Starting phenix.real_space_refine on Sat Jun 21 05:53:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gc2_29926/06_2025/8gc2_29926.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gc2_29926/06_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_29926/06_2025/8gc2_29926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gc2_29926/06_2025/8gc2_29926.map" model { file = "/net/cci-nas-00/data/ceres_data/8gc2_29926/06_2025/8gc2_29926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gc2_29926/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 16.13, per 1000 atoms: 0.66 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: 6.65 Conformation dependent library (CDL) restraints added in 3.2 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: 2.87 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: 9.53 Time building geometry restraints manager: 7.69 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: 342.450 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: 0.030 Extract box with map and model: 0.940 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 57.950 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 406.740 ------------------------------------------------------------------------------- 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 : 2.617 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: 0.3254 time to fit residues: 58.5322 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 : 3.541 ------------------------------------------------------------------------------- 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 = 52)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.023391 restraints weight = 322395.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.023973 restraints weight = 187784.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.024371 restraints weight = 130808.197| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 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 : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8624 (mpp) cc_final: 0.8408 (mpp) REVERT: A 360 MET cc_start: 0.9478 (tpt) cc_final: 0.9115 (tpt) REVERT: A 534 MET cc_start: 0.8500 (ppp) cc_final: 0.8043 (ppp) REVERT: B 247 MET cc_start: 0.9177 (mmt) cc_final: 0.8533 (mmt) REVERT: B 770 MET cc_start: 0.9366 (pmm) cc_final: 0.8982 (mpp) REVERT: B 794 MET cc_start: 0.7984 (ttp) cc_final: 0.7722 (ttp) REVERT: C 247 MET cc_start: 0.9160 (tpp) cc_final: 0.8686 (tpp) REVERT: C 413 MET cc_start: 0.8128 (tpp) cc_final: 0.7628 (tmm) REVERT: C 501 MET cc_start: 0.8825 (mmp) cc_final: 0.8620 (mmt) REVERT: C 794 MET cc_start: 0.8952 (ppp) cc_final: 0.8394 (ppp) REVERT: D 247 MET cc_start: 0.9050 (mmp) cc_final: 0.8793 (mmt) REVERT: D 534 MET cc_start: 0.7822 (mpp) cc_final: 0.7318 (ptp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3394 time to fit residues: 58.5371 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 : 3.288 ------------------------------------------------------------------------------- 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: 0.0070 chunk 27 optimal weight: 0.0970 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: 10.0000 chunk 26 optimal weight: 6.9990 overall best weight: 3.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS C 367 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.032009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.023110 restraints weight = 323383.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.023678 restraints weight = 189537.