Starting phenix.real_space_refine on Fri May 23 18:56:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gc2_29926/05_2025/8gc2_29926.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gc2_29926/05_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_29926/05_2025/8gc2_29926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gc2_29926/05_2025/8gc2_29926.map" model { file = "/net/cci-nas-00/data/ceres_data/8gc2_29926/05_2025/8gc2_29926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gc2_29926/05_2025/8gc2_29926.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.06, per 1000 atoms: 0.62 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: 6.21 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 3.33 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: 11.16 Time building geometry restraints manager: 7.09 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 839 or resid 1001 through 1002)) selection = (chain 'B' and (resid 35 through 839 or resid 1001 through 1002)) selection = (chain 'C' and (resid 35 through 839 or resid 1001 through 1002)) selection = (chain 'D' and (resid 35 through 800 or resid 817 through 839 or resid 1001 thro \ ugh 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: 6.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.850 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 57.660 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.010 ------------------------------------------------------------------------------- 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 : 5.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.002 TRP D 641 HIS 0.016 0.002 HIS C 328 PHE 0.048 0.002 PHE A 658 TYR 0.023 0.002 TYR C 324 ARG 0.007 0.000 ARG C 358 Details of bonding type rmsd link_NAG-ASN : bond 0.00754 ( 16) link_NAG-ASN : angle 3.39663 ( 48) 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_BETA1-4 : bond 0.00177 ( 11) link_BETA1-4 : angle 1.60317 ( 33) link_ALPHA1-3 : bond 0.00164 ( 5) link_ALPHA1-3 : angle 0.86091 ( 15) hydrogen bonds : bond 0.15773 ( 1059) hydrogen bonds : angle 6.81158 ( 3099) SS BOND : bond 0.00176 ( 5) SS BOND : angle 1.07038 ( 10) link_BETA1-3 : bond 0.00025 ( 1) link_BETA1-3 : angle 0.65643 ( 3) covalent geometry : bond 0.00452 (24861) covalent geometry : angle 0.81079 (33664) *********************** 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 : 2.664 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: 0.8930 (mpp) REVERT: B 793 MET cc_start: 0.9287 (ppp) cc_final: 0.9073 (ppp) REVERT: C 247 MET cc_start: 0.9175 (tpp) cc_final: 0.8567 (tpp) REVERT: C 323 MET cc_start: 0.9193 (tpp) cc_final: 0.8985 (tpp) REVERT: C 413 MET cc_start: 0.8210 (tpp) cc_final: 0.7687 (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: 0.3272 time to fit residues: 57.9633 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 : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 270 optimal weight: 0.0980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 549 ASN B 81 GLN B 165 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.032371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.023391 restraints weight = 322395.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.023976 restraints weight = 187818.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.024382 restraints weight = 130834.461| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24908 Z= 0.148 Angle : 0.627 13.315 33800 Z= 0.299 Chirality : 0.043 0.587 3929 Planarity : 0.004 0.070 4184 Dihedral : 12.825 121.906 4173 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 2971 helix: 0.36 (0.13), residues: 1323 sheet: -1.37 (0.26), residues: 426 loop : -1.23 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 641 HIS 0.007 0.001 HIS C 253 PHE 0.020 0.001 PHE B 643 TYR 0.013 0.001 TYR C 324 ARG 0.006 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00748 ( 16) link_NAG-ASN : angle 4.14693 ( 48) link_ALPHA1-4 : bond 0.00349 ( 3) link_ALPHA1-4 : angle 3.22901 ( 9) link_ALPHA1-6 : bond 0.00711 ( 6) link_ALPHA1-6 : angle 1.69263 ( 18) link_BETA1-4 : bond 0.00984 ( 11) link_BETA1-4 : angle 2.51380 ( 33) link_ALPHA1-3 : bond 0.00988 ( 5) link_ALPHA1-3 : angle 2.27349 ( 15) hydrogen bonds : bond 0.03835 ( 1059) hydrogen bonds : angle 4.89972 ( 3099) SS BOND : bond 0.00141 ( 5) SS BOND : angle 1.01455 ( 10) link_BETA1-3 : bond 0.01542 ( 1) link_BETA1-3 : angle 3.52415 ( 3) covalent geometry : bond 0.00303 (24861) covalent geometry : angle 0.59661 (33664) *********************** 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 : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8620 (mpp) cc_final: 0.8407 (mpp) REVERT: A 360 MET cc_start: 0.9480 (tpt) cc_final: 0.9116 (tpt) REVERT: A 534 MET cc_start: 0.8495 (ppp) cc_final: 0.8038 (ppp) REVERT: B 247 MET cc_start: 0.9177 (mmt) cc_final: 0.8532 (mmt) REVERT: B 770 MET cc_start: 0.9365 (pmm) cc_final: 0.8978 (mpp) REVERT: B 794 MET cc_start: 0.7998 (ttp) cc_final: 0.7736 (ttp) REVERT: C 247 MET cc_start: 0.9160 (tpp) cc_final: 0.8686 (tpp) REVERT: C 413 MET cc_start: 0.8117 (tpp) cc_final: 0.7624 (tmm) REVERT: C 501 MET cc_start: 0.8826 (mmp) cc_final: 0.8620 (mmt) REVERT: C 794 MET cc_start: 0.8954 (ppp) cc_final: 0.8393 (ppp) REVERT: D 247 MET cc_start: 0.9050 (mmp) cc_final: 0.8794 (mmt) REVERT: D 534 MET cc_start: 0.7825 (mpp) cc_final: 0.7325 (ptp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3193 time to fit residues: 53.1786 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 : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 136 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 206 optimal weight: 0.8980 chunk 27 optimal weight: 0.0870 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 overall best weight: 3.3964 ------------------------------------------------------------------------------- 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** A 491 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.031966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.023077 restraints weight = 323823.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.023649 restraints weight = 189885.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.024028 restraints weight = 132173.423| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24908 Z= 0.207 Angle : 0.629 9.980 33800 Z= 0.306 Chirality : 0.043 0.491 3929 Planarity : 0.004 0.065 4184 Dihedral : 11.332 118.316 4173 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2971 helix: 1.07 (0.14), residues: 1345 sheet: -1.44 (0.27), residues: 396 loop : -1.08 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 641 HIS 0.008 0.001 HIS D 225 PHE 0.020 0.002 PHE C 256 TYR 0.012 0.001 TYR D 462 ARG 0.004 0.000 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 16) link_NAG-ASN : angle 3.28490 ( 48) link_ALPHA1-4 : bond 0.00741 ( 3) link_ALPHA1-4 : angle 3.25934 ( 9) link_ALPHA1-6 : bond 0.00656 ( 6) link_ALPHA1-6 : angle 1.71158 ( 18) link_BETA1-4 : bond 0.00547 ( 11) link_BETA1-4 : angle 1.98516 ( 33) link_ALPHA1-3 : bond 0.01120 ( 5) link_ALPHA1-3 : angle 1.91209 ( 15) hydrogen bonds : bond 0.03577 ( 1059) hydrogen bonds : angle 4.70856 ( 3099) SS BOND : bond 0.01407 ( 5) SS BOND : angle 1.31233 ( 10) link_BETA1-3 : bond 0.01113 ( 1) link_BETA1-3 : angle 2.40481 ( 3) covalent geometry : bond 0.00425 (24861) covalent geometry : angle 0.60946 (33664) *********************** 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 : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8776 (mpp) cc_final: 0.8444 (mpp) REVERT: A 360 MET cc_start: 0.9508 (tpt) cc_final: 0.9080 (tpt) REVERT: A 794 MET cc_start: 0.9111 (ttt) cc_final: 0.8852 (ttt) REVERT: B 247 MET cc_start: 0.9234 (mmt) cc_final: 0.8396 (mmt) REVERT: B 770 MET cc_start: 0.9331 (pmm) cc_final: 0.8985 (mpp) REVERT: B 794 MET cc_start: 0.8189 (ttp) cc_final: 0.7987 (ttt) REVERT: C 234 MET cc_start: 0.9126 (mmp) cc_final: 0.8922 (mmm) REVERT: C 247 MET cc_start: 0.9224 (tpp) cc_final: 0.8752 (tpp) REVERT: C 794 MET cc_start: 0.8925 (ppp) cc_final: 0.8410 (ppp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3111 time to fit residues: 51.6738 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 : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 16 optimal weight: 3.9990 chunk 281 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 217 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.032182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.023243 restraints weight = 324700.