66 -9.86 2.44e+00 1.68e-01 1.63e+01 ... (remaining 33659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.69: 14259 22.69 - 45.38: 951 45.38 - 68.07: 120 68.07 - 90.76: 50 90.76 - 113.45: 50 Dihedral angle restraints: 15430 sinusoidal: 6742 harmonic: 8688 Sorted by residual: dihedral pdb=" CA HIS C 111 " pdb=" C HIS C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CB CYS C 96 " pdb=" SG CYS C 96 " pdb=" SG CYS C 347 " pdb=" CB CYS C 347 " ideal model delta sinusoidal sigma weight residual 93.00 137.38 -44.38 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CA VAL D 45 " pdb=" C VAL D 45 " pdb=" N GLU D 46 " pdb=" CA GLU D 46 " ideal model delta harmonic sigma weight residual 180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 15427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.965: 3927 0.965 - 1.929: 0 1.929 - 2.894: 0 2.894 - 3.858: 0 3.858 - 4.823: 2 Chirality restraints: 3929 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 2.42 -4.82 2.00e-02 2.50e+03 5.81e+04 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 275 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 1.61 -4.01 2.00e-01 2.50e+01 4.02e+02 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.22e+02 ... (remaining 3926 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.360 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C7 NAG H 2 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.142 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.548 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.353 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG H 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.089 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.540 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1001 " 0.342 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG B1001 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B1001 " 0.083 2.00e-02 2.50e+03 pdb=" N2 NAG B1001 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG B1001 " 0.181 2.00e-02 2.50e+03 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 7940 2.84 - 3.35: 21693 3.35 - 3.87: 42127 3.87 - 4.38: 45367 4.38 - 4.90: 76613 Nonbonded interactions: 193740 Sorted by model distance: nonbonded pdb=" OE2 GLU D 738 " pdb=" OG1 THR D 740 " model vdw 2.321 3.040 nonbonded pdb=" O VAL B 327 " pdb=" OG SER B 331 " model vdw 2.327 3.040 nonbonded pdb=" OG SER C 670 " pdb=" OD1 ASP C 672 " model vdw 2.330 3.040 nonbonded pdb=" O VAL B 716 " pdb=" OH TYR B 733 " model vdw 2.331 3.040 nonbonded pdb=" O PHE A 59 " pdb=" OG1 THR A 63 " model vdw 2.332 3.040 ... (remaining 193735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 35 through 1002) selection = (chain 'B' and resid 35 through 1002) selection = (chain 'C' and resid 35 through 1002) selection = (chain 'D' and (resid 35 through 800 or resid 817 through 1002)) } ncs_group { reference = (chain 'E' and (resid 1 through 2 or resid 5)) selection = (chain 'G' and (resid 1 through 2 or resid 5)) selection = (chain 'H' and (resid 1 through 2 or resid 5)) selection = (chain 'I' and (resid 1 through 2 or resid 5)) selection = (chain 'K' and (resid 1 through 2 or resid 5)) selection = (chain 'L' and (resid 1 through 2 or resid 5)) } ncs_group { reference = chain 'F' selection = chain 'J' } 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 group one per residue 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: 6.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.840 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24908 Z= 0.245 Angle : 0.822 9.951 33800 Z= 0.446 Chirality : 0.113 4.823 3929 Planarity : 0.017 0.309 4184 Dihedral : 16.859 113.454 9821 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.15 % Allowed : 0.54 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.13), residues: 2971 helix: -1.47 (0.11), residues: 1306 sheet: -1.36 (0.26), residues: 417 loop : -1.61 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 358 TYR 0.023 0.002 TYR C 324 PHE 0.048 0.002 PHE A 658 TRP 0.019 0.002 TRP D 641 HIS 0.016 0.002 