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.024072 restraints weight = 132364.857| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24908 Z= 0.196 Angle : 0.618 9.607 33800 Z= 0.301 Chirality : 0.043 0.486 3929 Planarity : 0.004 0.065 4184 Dihedral : 11.228 118.061 4173 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: -0.25 (0.16), residues: 2971 helix: 1.11 (0.14), residues: 1332 sheet: -1.43 (0.27), residues: 395 loop : -1.09 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 641 HIS 0.009 0.001 HIS D 225 PHE 0.026 0.002 PHE D 337 TYR 0.011 0.001 TYR A 195 ARG 0.004 0.000 ARG B 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 16) link_NAG-ASN : angle 3.29237 ( 48) link_ALPHA1-4 : bond 0.00791 ( 3) link_ALPHA1-4 : angle 3.21786 ( 9) link_ALPHA1-6 : bond 0.00745 ( 6) link_ALPHA1-6 : angle 1.72274 ( 18) link_BETA1-4 : bond 0.00576 ( 11) link_BETA1-4 : angle 1.95944 ( 33) link_ALPHA1-3 : bond 0.01065 ( 5) link_ALPHA1-3 : angle 1.96266 ( 15) hydrogen bonds : bond 0.03525 ( 1059) hydrogen bonds : angle 4.67798 ( 3099) SS BOND : bond 0.00704 ( 5) SS BOND : angle 1.33066 ( 10) link_BETA1-3 : bond 0.01135 ( 1) link_BETA1-3 : angle 2.44308 ( 3) covalent geometry : bond 0.00402 (24861) covalent geometry : angle 0.59790 (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 : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8763 (mpp) cc_final: 0.8436 (mpp) REVERT: A 360 MET cc_start: 0.9505 (tpt) cc_final: 0.9082 (tpt) REVERT: A 794 MET cc_start: 0.9103 (ttt) cc_final: 0.8855 (ttt) REVERT: B 247 MET cc_start: 0.9232 (mmt) cc_final: 0.8380 (mmt) REVERT: B 770 MET cc_start: 0.9324 (pmm) cc_final: 0.8976 (mpp) REVERT: C 50 MET cc_start: 0.8051 (ppp) cc_final: 0.7830 (ppp) REVERT: C 234 MET cc_start: 0.9125 (mmp) cc_final: 0.8914 (mmm) REVERT: C 247 MET cc_start: 0.9196 (tpp) cc_final: 0.8738 (tpp) REVERT: C 794 MET cc_start: 0.8919 (ppp) cc_final: 0.8406 (ppp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.4161 time to fit residues: 70.1061 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 : 3.146 ------------------------------------------------------------------------------- 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: 2.9990 chunk 281 optimal weight: 30.0000 chunk 117 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 289 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 136 HIS ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.031822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.022942 restraints weight = 328706.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.023513 restraints weight = 191726.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.023896 restraints weight = 133065.467| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1969 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= 0.225 Angle : 0.636 9.803 33800 Z= 0.311 Chirality : 0.043 0.574 3929 Planarity : 0.004 0.061 4184 Dihedral : 10.364 116.491 4173 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.16), residues: 2971 helix: 1.31 (0.14), residues: 1344 sheet: -1.50 (0.27), residues: 387 loop : -1.02 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 641 HIS 0.010 0.002 HIS A 136 PHE 0.023 0.002 PHE B 359 TYR 0.015 0.001 TYR C 488 ARG 0.010 0.001 ARG A 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 16) link_NAG-ASN : angle 3.34423 ( 48) link_ALPHA1-4 : bond 0.00676 ( 3) link_ALPHA1-4 : angle 3.25823 ( 9) link_ALPHA1-6 : bond 0.00581 ( 6) link_ALPHA1-6 : angle 1.76078 ( 18) link_BETA1-4 : bond 0.00545 ( 11) link_BETA1-4 : angle 1.97021 ( 33) link_ALPHA1-3 : bond 0.01005 ( 5) link_ALPHA1-3 : angle 1.97660 ( 15) hydrogen bonds : bond 0.03465 ( 1059) hydrogen bonds : angle 4.69076 ( 3099) SS BOND : bond 0.00616 ( 5) SS BOND : angle 1.24758 ( 10) link_BETA1-3 : bond 0.00997 ( 1) link_BETA1-3 : angle 2.52977 ( 3) covalent geometry : bond 0.00466 (24861) covalent geometry : angle 0.61582 (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 97 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 3.