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.023816 restraints weight = 189859.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.024217 restraints weight = 131926.462| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1798 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= 0.143 Angle : 0.571 9.738 33800 Z= 0.276 Chirality : 0.042 0.497 3929 Planarity : 0.004 0.062 4184 Dihedral : 10.484 116.903 4173 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 2971 helix: 1.38 (0.14), residues: 1339 sheet: -1.37 (0.27), residues: 398 loop : -0.99 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 641 HIS 0.009 0.001 HIS A 253 PHE 0.023 0.001 PHE B 735 TYR 0.014 0.001 TYR C 488 ARG 0.007 0.000 ARG A 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 16) link_NAG-ASN : angle 3.28986 ( 48) link_ALPHA1-4 : bond 0.00802 ( 3) link_ALPHA1-4 : angle 3.16079 ( 9) link_ALPHA1-6 : bond 0.00677 ( 6) link_ALPHA1-6 : angle 1.66196 ( 18) link_BETA1-4 : bond 0.00551 ( 11) link_BETA1-4 : angle 1.87438 ( 33) link_ALPHA1-3 : bond 0.01155 ( 5) link_ALPHA1-3 : angle 1.90958 ( 15) hydrogen bonds : bond 0.03240 ( 1059) hydrogen bonds : angle 4.52626 ( 3099) SS BOND : bond 0.00158 ( 5) SS BOND : angle 1.09594 ( 10) link_BETA1-3 : bond 0.01084 ( 1) link_BETA1-3 : angle 2.78727 ( 3) covalent geometry : bond 0.00300 (24861) covalent geometry : angle 0.54914 (33664) *********************** 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 : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 CYS cc_start: 0.9212 (m) cc_final: 0.8968 (p) REVERT: A 534 MET cc_start: 0.8378 (ppp) cc_final: 0.7998 (ppp) REVERT: A 794 MET cc_start: 0.9055 (ttt) cc_final: 0.8800 (ttt) REVERT: B 247 MET cc_start: 0.9215 (mmt) cc_final: 0.8340 (mmt) REVERT: B 770 MET cc_start: 0.9313 (pmm) cc_final: 0.8971 (mpp) REVERT: B 793 MET cc_start: 0.9317 (ppp) cc_final: 0.9105 (ppp) REVERT: C 247 MET cc_start: 0.9148 (tpp) cc_final: 0.8685 (tpp) REVERT: C 794 MET cc_start: 0.8891 (ppp) cc_final: 0.8371 (ppp) REVERT: D 247 MET cc_start: 0.9045 (mmp) cc_final: 0.8732 (mmt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3278 time to fit residues: 55.4382 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 : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 286 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 chunk 296 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 273 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 137 GLN B 417 GLN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.031744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.022833 restraints weight = 330572.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.023385 restraints weight = 193563.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.023760 restraints weight = 135381.044| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24908 Z= 0.270 Angle : 0.691 9.816 33800 Z= 0.337 Chirality : 0.044 0.518 3929 Planarity : 0.004 0.058 4184 Dihedral : 9.794 114.253 4173 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2971 helix: 1.36 (0.14), residues: 1341 sheet: -1.43 (0.28), residues: 372 loop : -1.07 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 641 HIS 0.011 0.002 HIS A 253 PHE 0.019 0.002 PHE D 337 TYR 0.014 0.002 TYR C 252 ARG 0.006 0.001 ARG A 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 16) link_NAG-ASN : angle 3.28117 ( 48) link_ALPHA1-4 : bond 0.00747 ( 3) link_ALPHA1-4 : angle 3.31862 ( 9) link_ALPHA1-6 : bond 0.00532 ( 6) link_ALPHA1-6 : angle 1.84164 ( 18) link_BETA1-4 : bond 0.00647 ( 11) link_BETA1-4 : angle 2.01063 ( 33) link_ALPHA1-3 : bond 0.01028 ( 5) link_ALPHA1-3 : angle 2.06137 ( 15) hydrogen bonds : bond 0.03556 ( 1059) hydrogen bonds : angle 4.77651 ( 3099) SS BOND : bond 0.00089 ( 5) SS BOND : angle 1.34484 ( 10) link_BETA1-3 : bond 0.01697 ( 1) link_BETA1-3 : angle 2.70389 ( 3) covalent geometry : bond 0.00555 (24861) covalent geometry : angle 0.67202 (33664) *********************** 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 97 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.9539 (tpt) cc_final: 0.9049 (tpt) REVERT: A 794 MET cc_start: 0.9044 (ttt) cc_final: 0.8773 (ttt) REVERT: B 50 MET cc_start: 0.9047 (ptm) cc_final: 0.8614 (tmm) REVERT: B 247 MET cc_start: 0.9252 (mmt) cc_final: 0.8405 (mmt) REVERT: B 770 MET cc_start: 0.9278 (pmm) cc_final: 0.8970 (mpp) REVERT: B 793 MET cc_start: 0.9257 (ppp) cc_final: 0.9027 (ppp) REVERT: C 664 MET cc_start: 0.9331 (mmt) cc_final: 0.8805 (ptp) REVERT: C 794 MET cc_start: 0.8933 (ppp) cc_final: 0.8517 (ppp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3276 time to fit residues: 54.2299 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 : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 253 optimal weight: 0.7980 chunk 294 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 257 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 281 optimal weight: 30.0000 chunk 163 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 81 GLN B 129 HIS 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** D 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.032277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.023303 restraints weight = 324896.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.023888 restraints weight = 189472.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.024280 restraints weight = 131632.926| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24908 Z= 0.125 Angle : 0.582 10.314 33800 Z= 0.278 Chirality : 0.042 0.442 3929 Planarity : 0.003 0.059 4184 Dihedral : 9.179 116.050 4173 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2971 helix: 1.58 (0.14), residues: 1337 sheet: -1.40 (0.28), residues: 386 loop : -0.99 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP D 169 HIS 0.017 0.001 HIS C 253 PHE 0.023 0.001 PHE B 643 TYR 0.021 0.001 TYR D 324 ARG 0.005 0.000 ARG B 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 16) link_NAG-ASN : angle 3.75659 ( 48) link_ALPHA1-4 : bond 0.00937 ( 3) link_ALPHA1-4 : angle 3.21981 ( 9) link_ALPHA1-6 : bond 0.00595 ( 6) link_ALPHA1-6 : angle 1.84154 ( 18) link_BETA1-4 : bond 0.00503 ( 11) link_BETA1-4 : angle 1.85193 ( 33) link_ALPHA1-3 : bond 0.01110 ( 5) link_ALPHA1-3 : angle 2.14441 ( 15) hydrogen bonds : bond 0.03136 ( 1059) hydrogen bonds : angle 4.47693 ( 3099) SS BOND : bond 0.00153 ( 5) SS BOND : angle 1.25553 ( 10) link_BETA1-3 : bond 0.01138 ( 1) link_BETA1-3 : angle 3.08620 ( 3) covalent geometry : bond 0.00265 (24861) covalent geometry : angle 0.55539 (33664) *********************** 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 : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.9461 (tpt) cc_final: 0.9106 (tpt) REVERT: A 463 CYS cc_start: 0.9170 (m) cc_final: 0.8907 (p) REVERT: A 534 MET cc_start: 0.8457 (ppp) cc_final: 0.8099 (ppp) REVERT: A 565 MET cc_start: 0.8810 (mpp) cc_final: 0.8562 (ptp) REVERT: A 794 MET cc_start: 0.8997 (ttt) cc_final: 0.8729 (ttt) REVERT: B 50 MET cc_start: 0.9061 (ptm) cc_final: 0.8633 (tmm) REVERT: B 247 MET cc_start: 0.9182 (mmt) cc_final: 0.8317 (mmt) REVERT: B 793 MET cc_start: 0.9294 (ppp) cc_final: 0.9068 (ppp) REVERT: C 234 MET cc_start: 0.9187 (mmp) cc_final: 0.8948 (mmm) REVERT: C 247 MET cc_start: 0.9016 (tpp) cc_final: 0.8342 (tpp) REVERT: C 664 MET cc_start: 0.9271 (mmt) cc_final: 0.9062 (mmm) REVERT: C 794 MET cc_start: 0.8851 (ppp) cc_final: 0.8466 (ppp) REVERT: D 247 MET cc_start: 0.8996 (mmp) cc_final: 0.8305 (mmt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3333 time to fit residues: 56.3407 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 : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 289 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 230 optimal weight: 0.7980 chunk 257 optimal weight: 0.8980 chunk 269 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 259 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 B 721 ASN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.032549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.023509 restraints weight = 324994.