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00452 (24861) covalent geometry : angle 0.81079 (33664) SS BOND : bond 0.00176 ( 5) SS BOND : angle 1.07038 ( 10) hydrogen bonds : bond 0.15773 ( 1059) hydrogen bonds : angle 6.81158 ( 3099) link_ALPHA1-3 : bond 0.00164 ( 5) link_ALPHA1-3 : angle 0.86091 ( 15) link_ALPHA1-4 : bond 0.00144 ( 3) link_ALPHA1-4 : angle 2.36761 ( 9) link_ALPHA1-6 : bond 0.00303 ( 6) link_ALPHA1-6 : angle 1.05038 ( 18) link_BETA1-3 : bond 0.00025 ( 1) link_BETA1-3 : angle 0.65643 ( 3) link_BETA1-4 : bond 0.00177 ( 11) link_BETA1-4 : angle 1.60317 ( 33) link_NAG-ASN : bond 0.00754 ( 16) link_NAG-ASN : angle 3.39663 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 MET cc_start: 0.9148 (ttt) cc_final: 0.8935 (ttt) REVERT: B 247 MET cc_start: 0.9001 (mmt) cc_final: 0.8516 (mmt) REVERT: B 248 MET cc_start: 0.9406 (mmp) cc_final: 0.9155 (mmm) REVERT: B 770 MET cc_start: 0.9365 (pmm) cc_final: 0.8929 (mpp) REVERT: B 793 MET cc_start: 0.9287 (ppp) cc_final: 0.9074 (ppp) REVERT: C 247 MET cc_start: 0.9175 (tpp) cc_final: 0.8565 (tpp) REVERT: C 323 MET cc_start: 0.9193 (tpp) cc_final: 0.8981 (tpp) REVERT: C 413 MET cc_start: 0.8210 (tpp) cc_final: 0.7741 (tmm) REVERT: C 501 MET cc_start: 0.8747 (mmp) cc_final: 0.8509 (mmt) REVERT: C 793 MET cc_start: 0.9580 (tmm) cc_final: 0.9371 (tmm) REVERT: C 794 MET cc_start: 0.9120 (ppp) cc_final: 0.8529 (ppp) REVERT: D 534 MET cc_start: 0.7767 (mpp) cc_final: 0.7535 (ptp) outliers start: 4 outliers final: 2 residues processed: 104 average time/residue: 0.1344 time to fit residues: 23.5907 Evaluate side-chains 98 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.0870 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN A 137 GLN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN A 549 ASN B 81 GLN B 165 GLN B 677 GLN B 792 HIS C 67 ASN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN C 335 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.032120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.023158 restraints weight = 326271.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.023742 restraints weight = 190515.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.024132 restraints weight = 132281.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.024366 restraints weight = 103273.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.024575 restraints weight = 87665.493| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24908 Z= 0.196 Angle : 0.666 12.882 33800 Z= 0.319 Chirality : 0.044 0.585 3929 Planarity : 0.004 0.069 4184 Dihedral : 12.822 121.821 4173 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.15), residues: 2971 helix: 0.35 (0.13), residues: 1337 sheet: -1.42 (0.25), residues: 431 loop : -1.20 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 583 TYR 0.012 0.001 TYR D 462 PHE 0.019 0.001 PHE B 643 TRP 0.020 0.001 TRP A 296 HIS 0.008 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00396 (24861) covalent geometry : angle 0.63802 (33664) SS BOND : bond 0.00133 ( 5) SS BOND : angle 1.06963 ( 10) hydrogen bonds : bond 0.03927 ( 1059) hydrogen bonds : angle 4.95706 ( 3099) link_ALPHA1-3 : bond 0.01127 ( 5) link_ALPHA1-3 : angle 2.36153 ( 15) link_ALPHA1-4 : bond 0.00303 ( 3) link_ALPHA1-4 : angle 3.03205 ( 9) link_ALPHA1-6 : bond 0.00800 ( 6) link_ALPHA1-6 : angle 1.74460 ( 18) link_BETA1-3 : bond 0.01522 ( 1) link_BETA1-3 : angle 3.53159 ( 3) link_BETA1-4 : bond 0.00954 ( 11) link_BETA1-4 : angle 2.52098 ( 33) link_NAG-ASN : bond 0.00739 ( 16) link_NAG-ASN : angle 4.13940 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8701 (mpp) cc_final: 0.8440 (mpp) REVERT: A 534 MET cc_start: 0.8548 (ppp) cc_final: 0.8021 (ppp) REVERT: B 247 MET cc_start: 0.9212 (mmt) cc_final: 0.8499 (mmt) REVERT: B 770 MET cc_start: 0.9373 (pmm) cc_final: 0.8995 (mpp) REVERT: C 234 MET cc_start: 0.9090 (mmp) cc_final: 0.8848 (mmm) REVERT: C 413 MET cc_start: 0.8127 (tpp) cc_final: 0.7621 (tmm) REVERT: C 501 MET cc_start: 0.8834 (mmp) cc_final: 0.8629 (mmt) REVERT: C 794 MET cc_start: 0.8957 (ppp) cc_final: 0.8385 (ppp) REVERT: D 247 MET cc_start: 0.9050 (mmp) cc_final: 0.8710 (mmt) REVERT: D 534 MET cc_start: 0.7846 (mpp) cc_final: 0.7341 (ptp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1326 time to fit residues: 22.3503 Evaluate side-chains 96 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 257 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 297 optimal weight: 9.9990 chunk 274 optimal weight: 5.9990 chunk 211 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 114 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 263 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS C 367 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.031772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.022896 restraints weight = 328126.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.023458 restraints weight = 192021.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.023852 restraints weight = 133825.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.024127 restraints weight = 104052.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.024261 restraints weight = 87091.295| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24908 Z= 0.236 Angle : 0.660 9.826 33800 Z= 0.323 Chirality : 0.043 0.486 3929 Planarity : 0.004 0.064 4184 Dihedral : 11.311 118.549 4173 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.16), residues: 2971 helix: 1.05 (0.14), residues: 1340 sheet: -1.48 (0.28), residues: 374 loop : -1.15 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 184 TYR 0.014 0.001 TYR B 462 PHE 0.019 0.002 PHE C 256 TRP 0.020 0.001 TRP D 641 HIS 0.010 0.002 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00484 (24861) covalent geometry : angle 0.64035 (33664) SS BOND : bond 0.00664 ( 5) SS BOND : angle 1.17675 ( 10) hydrogen bonds : bond 0.03704 ( 1059) hydrogen bonds : angle 4.80468 ( 3099) link_ALPHA1-3 : bond 0.00949 ( 5) link_ALPHA1-3 : angle 1.93039 ( 15) link_ALPHA1-4 : bond 0.00769 ( 3) link_ALPHA1-4 : angle 3.30638 ( 9) link_ALPHA1-6 : bond 0.00695 ( 6) link_ALPHA1-6 : angle 1.77788 ( 18) link_BETA1-3 : bond 0.01042 ( 1) link_BETA1-3 : angle 2.20304 ( 3) link_BETA1-4 : bond 0.00603 ( 11) link_BETA1-4 : angle 1.97662 ( 33) link_NAG-ASN : bond 0.00594 ( 16) link_NAG-ASN : angle 3.37593 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8862 (mpp) cc_final: 0.8466 (mpp) REVERT: A 360 MET cc_start: 0.9494 (tpt) cc_final: 0.9072 (tpt) REVERT: A 794 MET cc_start: 0.9138 (ttt) cc_final: 0.8873 (ttt) REVERT: B 247 MET cc_start: 0.9245 (mmt) cc_final: 0.8364 (mmt) REVERT: B 770 MET cc_start: 0.9336 (pmm) cc_final: 0.8989 (mpp) REVERT: C 247 MET cc_start: 0.8856 (tpp) cc_final: 0.8465 (tpp) REVERT: C 794 MET cc_start: 0.8890 (ppp) cc_final: 0.8354 (ppp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1286 time to fit residues: 20.9673 Evaluate side-chains 96 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 91 optimal weight: 0.0980 chunk 279 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 236 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 129 HIS B 131 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.032340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.023388 restraints weight = 322309.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.023974 restraints weight = 187025.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.024370 restraints weight = 129600.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.024617 restraints weight = 100634.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.024818 restraints weight = 85214.695| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24908 Z= 0.104 Angle : 0.560 10.687 33800 Z= 0.268 Chirality : 0.042 0.488 3929 Planarity : 0.003 0.062 4184 Dihedral : 10.455 117.463 4173 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.16), residues: 2971 helix: 1.33 (0.14), residues: 1339 sheet: -1.34 (0.27), residues: 404 loop : -1.01 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 384 TYR 0.020 0.001 TYR A 254 PHE 0.026 0.001 PHE B 735 TRP 0.017 0.001 TRP D 641 HIS 0.012 