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.9507 (tpt) cc_final: 0.9109 (tpt) REVERT: A 565 MET cc_start: 0.8817 (mtm) cc_final: 0.8521 (mmm) REVERT: A 794 MET cc_start: 0.9046 (ttt) cc_final: 0.8783 (ttt) REVERT: B 247 MET cc_start: 0.9257 (mmt) cc_final: 0.8358 (mmt) REVERT: B 770 MET cc_start: 0.9298 (pmm) cc_final: 0.8971 (mpp) REVERT: B 793 MET cc_start: 0.9303 (ppp) cc_final: 0.9086 (ppp) REVERT: C 794 MET cc_start: 0.8902 (ppp) cc_final: 0.8375 (ppp) REVERT: D 247 MET cc_start: 0.9032 (mmp) cc_final: 0.8758 (mmp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.5395 time to fit residues: 88.3856 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 : 3.400 ------------------------------------------------------------------------------- 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: 10.0000 chunk 296 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 213 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 273 optimal weight: 0.9980 chunk 256 optimal weight: 0.0970 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- 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 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 = 0.3252 r_free = 0.3252 target = 0.032282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.023282 restraints weight = 327543.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.023868 restraints weight = 191097.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.024259 restraints weight = 132673.370| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24908 Z= 0.136 Angle : 0.575 9.989 33800 Z= 0.278 Chirality : 0.042 0.465 3929 Planarity : 0.003 0.059 4184 Dihedral : 9.726 116.495 4173 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.12 (0.16), residues: 2971 helix: 1.50 (0.14), residues: 1341 sheet: -1.43 (0.27), residues: 407 loop : -0.95 (0.18), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 169 HIS 0.011 0.001 HIS A 253 PHE 0.020 0.001 PHE D 89 TYR 0.013 0.001 TYR C 488 ARG 0.005 0.000 ARG B 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 16) link_NAG-ASN : angle 3.09526 ( 48) link_ALPHA1-4 : bond 0.00809 ( 3) link_ALPHA1-4 : angle 3.30660 ( 9) link_ALPHA1-6 : bond 0.00618 ( 6) link_ALPHA1-6 : angle 1.68784 ( 18) link_BETA1-4 : bond 0.00505 ( 11) link_BETA1-4 : angle 1.83869 ( 33) link_ALPHA1-3 : bond 0.01113 ( 5) link_ALPHA1-3 : angle 2.03979 ( 15) hydrogen bonds : bond 0.03154 ( 1059) hydrogen bonds : angle 4.50562 ( 3099) SS BOND : bond 0.00101 ( 5) SS BOND : angle 1.07802 ( 10) link_BETA1-3 : bond 0.01085 ( 1) link_BETA1-3 : angle 2.86889 ( 3) covalent geometry : bond 0.00287 (24861) covalent geometry : angle 0.55514 (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 99 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 CYS cc_start: 0.9206 (m) cc_final: 0.8954 (p) REVERT: A 534 MET cc_start: 0.8553 (ppp) cc_final: 0.8033 (ppp) REVERT: A 794 MET cc_start: 0.9027 (ttt) cc_final: 0.8767 (ttt) REVERT: B 50 MET cc_start: 0.9077 (ptm) cc_final: 0.8596 (tmm) REVERT: B 247 MET cc_start: 0.9208 (mmt) cc_final: 0.8247 (mmt) REVERT: B 770 MET cc_start: 0.9267 (pmm) cc_final: 0.9036 (mpp) REVERT: B 793 MET cc_start: 0.9320 (ppp) cc_final: 0.9101 (ppp) REVERT: C 234 MET cc_start: 0.9263 (mmp) cc_final: 0.8972 (mmm) REVERT: C 247 MET cc_start: 0.8815 (tpp) cc_final: 0.8350 (tpp) REVERT: C 276 MET cc_start: 0.8995 (mmm) cc_final: 0.8748 (mmm) REVERT: C 664 MET cc_start: 0.9329 (mmt) cc_final: 0.8924 (mmm) REVERT: C 794 MET cc_start: 0.8903 (ppp) cc_final: 0.8518 (ppp) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.5042 time to fit residues: 86.7889 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 : 4.085 ------------------------------------------------------------------------------- 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: 1.9990 chunk 294 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 257 optimal weight: 3.9990 chunk 232 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 281 optimal weight: 30.0000 chunk 163 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 350 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.032242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.023251 restraints weight = 325493.