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.024111 restraints weight = 188926.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.024503 restraints weight = 130292.666| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24908 Z= 0.099 Angle : 0.563 11.023 33800 Z= 0.266 Chirality : 0.042 0.429 3929 Planarity : 0.003 0.060 4184 Dihedral : 8.387 115.511 4173 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2971 helix: 1.74 (0.14), residues: 1337 sheet: -1.28 (0.28), residues: 377 loop : -0.97 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 564 HIS 0.012 0.001 HIS D 225 PHE 0.025 0.001 PHE B 643 TYR 0.018 0.001 TYR D 324 ARG 0.006 0.000 ARG C 184 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 16) link_NAG-ASN : angle 3.60718 ( 48) link_ALPHA1-4 : bond 0.00933 ( 3) link_ALPHA1-4 : angle 3.19416 ( 9) link_ALPHA1-6 : bond 0.00588 ( 6) link_ALPHA1-6 : angle 1.87908 ( 18) link_BETA1-4 : bond 0.00523 ( 11) link_BETA1-4 : angle 1.76266 ( 33) link_ALPHA1-3 : bond 0.01308 ( 5) link_ALPHA1-3 : angle 2.32360 ( 15) hydrogen bonds : bond 0.02878 ( 1059) hydrogen bonds : angle 4.24896 ( 3099) SS BOND : bond 0.00253 ( 5) SS BOND : angle 1.01317 ( 10) link_BETA1-3 : bond 0.01248 ( 1) link_BETA1-3 : angle 3.67240 ( 3) covalent geometry : bond 0.00211 (24861) covalent geometry : angle 0.53645 (33664) *********************** 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 : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.9429 (tpt) cc_final: 0.9095 (tpt) REVERT: A 463 CYS cc_start: 0.9203 (m) cc_final: 0.8947 (p) REVERT: A 534 MET cc_start: 0.8438 (ppp) cc_final: 0.7907 (ppp) REVERT: A 565 MET cc_start: 0.8834 (mpp) cc_final: 0.8512 (ptt) REVERT: A 794 MET cc_start: 0.8935 (ttt) cc_final: 0.8647 (ttt) REVERT: B 247 MET cc_start: 0.9147 (mmt) cc_final: 0.8465 (mmt) REVERT: B 793 MET cc_start: 0.9325 (ppp) cc_final: 0.9101 (ppp) REVERT: C 234 MET cc_start: 0.9136 (mmp) cc_final: 0.8891 (mmm) REVERT: C 247 MET cc_start: 0.8983 (tpp) cc_final: 0.8093 (tpp) REVERT: C 664 MET cc_start: 0.9314 (mmt) cc_final: 0.9035 (mmm) REVERT: C 794 MET cc_start: 0.8831 (ppp) cc_final: 0.8483 (ppp) REVERT: D 247 MET cc_start: 0.8976 (mmp) cc_final: 0.8427 (mmt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3163 time to fit residues: 54.0338 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 : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 17 optimal weight: 6.9990 chunk 270 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 274 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 82 optimal weight: 0.3980 chunk 254 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 350 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 = 0.3250 r_free = 0.3250 target = 0.032225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.023245 restraints weight = 326185.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.023817 restraints weight = 190925.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.024211 restraints weight = 133194.273| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2351 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= 0.156 Angle : 0.584 10.918 33800 Z= 0.280 Chirality : 0.042 0.450 3929 Planarity : 0.003 0.058 4184 Dihedral : 8.116 115.042 4173 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 2971 helix: 1.80 (0.14), residues: 1340 sheet: -1.28 (0.28), residues: 378 loop : -0.97 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP D 169 HIS 0.014 0.001 HIS C 253 PHE 0.025 0.001 PHE B 643 TYR 0.012 0.001 TYR D 462 ARG 0.005 0.000 ARG D 58 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 16) link_NAG-ASN : angle 3.57220 ( 48) link_ALPHA1-4 : bond 0.00900 ( 3) link_ALPHA1-4 : angle 3.17547 ( 9) link_ALPHA1-6 : bond 0.00495 ( 6) link_ALPHA1-6 : angle 1.91773 ( 18) link_BETA1-4 : bond 0.00490 ( 11) link_BETA1-4 : angle 1.81975 ( 33) link_ALPHA1-3 : bond 0.01280 ( 5) link_ALPHA1-3 : angle 