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00221 (24861) covalent geometry : angle 0.53696 (33664) SS BOND : bond 0.00210 ( 5) SS BOND : angle 1.43285 ( 10) hydrogen bonds : bond 0.03188 ( 1059) hydrogen bonds : angle 4.50422 ( 3099) link_ALPHA1-3 : bond 0.01082 ( 5) link_ALPHA1-3 : angle 1.90331 ( 15) link_ALPHA1-4 : bond 0.00849 ( 3) link_ALPHA1-4 : angle 3.15695 ( 9) link_ALPHA1-6 : bond 0.00712 ( 6) link_ALPHA1-6 : angle 1.59796 ( 18) link_BETA1-3 : bond 0.01083 ( 1) link_BETA1-3 : angle 2.87216 ( 3) link_BETA1-4 : bond 0.00487 ( 11) link_BETA1-4 : angle 1.83551 ( 33) link_NAG-ASN : bond 0.00456 ( 16) link_NAG-ASN : angle 3.36770 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 CYS cc_start: 0.9200 (m) cc_final: 0.8952 (p) REVERT: A 534 MET cc_start: 0.8368 (ppp) cc_final: 0.7976 (ppp) REVERT: A 565 MET cc_start: 0.8874 (mpp) cc_final: 0.8643 (ptp) REVERT: A 794 MET cc_start: 0.9079 (ttt) cc_final: 0.8832 (ttt) REVERT: B 247 MET cc_start: 0.9187 (mmt) cc_final: 0.8385 (mmt) REVERT: B 770 MET cc_start: 0.9323 (pmm) cc_final: 0.8978 (mpp) REVERT: B 793 MET cc_start: 0.9309 (ppp) cc_final: 0.9096 (ppp) REVERT: C 234 MET cc_start: 0.9133 (mmp) cc_final: 0.8858 (mmm) REVERT: C 247 MET cc_start: 0.8653 (tpp) cc_final: 0.8039 (tpp) REVERT: C 794 MET cc_start: 0.8857 (ppp) cc_final: 0.8444 (ppp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1279 time to fit residues: 21.6352 Evaluate side-chains 97 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 111 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 158 optimal weight: 0.7980 chunk 223 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 267 optimal weight: 40.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN C 328 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.032241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.023229 restraints weight = 326302.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.023806 restraints weight = 190963.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.024200 restraints weight = 133142.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.024437 restraints weight = 103415.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.024643 restraints weight = 87725.774| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24908 Z= 0.154 Angle : 0.578 10.030 33800 Z= 0.279 Chirality : 0.042 0.488 3929 Planarity : 0.003 0.060 4184 Dihedral : 9.783 114.437 4173 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.16), residues: 2971 helix: 1.52 (0.14), residues: 1342 sheet: -1.31 (0.27), residues: 408 loop : -1.02 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 384 TYR 0.012 0.001 TYR C 488 PHE 0.017 0.001 PHE A 643 TRP 0.037 0.001 TRP D 169 HIS 0.017 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00323 (24861) covalent geometry : angle 0.55726 (33664) SS BOND : bond 0.00107 ( 5) SS BOND : angle 1.09182 ( 10) hydrogen bonds : bond 0.03158 ( 1059) hydrogen bonds : angle 4.47365 ( 3099) link_ALPHA1-3 : bond 0.01078 ( 5) link_ALPHA1-3 : angle 1.95957 ( 15) link_ALPHA1-4 : bond 0.00870 ( 3) link_ALPHA1-4 : angle 3.24743 ( 9) link_ALPHA1-6 : bond 0.00604 ( 6) link_ALPHA1-6 : angle 1.71585 ( 18) link_BETA1-3 : bond 0.01141 ( 1) link_BETA1-3 : angle 2.86022 ( 3) link_BETA1-4 : bond 0.00576 ( 11) link_BETA1-4 : angle 1.88086 ( 33) link_NAG-ASN : bond 0.00397 ( 16) link_NAG-ASN : angle 3.17770 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 CYS cc_start: 0.9176 (m) cc_final: 0.8940 (p) REVERT: A 794 MET cc_start: 0.9019 (ttt) cc_final: 0.8750 (ttt) REVERT: B 50 MET cc_start: 0.9013 (ptm) cc_final: 0.8635 (tmm) REVERT: B 247 MET cc_start: 0.9235 (mmt) cc_final: 0.8335 (mmt) REVERT: B 770 MET cc_start: 0.9327 (pmm) cc_final: 0.9072 (mpp) REVERT: B 793 MET cc_start: 0.9279 (ppp) cc_final: 0.9052 (ppp) REVERT: C 234 MET cc_start: 0.9211 (mmp) cc_final: 0.8939 (mmm) REVERT: C 247 MET cc_start: 0.8700 (tpp) cc_final: 0.8118 (tpp) REVERT: C 794 MET cc_start: 0.8893 (ppp) cc_final: 0.8511 (ppp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1351 time to fit residues: 22.7752 Evaluate side-chains 97 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 119 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 chunk 208 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 218 optimal weight: 0.9980 chunk 247 optimal weight: 0.0370 chunk 77 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 721 ASN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.032587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.023562 restraints weight = 325879.