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.023835 restraints weight = 189834.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.024220 restraints weight = 131739.116| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 0.037 24908 Z= 0.145 Angle : 0.575 9.812 33800 Z= 0.277 Chirality : 0.042 0.460 3929 Planarity : 0.003 0.058 4184 Dihedral : 8.898 114.518 4173 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.24 (0.16), residues: 2971 helix: 1.66 (0.14), residues: 1338 sheet: -1.37 (0.28), residues: 385 loop : -0.97 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 169 HIS 0.011 0.001 HIS A 253 PHE 0.022 0.001 PHE B 643 TYR 0.011 0.001 TYR D 462 ARG 0.003 0.000 ARG A 384 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 16) link_NAG-ASN : angle 2.98887 ( 48) link_ALPHA1-4 : bond 0.00902 ( 3) link_ALPHA1-4 : angle 3.26031 ( 9) link_ALPHA1-6 : bond 0.00563 ( 6) link_ALPHA1-6 : angle 1.92837 ( 18) link_BETA1-4 : bond 0.00562 ( 11) link_BETA1-4 : angle 1.86076 ( 33) link_ALPHA1-3 : bond 0.01221 ( 5) link_ALPHA1-3 : angle 2.15692 ( 15) hydrogen bonds : bond 0.03060 ( 1059) hydrogen bonds : angle 4.40264 ( 3099) SS BOND : bond 0.00628 ( 5) SS BOND : angle 1.21955 ( 10) link_BETA1-3 : bond 0.01201 ( 1) link_BETA1-3 : angle 3.31486 ( 3) covalent geometry : bond 0.00304 (24861) covalent geometry : angle 0.55452 (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 : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 CYS cc_start: 0.9232 (m) cc_final: 0.8966 (p) REVERT: A 534 MET cc_start: 0.8571 (ppp) cc_final: 0.8099 (ppp) REVERT: A 794 MET cc_start: 0.9033 (ttt) cc_final: 0.8759 (ttt) REVERT: B 50 MET cc_start: 0.9193 (ptm) cc_final: 0.8644 (tmm) REVERT: B 247 MET cc_start: 0.9231 (mmt) cc_final: 0.8391 (mmt) REVERT: B 793 MET cc_start: 0.9321 (ppp) cc_final: 0.9098 (ppp) REVERT: C 234 MET cc_start: 0.9288 (mmp) cc_final: 0.9001 (mmm) REVERT: C 247 MET cc_start: 0.8799 (tpp) cc_final: 0.8378 (tpp) REVERT: C 794 MET cc_start: 0.8902 (ppp) cc_final: 0.8544 (ppp) REVERT: D 247 MET cc_start: 0.9073 (mmp) cc_final: 0.8406 (mmt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3264 time to fit residues: 55.5582 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 : 2.569 ------------------------------------------------------------------------------- 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: 0.9980 chunk 122 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 230 optimal weight: 0.7980 chunk 257 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** D 721 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.032498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.023464 restraints weight = 325640.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.024045 restraints weight = 189494.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.024461 restraints weight = 130677.972| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24908 Z= 0.106 Angle : 0.563 12.257 33800 Z= 0.266 Chirality : 0.042 0.431 3929 Planarity : 0.003 0.059 4184 Dihedral : 8.397 115.766 4173 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: 0.34 (0.16), residues: 2971 helix: 1.77 (0.14), residues: 1337 sheet: -1.33 (0.27), residues: 398 loop : -0.93 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 564 HIS 0.019 0.001 HIS C 253 PHE 0.025 0.001 PHE B 643 TYR 0.020 0.001 TYR D 324 ARG 0.005 0.000 ARG C 184 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 16) link_NAG-ASN : angle 3.88266 ( 48) link_ALPHA1-4 : bond 0.00921 ( 3) link_ALPHA1-4 : angle 3.15376 ( 9) link_ALPHA1-6 : bond 0.00556 ( 6) link_ALPHA1-6 : angle 1.86886 ( 18) link_BETA1-4 : bond 0.00509 ( 11) link_BETA1-4 : angle 1.79118 ( 33) link_ALPHA1-3 : bond 0.01256 ( 5) link_ALPHA1-3 : angle 2.24709 ( 15) hydrogen