2.25066 ( 15) hydrogen bonds : bond 0.03007 ( 1059) hydrogen bonds : angle 4.29687 ( 3099) SS BOND : bond 0.00175 ( 5) SS BOND : angle 1.03607 ( 10) link_BETA1-3 : bond 0.01134 ( 1) link_BETA1-3 : angle 3.50208 ( 3) covalent geometry : bond 0.00329 (24861) covalent geometry : angle 0.55963 (33664) *********************** 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 : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8837 (mpp) cc_final: 0.8517 (ptt) REVERT: A 794 MET cc_start: 0.8984 (ttt) cc_final: 0.8703 (ttt) REVERT: B 247 MET cc_start: 0.9136 (mmt) cc_final: 0.8400 (mmt) REVERT: B 793 MET cc_start: 0.9311 (ppp) cc_final: 0.9106 (ppp) REVERT: C 234 MET cc_start: 0.9165 (mmp) cc_final: 0.8922 (mmm) REVERT: C 247 MET cc_start: 0.8993 (tpp) cc_final: 0.8234 (tpp) REVERT: C 360 MET cc_start: 0.9173 (mtp) cc_final: 0.8864 (mtp) REVERT: C 794 MET cc_start: 0.8859 (ppp) cc_final: 0.8500 (ppp) REVERT: D 247 MET cc_start: 0.9007 (mmp) cc_final: 0.8473 (mmt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3495 time to fit residues: 58.4556 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 : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 91 optimal weight: 0.6980 chunk 271 optimal weight: 0.0040 chunk 292 optimal weight: 8.9990 chunk 170 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3269 r_free = 0.3269 target = 0.032614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.023582 restraints weight = 324780.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.024174 restraints weight = 188831.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.024580 restraints weight = 130856.787| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24908 Z= 0.094 Angle : 0.558 11.092 33800 Z= 0.263 Chirality : 0.042 0.423 3929 Planarity : 0.003 0.055 4184 Dihedral : 7.900 115.946 4173 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2971 helix: 1.82 (0.14), residues: 1339 sheet: -1.22 (0.29), residues: 377 loop : -0.91 (0.18), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 169 HIS 0.011 0.001 HIS C 253 PHE 0.028 0.001 PHE B 643 TYR 0.014 0.001 TYR D 324 ARG 0.004 0.000 ARG A 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 16) link_NAG-ASN : angle 3.54035 ( 48) link_ALPHA1-4 : bond 0.00969 ( 3) link_ALPHA1-4 : angle 3.12927 ( 9) link_ALPHA1-6 : bond 0.00592 ( 6) link_ALPHA1-6 : angle 1.86341 ( 18) link_BETA1-4 : bond 0.00507 ( 11) link_BETA1-4 : angle 1.74798 ( 33) link_ALPHA1-3 : bond 0.01232 ( 5) link_ALPHA1-3 : angle 2.10024 ( 15) hydrogen bonds : bond 0.02826 ( 1059) hydrogen bonds : angle 4.17196 ( 3099) SS BOND : bond 0.00167 ( 5) SS BOND : angle 0.87987 ( 10) link_BETA1-3 : bond 0.01084 ( 1) link_BETA1-3 : angle 3.60454 ( 3) covalent geometry : bond 0.00201 (24861) covalent geometry : angle 0.53283 (33664) *********************** 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 : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8757 (mpp) cc_final: 0.8469 (ptt) REVERT: A 691 MET cc_start: 0.9522 (ptp) cc_final: 0.9049 (pmm) REVERT: A 794 MET cc_start: 0.8971 (ttt) cc_final: 0.8701 (ttt) REVERT: B 50 MET cc_start: 0.9116 (ptm) cc_final: 0.8696 (tmm) REVERT: B 247 MET cc_start: 0.9148 (mmt) cc_final: 0.8503 (mmt) REVERT: C 234 MET cc_start: 0.9147 (mmp) cc_final: 0.8925 (mmm) REVERT: C 247 MET cc_start: 0.8936 (tpp) cc_final: 0.8014 (tpp) REVERT: C 664 MET cc_start: 0.9308 (mmt) cc_final: 0.8871 (mmm) REVERT: C 794 MET cc_start: 0.8826 (ppp) cc_final: 0.8480 (ppp) REVERT: D 247 MET cc_start: 0.8977 (mmp) cc_final: 0.8433 (mmt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3259 time to fit residues: 55.1917 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 : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 282 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 266 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 186 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3241 r_free = 0.3241 target = 0.032050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.023106 restraints weight = 328282.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.023673 restraints weight = 192340.