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.024152 restraints weight = 189124.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.024549 restraints weight = 130736.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.024839 restraints weight = 101838.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.024993 restraints weight = 84800.132| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24908 Z= 0.101 Angle : 0.558 10.785 33800 Z= 0.266 Chirality : 0.042 0.439 3929 Planarity : 0.003 0.060 4184 Dihedral : 9.138 114.254 4173 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.16), residues: 2971 helix: 1.70 (0.14), residues: 1325 sheet: -1.30 (0.28), residues: 398 loop : -0.93 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.019 0.001 TYR D 324 PHE 0.023 0.001 PHE B 643 TRP 0.035 0.001 TRP D 169 HIS 0.013 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00214 (24861) covalent geometry : angle 0.53389 (33664) SS BOND : bond 0.00099 ( 5) SS BOND : angle 1.06349 ( 10) hydrogen bonds : bond 0.02953 ( 1059) hydrogen bonds : angle 4.30075 ( 3099) link_ALPHA1-3 : bond 0.01286 ( 5) link_ALPHA1-3 : angle 2.04832 ( 15) link_ALPHA1-4 : bond 0.00931 ( 3) link_ALPHA1-4 : angle 3.20305 ( 9) link_ALPHA1-6 : bond 0.00611 ( 6) link_ALPHA1-6 : angle 1.85644 ( 18) link_BETA1-3 : bond 0.01474 ( 1) link_BETA1-3 : angle 3.40477 ( 3) link_BETA1-4 : bond 0.00533 ( 11) link_BETA1-4 : angle 1.80092 ( 33) link_NAG-ASN : bond 0.00591 ( 16) link_NAG-ASN : angle 3.42246 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.9399 (tpt) cc_final: 0.9105 (tpt) REVERT: A 463 CYS cc_start: 0.9193 (m) cc_final: 0.8966 (p) REVERT: A 534 MET cc_start: 0.8383 (ppp) cc_final: 0.8161 (ppp) REVERT: A 794 MET cc_start: 0.8976 (ttt) cc_final: 0.8697 (ttt) REVERT: B 50 MET cc_start: 0.9014 (ptm) cc_final: 0.8672 (tmm) REVERT: B 247 MET cc_start: 0.9166 (mmt) cc_final: 0.8333 (mmt) REVERT: B 793 MET cc_start: 0.9300 (ppp) cc_final: 0.9099 (ppp) REVERT: B 794 MET cc_start: 0.7943 (tmm) cc_final: 0.7384 (ppp) REVERT: C 234 MET cc_start: 0.9158 (mmp) cc_final: 0.8914 (mmm) REVERT: C 247 MET cc_start: 0.8593 (tpp) cc_final: 0.8065 (tpp) REVERT: C 276 MET cc_start: 0.8825 (mmm) cc_final: 0.8624 (mmm) REVERT: C 664 MET cc_start: 0.9283 (mmt) cc_final: 0.8726 (ptp) REVERT: C 794 MET cc_start: 0.8856 (ppp) cc_final: 0.8494 (ppp) REVERT: D 247 MET cc_start: 0.8962 (mmp) cc_final: 0.8544 (mmt) REVERT: D 276 MET cc_start: 0.9069 (mmp) cc_final: 0.8861 (mmp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1337 time to fit residues: 22.5535 Evaluate side-chains 97 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 259 optimal weight: 2.9990 chunk 294 optimal weight: 8.9990 chunk 237 optimal weight: 0.0570 chunk 84 optimal weight: 2.9990 chunk 268 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 chunk 297 optimal weight: 20.0000 chunk 239 optimal weight: 0.9980 chunk 181 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 280 optimal weight: 10.0000 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.032428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.023426 restraints weight = 325126.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.024003 restraints weight = 190004.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.024408 restraints weight = 132056.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.024636 restraints weight = 102393.