bonds : bond 0.02886 ( 1059) hydrogen bonds : angle 4.25776 ( 3099) SS BOND : bond 0.00325 ( 5) SS BOND : angle 1.03871 ( 10) link_BETA1-3 : bond 0.01282 ( 1) link_BETA1-3 : angle 3.59669 ( 3) covalent geometry : bond 0.00227 (24861) covalent geometry : angle 0.53385 (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 : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 CYS cc_start: 0.9191 (m) cc_final: 0.8941 (p) REVERT: A 794 MET cc_start: 0.8965 (ttt) cc_final: 0.8690 (ttt) REVERT: B 50 MET cc_start: 0.9068 (ptm) cc_final: 0.8732 (tmm) REVERT: B 247 MET cc_start: 0.9188 (mmt) cc_final: 0.8425 (mmt) REVERT: B 793 MET cc_start: 0.9323 (ppp) cc_final: 0.9100 (ppp) REVERT: C 234 MET cc_start: 0.9152 (mmp) cc_final: 0.8911 (mmm) REVERT: C 247 MET cc_start: 0.8677 (tpp) cc_final: 0.8306 (tpp) REVERT: C 664 MET cc_start: 0.9292 (mmt) cc_final: 0.8725 (ptp) REVERT: C 794 MET cc_start: 0.8842 (ppp) cc_final: 0.8492 (ppp) REVERT: D 247 MET cc_start: 0.8992 (mmp) cc_final: 0.8415 (mmt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.3704 time to fit residues: 63.7611 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 : 3.230 ------------------------------------------------------------------------------- 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: 0.0970 chunk 270 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 274 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 222 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 chunk 254 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.032512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.023510 restraints weight = 324578.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.024086 restraints weight = 188396.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.024495 restraints weight = 131082.726| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2294 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= 0.105 Angle : 0.555 10.737 33800 Z= 0.263 Chirality : 0.041 0.434 3929 Planarity : 0.003 0.058 4184 Dihedral : 8.013 115.352 4173 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % 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: 0.46 (0.16), residues: 2971 helix: 1.86 (0.14), residues: 1339 sheet: -1.25 (0.28), residues: 398 loop : -0.88 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 564 HIS 0.015 0.001 HIS C 253 PHE 0.026 0.001 PHE B 643 TYR 0.017 0.001 TYR D 324 ARG 0.003 0.000 ARG B 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 16) link_NAG-ASN : angle 3.67479 ( 48) link_ALPHA1-4 : bond 0.00950 ( 3) link_ALPHA1-4 : angle 3.14476 ( 9) link_ALPHA1-6 : bond 0.00576 ( 6) link_ALPHA1-6 : angle 1.88621 ( 18) link_BETA1-4 : bond 0.00487 ( 11) link_BETA1-4 : angle 1.78543 ( 33) link_ALPHA1-3 : bond 0.01219 ( 5) link_ALPHA1-3 : angle 2.18634 ( 15) hydrogen bonds : bond 0.02827 ( 1059) hydrogen bonds : angle 4.17361 ( 3099) SS BOND : bond 0.00225 ( 5) SS BOND : angle 0.95338 ( 10) link_BETA1-3 : bond 0.01146 ( 1) link_BETA1-3 : angle 3.63040 ( 3) covalent geometry : bond 0.00226 (24861) covalent geometry : angle 0.52829 (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 : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8681 (mtm) cc_final: 0.8296 (mmp) REVERT: A 794 MET cc_start: 0.8959 (ttt) cc_final: 0.8688 (ttt) REVERT: B 247 MET cc_start: 0.9164 (mmt) cc_final: 0.8319 (mmt) REVERT: B 793 MET cc_start: 0.9322 (ppp) cc_final: 0.9098 (ppp) REVERT: C 234 MET cc_start: 0.9143 (mmp) cc_final: 0.8902 (mmm) REVERT: C 247 MET cc_start: 0.8624 (tpp) cc_final: 0.8280 (tpp) REVERT: C 664 MET cc_start: 0.9311 (mmt) cc_final: 0.9092 (mmm) REVERT: C 794 MET cc_start: 0.8837 (ppp) cc_final: 0.8496 (ppp) REVERT: D 247 MET cc_start: 0.8989 (mmp) cc_final: 0.8407 (mmt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3188 time to fit residues: 54.0600 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 : 2.884 ------------------------------------------------------------------------------- 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: 0.2980 chunk 271 optimal weight: 1.9990 chunk 292 optimal weight: 8.9990 chunk 170 optimal weight: 0.8980 chunk 232 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 288 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.032364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.023360 restraints weight = 326551.