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.024064 restraints weight = 133486.652| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24908 Z= 0.202 Angle : 0.615 10.878 33800 Z= 0.298 Chirality : 0.042 0.473 3929 Planarity : 0.004 0.049 4184 Dihedral : 7.618 113.075 4173 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2971 helix: 1.87 (0.15), residues: 1335 sheet: -1.31 (0.28), residues: 385 loop : -0.92 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 169 HIS 0.015 0.002 HIS D 225 PHE 0.026 0.001 PHE B 643 TYR 0.012 0.001 TYR D 462 ARG 0.004 0.000 ARG B 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 16) link_NAG-ASN : angle 3.66826 ( 48) link_ALPHA1-4 : bond 0.00887 ( 3) link_ALPHA1-4 : angle 3.23215 ( 9) link_ALPHA1-6 : bond 0.00485 ( 6) link_ALPHA1-6 : angle 1.88949 ( 18) link_BETA1-4 : bond 0.00518 ( 11) link_BETA1-4 : angle 1.86119 ( 33) link_ALPHA1-3 : bond 0.01134 ( 5) link_ALPHA1-3 : angle 2.21418 ( 15) hydrogen bonds : bond 0.03091 ( 1059) hydrogen bonds : angle 4.35051 ( 3099) SS BOND : bond 0.00362 ( 5) SS BOND : angle 1.24757 ( 10) link_BETA1-3 : bond 0.01065 ( 1) link_BETA1-3 : angle 3.29613 ( 3) covalent geometry : bond 0.00423 (24861) covalent geometry : angle 0.59061 (33664) ********************** 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 : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8860 (ppp) cc_final: 0.8464 (ppp) REVERT: A 565 MET cc_start: 0.8813 (mpp) cc_final: 0.8584 (ptp) REVERT: A 794 MET cc_start: 0.8968 (ttt) cc_final: 0.8688 (ttt) REVERT: B 50 MET cc_start: 0.9137 (ptm) cc_final: 0.8602 (tmm) REVERT: B 247 MET cc_start: 0.9159 (mmt) cc_final: 0.8467 (mmt) REVERT: C 234 MET cc_start: 0.9196 (mmp) cc_final: 0.8957 (mmm) REVERT: C 664 MET cc_start: 0.9318 (mmt) cc_final: 0.9095 (mmm) REVERT: C 794 MET cc_start: 0.8872 (ppp) cc_final: 0.8508 (ppp) REVERT: D 247 MET cc_start: 0.9032 (mmp) cc_final: 0.8228 (mmt) REVERT: D 565 MET cc_start: 0.8654 (mpp) cc_final: 0.8348 (mpp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3331 time to fit residues: 55.7296 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 : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 17 optimal weight: 0.6980 chunk 257 optimal weight: 3.9990 chunk 292 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 283 optimal weight: 7.9990 chunk 241 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 294 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN D 721 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.031924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.023003 restraints weight = 329190.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.023564 restraints weight = 193122.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.023951 restraints weight = 134558.948| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24908 Z= 0.218 Angle : 0.646 10.813 33800 Z= 0.314 Chirality : 0.043 0.489 3929 Planarity : 0.004 0.049 4184 Dihedral : 7.579 113.256 4173 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2971 helix: 1.74 (0.14), residues: 1328 sheet: -1.51 (0.27), residues: 405 loop : -0.90 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 169 HIS 0.017 0.002 HIS D 225 PHE 0.034 0.002 PHE D 166 TYR 0.012 0.001 TYR D 651 ARG 0.005 0.000 ARG B 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 16) link_NAG-ASN : angle 3.77381 ( 48) link_ALPHA1-4 : bond 0.00874 ( 3) link_ALPHA1-4 : angle 3.26232 ( 9) link_ALPHA1-6 : bond 0.00443 ( 6) link_ALPHA1-6 : angle 1.84239 ( 18) link_BETA1-4 : bond 0.00502 ( 11) link_BETA1-4 : angle 1.86259 ( 33) link_ALPHA1-3 : bond 0.01001 ( 5) link_ALPHA1-3 : angle 2.20720 ( 15) hydrogen bonds : bond 0.03267 ( 1059) hydrogen bonds : angle 4.54313 ( 3099) SS BOND : bond 0.00341 ( 5) SS BOND : angle 1.32106 ( 10) link_BETA1-3 : bond 0.00760 ( 1) link_BETA1-3 : angle 2.96712 ( 3) covalent geometry : bond 0.00455 (24861) covalent geometry : angle 0.62267 (33664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6388.23 seconds wall clock time: 114 minutes 12.43 seconds (6852.43 seconds total)