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.024846 restraints weight = 87110.675| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24908 Z= 0.129 Angle : 0.562 10.901 33800 Z= 0.269 Chirality : 0.042 0.446 3929 Planarity : 0.003 0.058 4184 Dihedral : 8.793 113.592 4173 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.16), residues: 2971 helix: 1.80 (0.14), residues: 1332 sheet: -1.26 (0.28), residues: 377 loop : -1.00 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 543 TYR 0.020 0.001 TYR D 324 PHE 0.024 0.001 PHE B 643 TRP 0.029 0.001 TRP D 564 HIS 0.010 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00276 (24861) covalent geometry : angle 0.53740 (33664) SS BOND : bond 0.00195 ( 5) SS BOND : angle 1.04413 ( 10) hydrogen bonds : bond 0.02945 ( 1059) hydrogen bonds : angle 4.27054 ( 3099) link_ALPHA1-3 : bond 0.01087 ( 5) link_ALPHA1-3 : angle 2.03788 ( 15) link_ALPHA1-4 : bond 0.00932 ( 3) link_ALPHA1-4 : angle 3.23015 ( 9) link_ALPHA1-6 : bond 0.00565 ( 6) link_ALPHA1-6 : angle 1.89584 ( 18) link_BETA1-3 : bond 0.01230 ( 1) link_BETA1-3 : angle 3.44464 ( 3) link_BETA1-4 : bond 0.00526 ( 11) link_BETA1-4 : angle 1.79749 ( 33) link_NAG-ASN : bond 0.00499 ( 16) link_NAG-ASN : angle 3.43278 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.9430 (tpt) cc_final: 0.9109 (tpt) REVERT: A 413 MET cc_start: 0.8806 (tpp) cc_final: 0.8485 (tmm) REVERT: A 463 CYS cc_start: 0.9199 (m) cc_final: 0.8962 (p) REVERT: A 534 MET cc_start: 0.8473 (ppp) cc_final: 0.7961 (ppp) REVERT: A 794 MET cc_start: 0.8971 (ttt) cc_final: 0.8687 (ttt) REVERT: B 50 MET cc_start: 0.9051 (ptm) cc_final: 0.8674 (tmm) REVERT: B 247 MET cc_start: 0.9161 (mmt) cc_final: 0.8376 (mmt) REVERT: B 793 MET cc_start: 0.9276 (ppp) cc_final: 0.9052 (ppp) REVERT: B 794 MET cc_start: 0.7948 (tmm) cc_final: 0.7745 (tmm) REVERT: C 234 MET cc_start: 0.9165 (mmp) cc_final: 0.8925 (mmm) REVERT: C 247 MET cc_start: 0.8627 (tpp) cc_final: 0.8108 (tpp) REVERT: C 664 MET cc_start: 0.9293 (mmt) cc_final: 0.9069 (mmm) REVERT: C 794 MET cc_start: 0.8847 (ppp) cc_final: 0.8500 (ppp) REVERT: D 247 MET cc_start: 0.9002 (mmp) cc_final: 0.8499 (mmt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1315 time to fit residues: 22.4126 Evaluate side-chains 97 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 280 optimal weight: 9.9990 chunk 247 optimal weight: 0.9990 chunk 275 optimal weight: 8.9990 chunk 271 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 252 optimal weight: 0.0370 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.032393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.023371 restraints weight = 324548.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.023953 restraints weight = 189160.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.024342 restraints weight = 131979.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.024615 restraints weight = 102780.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.024768 restraints weight = 86250.872| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24908 Z= 0.134 Angle : 0.573 10.948 33800 Z= 0.273 Chirality : 0.042 0.445 3929 Planarity : 0.003 0.057 4184 Dihedral : 8.528 114.149 4173 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.16), residues: 2971 helix: 1.85 (0.14), residues: 1336 sheet: -1.24 (0.28), residues: 377 loop : -0.99 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.017 0.001 TYR D 324 PHE 0.026 0.001 PHE B 643 TRP 0.023 0.001 TRP D 564 HIS 0.020 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00285 (24861) covalent geometry : angle 0.54448 (33664) SS BOND : bond 0.00187 ( 5) SS BOND : angle 0.97579 ( 10) hydrogen bonds : bond 0.02927 ( 1059) hydrogen bonds : angle 4.25114 ( 3099) link_ALPHA1-3 : bond 0.01060 ( 5) link_ALPHA1-3 : angle 2.07615 ( 15) link_ALPHA1-4 : bond 0.00925 ( 3) link_ALPHA1-4 : angle 3.21299 ( 9) link_ALPHA1-6 : bond 0.00552 ( 6) link_ALPHA1-6 : angle 1.91838 ( 18) link_BETA1-3 : bond 0.01173 ( 1) link_BETA1-3 : angle 3.50280 ( 3) link_BETA1-4 : bond 0.00480 ( 11) link_BETA1-4 : angle 1.79667 ( 33) link_NAG-ASN : bond 0.00525 ( 16) link_NAG-ASN : angle 3.90638 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.9416 (tpt) cc_final: 0.9138 (tpt) REVERT: A 534 MET cc_start: 0.8441 (ppp) cc_final: 0.7853 (ppp) REVERT: A 737 MET cc_start: 0.8263 (ptp) cc_final: 0.7874 (ptp) REVERT: A 794 MET cc_start: 0.9000 (ttt) cc_final: 0.8723 (ttt) REVERT: B 247 MET cc_start: 0.9197 (mmt) cc_final: 0.8314 (mmt) REVERT: B 793 MET cc_start: 0.9259 (ppp) cc_final: 0.9044 (ppp) REVERT: C 234 MET cc_start: 0.9156 (mmp) cc_final: 0.8886 (mmm) REVERT: C 247 MET cc_start: 0.8623 (tpp) cc_final: 0.8074 (tpp) REVERT: C 664 MET cc_start: 0.9315 (mmt) cc_final: 0.9068 (mmm) REVERT: C 794 MET cc_start: 0.8851 (ppp) cc_final: 0.8486 (ppp) REVERT: D 247 MET cc_start: 0.8982 (mmp) cc_final: 0.8480 (mmt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1159 time to fit residues: 19.5732 Evaluate side-chains 96 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 181 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 273 optimal weight: 0.0170 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.032430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.023412 restraints weight = 326403.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.024016 restraints weight = 190677.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.024401 restraints weight = 131069.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.024636 restraints weight = 101852.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.024846 restraints weight = 86531.663| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24908 Z= 0.116 Angle : 0.556 10.919 33800 Z= 0.264 Chirality : 0.041 0.437 3929 Planarity : 0.003 0.057 4184 Dihedral : 8.279 114.626 4173 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.16), residues: 2971 helix: 1.89 (0.14), residues: 1340 sheet: -1.22 (0.28), residues: 377 loop : -0.96 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 349 TYR 0.016 0.001 TYR D 324 PHE 0.028 0.001 PHE B 643 TRP 0.018 0.001 TRP D 564 HIS 0.015 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00249 (24861) covalent geometry : angle 0.52843 (33664) SS BOND : bond 0.00171 ( 5) SS BOND : angle 0.93269 ( 10) hydrogen bonds : bond 0.02850 ( 1059) hydrogen bonds : angle 4.19153 ( 3099) link_ALPHA1-3 : bond 0.01065 ( 5) link_ALPHA1-3 : angle 1.98464 ( 15) link_ALPHA1-4 : bond 0.00958 ( 3) link_ALPHA1-4 : angle 3.17499 ( 9) link_ALPHA1-6 : bond 0.00568 ( 6) link_ALPHA1-6 : angle 1.90767 ( 18) link_BETA1-3 : bond 0.01118 ( 1) link_BETA1-3 : angle 3.50436 ( 3) link_BETA1-4 : bond 0.00494 ( 11) link_BETA1-4 : angle 1.76932 ( 33) link_NAG-ASN : bond 0.00540 ( 16) link_NAG-ASN : angle 3.78492 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.9408 (tpt) cc_final: 0.9157 (tpt) REVERT: A 534 MET cc_start: 0.8428 (ppp) cc_final: 0.7808 (ppp) REVERT: A 794 MET cc_start: 0.8981 (ttt) cc_final: 0.8708 (ttt) REVERT: B 50 MET cc_start: 0.9090 (ptm) cc_final: 0.8692 (tmm) REVERT: B 247 MET cc_start: 0.9166 (mmt) cc_final: 0.8332 (mmt) REVERT: B 793 MET cc_start: 0.9291 (ppp) cc_final: 0.9080 (ppp) REVERT: C 234 MET cc_start: 0.9177 (mmp) cc_final: 0.8919 (mmm) REVERT: C 664 MET cc_start: 0.9281 (mmt) cc_final: 0.9018 (mmm) REVERT: C 794 MET cc_start: 0.8821 (ppp) cc_final: 0.8464 (ppp) REVERT: D 247 MET cc_start: 0.8979 (mmp) cc_final: 0.8428 (mmt) REVERT: D 565 MET cc_start: 0.8518 (mpp) cc_final: 0.8211 (mpp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1208 time to fit residues: 20.2560 Evaluate side-chains 96 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 230 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 175 optimal weight: 0.0570 chunk 258 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 208 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.032613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.023607 restraints weight = 323893.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.024193 restraints weight = 188863.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.024586 restraints weight = 130992.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.024824 restraints weight = 102022.