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.023950 restraints weight = 190772.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.024335 restraints weight = 132010.903| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24908 Z= 0.134 Angle : 0.569 11.265 33800 Z= 0.271 Chirality : 0.041 0.443 3929 Planarity : 0.003 0.053 4184 Dihedral : 7.811 114.466 4173 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.16), residues: 2971 helix: 1.89 (0.14), residues: 1341 sheet: -1.19 (0.29), residues: 365 loop : -0.93 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 564 HIS 0.015 0.001 HIS C 253 PHE 0.027 0.001 PHE B 643 TYR 0.016 0.001 TYR D 324 ARG 0.004 0.000 ARG A 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 16) link_NAG-ASN : angle 3.67492 ( 48) link_ALPHA1-4 : bond 0.00929 ( 3) link_ALPHA1-4 : angle 3.17748 ( 9) link_ALPHA1-6 : bond 0.00540 ( 6) link_ALPHA1-6 : angle 1.91312 ( 18) link_BETA1-4 : bond 0.00502 ( 11) link_BETA1-4 : angle 1.80241 ( 33) link_ALPHA1-3 : bond 0.01134 ( 5) link_ALPHA1-3 : angle 2.14814 ( 15) hydrogen bonds : bond 0.02906 ( 1059) hydrogen bonds : angle 4.21404 ( 3099) SS BOND : bond 0.00326 ( 5) SS BOND : angle 1.30417 ( 10) link_BETA1-3 : bond 0.01112 ( 1) link_BETA1-3 : angle 3.50402 ( 3) covalent geometry : bond 0.00284 (24861) covalent geometry : angle 0.54214 (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 : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.8783 (ppp) cc_final: 0.8433 (ppp) REVERT: A 565 MET cc_start: 0.8730 (mtm) cc_final: 0.8366 (mmp) REVERT: A 737 MET cc_start: 0.8140 (ptp) cc_final: 0.7860 (ptp) REVERT: A 794 MET cc_start: 0.8967 (ttt) cc_final: 0.8700 (ttt) REVERT: B 50 MET cc_start: 0.9123 (ptm) cc_final: 0.8678 (tmm) REVERT: B 247 MET cc_start: 0.9174 (mmt) cc_final: 0.8408 (mmt) REVERT: B 793 MET cc_start: 0.9352 (ppp) cc_final: 0.9095 (ppp) REVERT: C 234 MET cc_start: 0.9170 (mmp) cc_final: 0.8936 (mmm) REVERT: C 247 MET cc_start: 0.8624 (tpp) cc_final: 0.8300 (tpp) REVERT: C 664 MET cc_start: 0.9315 (mmt) cc_final: 0.9075 (mmm) REVERT: C 794 MET cc_start: 0.8860 (ppp) cc_final: 0.8516 (ppp) REVERT: D 247 MET cc_start: 0.9006 (mmp) cc_final: 0.8431 (mmt) REVERT: D 565 MET cc_start: 0.8509 (mpp) cc_final: 0.8206 (mpp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3921 time to fit residues: 66.6315 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 : 3.546 ------------------------------------------------------------------------------- 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: 5.9990 chunk 247 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 138 optimal weight: 0.0470 chunk 110 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- 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 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 = 0.3231 r_free = 0.3231 target = 0.031901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.022914 restraints weight = 327345.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.023474 restraints weight = 192956.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.023858 restraints weight = 135229.342| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24908 Z= 0.238 Angle : 0.666 10.973 33800 Z= 0.324 Chirality : 0.043 0.496 3929 Planarity : 0.004 0.053 4184 Dihedral : 7.602 112.004 4173 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 0.31 (0.16), residues: 2971 helix: 1.76 (0.14), residues: 1332 sheet: -1.44 (0.28), residues: 374 loop : -0.95 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 564 HIS 0.017 0.002 HIS C 253 PHE 0.033 0.002 PHE C 153 TYR 0.019 0.002 TYR D 324 ARG 0.005 0.001 ARG B 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 16) link_NAG-ASN : angle 3.88902 ( 48) link_ALPHA1-4 : bond 0.00847 ( 3) link_ALPHA1-4 : angle 3.25043 ( 9) link_ALPHA1-6 : bond 0.00473 ( 6) link_ALPHA1-6 : angle 1.83144 ( 18) link_BETA1-4 : bond 0.00548 ( 11) link_BETA1-4 : angle 1.91901 ( 33) link_ALPHA1-3 : bond 0.01028 ( 5) link_ALPHA1-3 : angle 2.25479 ( 15) hydrogen bonds : bond 0.03283 ( 1059) hydrogen bonds : angle 4.49102 ( 3099) SS BOND : bond 0.00342 ( 5) SS BOND : angle 1.34765 ( 10) link_BETA1-3 : bond 0.00781 ( 1) link_BETA1-3 : angle 3.01065 ( 3) covalent geometry : bond 0.00495 (24861) covalent geometry : angle 0.64176 (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 97 residues out of total 2600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 MET cc_start: 0.8933 (tpp) cc_final: 0.8638 (tmm) REVERT: A 565 MET cc_start: 0.8764 (mtm) cc_final: 0.8393 (mmp) REVERT: A 737 MET cc_start: 0.8217 (ptp) cc_final: 0.7833 (ptp) REVERT: A 794 MET cc_start: 0.9028 (ttt) cc_final: 0.8727 (ttt) REVERT: B 247 MET cc_start: 0.9220 (mmt) cc_final: 0.8353 (mmt) REVERT: C 234 MET cc_start: 0.9251 (mmp) cc_final: 0.8993 (mmm) REVERT: C 247 MET cc_start: 0.8715 (tpp) cc_final: 0.8385 (tpp) REVERT: C 664 MET cc_start: 0.9334 (mmt) cc_final: 0.8925 (mmt) REVERT: C 794 MET cc_start: 0.8898 (ppp) cc_final: 0.8498 (ppp) REVERT: D 247 MET cc_start: 0.9055 (mmp) cc_final: 0.8416 (mmp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3491 time to fit residues: 58.9256 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 : 3.709 ------------------------------------------------------------------------------- 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: 5.9990 chunk 257 optimal weight: 6.9990 chunk 292 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 283 optimal weight: 5.9990 chunk 241 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 294 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 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** D 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.032184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.023212 restraints weight = 325693.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.023786 restraints weight = 190282.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.024183 restraints weight = 132357.269| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24908 Z= 0.151 Angle : 0.591 11.206 33800 Z= 0.285 Chirality : 0.042 0.468 3929 Planarity : 0.003 0.046 4184 Dihedral : 7.549 114.144 4173 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 0.34 (0.16), residues: 2971 helix: 1.80 (0.14), residues: 1328 sheet: -1.37 (0.29), residues: 374 loop : -0.95 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 564 HIS 0.016 0.001 HIS C 253 PHE 0.025 0.001 PHE C 153 TYR 0.014 0.001 TYR B 462 ARG 0.004 0.000 ARG B 543 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 16) link_NAG-ASN : angle 3.78752 ( 48) link_ALPHA1-4 : bond 0.00913 ( 3) link_ALPHA1-4 : angle 3.23653 ( 9) link_ALPHA1-6 : bond 0.00455 ( 6) link_ALPHA1-6 : angle 1.76951 ( 18) link_BETA1-4 : bond 0.00495 ( 11) link_BETA1-4 : angle 1.81159 ( 33) link_ALPHA1-3 : bond 0.01037 ( 5) link_ALPHA1-3 : angle 2.14328 ( 15) hydrogen bonds : bond 0.03063 ( 1059) hydrogen bonds : angle 4.37560 ( 3099) SS BOND : bond 0.00277 ( 5) SS BOND : angle 1.11524 ( 10) link_BETA1-3 : bond 0.00801 ( 1) link_BETA1-3 : angle 3.08858 ( 3) covalent geometry : bond 0.00320 (24861) covalent geometry : angle 0.56551 (33664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7872.86 seconds wall clock time: 145 minutes 53.41 seconds (8753.41 seconds total)