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.025039 restraints weight = 86592.546| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24908 Z= 0.095 Angle : 0.552 11.025 33800 Z= 0.261 Chirality : 0.041 0.425 3929 Planarity : 0.003 0.058 4184 Dihedral : 7.948 113.949 4173 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.16), residues: 2971 helix: 1.94 (0.14), residues: 1340 sheet: -1.18 (0.28), residues: 377 loop : -0.92 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 543 TYR 0.020 0.001 TYR D 324 PHE 0.029 0.001 PHE B 643 TRP 0.016 0.001 TRP D 564 HIS 0.014 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00204 (24861) covalent geometry : angle 0.52549 (33664) SS BOND : bond 0.00166 ( 5) SS BOND : angle 0.87347 ( 10) hydrogen bonds : bond 0.02740 ( 1059) hydrogen bonds : angle 4.10831 ( 3099) link_ALPHA1-3 : bond 0.01068 ( 5) link_ALPHA1-3 : angle 1.92491 ( 15) link_ALPHA1-4 : bond 0.01012 ( 3) link_ALPHA1-4 : angle 3.14814 ( 9) link_ALPHA1-6 : bond 0.00573 ( 6) link_ALPHA1-6 : angle 1.79101 ( 18) link_BETA1-3 : bond 0.01051 ( 1) link_BETA1-3 : angle 3.49472 ( 3) link_BETA1-4 : bond 0.00507 ( 11) link_BETA1-4 : angle 1.77684 ( 33) link_NAG-ASN : bond 0.00563 ( 16) link_NAG-ASN : angle 3.71062 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 534 MET cc_start: 0.8482 (ppp) cc_final: 0.7955 (ppp) REVERT: A 691 MET cc_start: 0.9450 (ptp) cc_final: 0.9215 (pmm) REVERT: A 794 MET cc_start: 0.8960 (ttt) cc_final: 0.8691 (ttt) REVERT: B 50 MET cc_start: 0.9057 (ptm) cc_final: 0.8633 (tmm) REVERT: B 247 MET cc_start: 0.9193 (mmt) cc_final: 0.8434 (mmt) REVERT: C 50 MET cc_start: 0.8631 (ppp) cc_final: 0.7895 (ppp) REVERT: C 234 MET cc_start: 0.9157 (mmp) cc_final: 0.8874 (mmm) REVERT: C 664 MET cc_start: 0.9281 (mmt) cc_final: 0.8984 (mmm) REVERT: C 770 MET cc_start: 0.8592 (mmm) cc_final: 0.8205 (mpp) REVERT: C 794 MET cc_start: 0.8811 (ppp) cc_final: 0.8473 (ppp) REVERT: D 247 MET cc_start: 0.8976 (mmp) cc_final: 0.8407 (mmt) REVERT: D 565 MET cc_start: 0.8489 (mpp) cc_final: 0.8182 (mpp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1117 time to fit residues: 18.8582 Evaluate side-chains 96 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 47 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 293 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 270 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 245 optimal weight: 0.4980 chunk 200 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.032501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.023498 restraints weight = 326105.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.024091 restraints weight = 190517.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.024475 restraints weight = 131967.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.024748 restraints weight = 102728.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.024899 restraints weight = 86440.740| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24908 Z= 0.110 Angle : 0.546 10.958 33800 Z= 0.259 Chirality : 0.041 0.434 3929 Planarity : 0.003 0.055 4184 Dihedral : 7.659 113.197 4173 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.16), residues: 2971 helix: 2.02 (0.14), residues: 1340 sheet: -1.13 (0.29), residues: 377 loop : -0.92 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 543 TYR 0.014 0.001 TYR D 324 PHE 0.019 0.001 PHE C 735 TRP 0.016 0.001 TRP D 564 HIS 0.015 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00236 (24861) covalent geometry : angle 0.51992 (33664) SS BOND : bond 0.00163 ( 5) SS BOND : angle 0.88398 ( 10) hydrogen bonds : bond 0.02745 ( 1059) hydrogen bonds : angle 4.08929 ( 3099) link_ALPHA1-3 : bond 0.01028 ( 5) link_ALPHA1-3 : angle 1.96199 ( 15) link_ALPHA1-4 : bond 0.00996 ( 3) link_ALPHA1-4 : angle 3.15252 ( 9) link_ALPHA1-6 : bond 0.00487 ( 6) link_ALPHA1-6 : angle 1.71748 ( 18) link_BETA1-3 : bond 0.00890 ( 1) link_BETA1-3 : angle 3.26189 ( 3) link_BETA1-4 : bond 0.00493 ( 11) link_BETA1-4 : angle 1.81546 ( 33) link_NAG-ASN : bond 0.00530 ( 16) link_NAG-ASN : angle 3.66493 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3097.69 seconds wall clock time: 54 minutes 51.60 seconds (3291.60 seconds total)