Starting phenix.real_space_refine on Sun Jul 5 00:16:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f0o_28775/07_2026/8f0o_28775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0o_28775/07_2026/8f0o_28775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8f0o_28775/07_2026/8f0o_28775.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f0o_28775/07_2026/8f0o_28775.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f0o_28775/07_2026/8f0o_28775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0o_28775/07_2026/8f0o_28775.map" model { file = "/net/cci-nas-00/data/ceres_data/8f0o_28775/07_2026/8f0o_28775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0o_28775/07_2026/8f0o_28775.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.052 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 120 5.16 5 C 15416 2.51 5 N 3940 2.21 5 O 4554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24030 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5888 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 27, 'TRANS': 714} Chain breaks: 2 Chain: "B" Number of atoms: 5888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5888 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 27, 'TRANS': 714} Chain breaks: 2 Chain: "C" Number of atoms: 5888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5888 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 27, 'TRANS': 714} Chain breaks: 2 Chain: "D" Number of atoms: 5888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5888 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 27, 'TRANS': 714} Chain breaks: 2 Chain: "E" 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 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 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 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 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 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 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 chiralities: 5 Chain: "L" 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 chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.19, per 1000 atoms: 0.22 Number of scatterers: 24030 At special positions: 0 Unit cell: (127.2, 146.28, 181.26, 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 120 16.00 O 4554 8.00 N 3940 7.00 C 15416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 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 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 " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG 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 L 2 " - " BMA L 3 " NAG-ASN " NAG A1001 " - " ASN A 412 " " NAG B1001 " - " ASN B 412 " " NAG C1001 " - " ASN C 412 " " NAG D1001 " - " ASN D 412 " " NAG E 1 " - " ASN A 381 " " 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: 2.12 Conformation dependent library (CDL) restraints added in 999.6 milliseconds 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5536 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 28 sheets defined 46.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 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 112 through 125 Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 210 through 220 removed outlier: 4.258A pdb=" N LEU A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.638A pdb=" N LEU A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.582A pdb=" N ALA A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 Processing helix chain 'A' and resid 423 through 427 removed outlier: 4.466A pdb=" N ASP A 426 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 427 " --> pdb=" O ILE A 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 427' Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 461 through 475 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.712A pdb=" N ARG A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.781A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 581 Processing helix chain 'A' and resid 632 through 664 Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.625A pdb=" N LEU A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.534A pdb=" N LYS A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.553A pdb=" N ARG A 712 " --> pdb=" O PHE A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 730 removed outlier: 3.758A pdb=" N THR A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 772 through 789 removed outlier: 4.094A pdb=" N ASP A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 Processing helix chain 'A' and resid 822 through 839 Processing helix chain 'B' and resid 51 through 66 Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.552A pdb=" N LEU B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 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 195 Proline residue: B 192 - end of helix Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 220 removed outlier: 4.565A 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 260 through 264 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.814A pdb=" N ARG B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 302 removed outlier: 4.073A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 334 removed outlier: 3.921A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 454 through 457 removed outlier: 3.880A pdb=" N ASP B 457 " --> pdb=" O TYR B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 457' Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.967A pdb=" N LEU B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 508 removed outlier: 4.016A pdb=" N ASP B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 Processing helix chain 'B' and resid 562 through 580 Processing helix chain 'B' and resid 632 through 665 Processing helix chain 'B' and resid 670 through 677 Processing helix chain 'B' and resid 691 through 696 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 720 through 730 removed outlier: 3.678A pdb=" N ILE B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 780 through 789 removed outlier: 4.036A pdb=" N GLU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 796 Processing helix chain 'B' and resid 818 through 839 Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 152 through 168 Processing helix chain 'C' and resid 178 through 184 removed outlier: 3.764A pdb=" N LEU C 182 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 195 removed outlier: 3.712A pdb=" N ILE C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Proline residue: C 192 - end of helix Processing helix chain 'C' and resid 210 through 220 removed outlier: 4.299A pdb=" N LEU C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 231 through 245 Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 286 through 301 removed outlier: 3.775A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU C 299 " --> pdb=" O LYS C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.716A pdb=" N ALA C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.583A pdb=" N ARG C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 552 through 557 Processing helix chain 'C' and resid 560 through 578 Processing helix chain 'C' and resid 632 through 664 Processing helix chain 'C' and resid 669 through 676 removed outlier: 3.700A pdb=" N ASP C 673 " --> pdb=" O ASP C 669 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 674 " --> pdb=" O SER C 670 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.689A pdb=" N THR C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 712 removed outlier: 3.892A pdb=" N ARG C 712 " --> pdb=" O PHE C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 717 removed outlier: 3.891A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 729 removed outlier: 3.733A pdb=" N GLY C 724 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 725 " --> pdb=" O ASN C 721 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 747 removed outlier: 4.064A pdb=" N ILE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU C 743 " --> pdb=" O SER C 739 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 788 Processing helix chain 'C' and resid 789 through 797 Processing helix chain 'C' and resid 818 through 839 removed outlier: 3.711A pdb=" N ILE C 823 " --> pdb=" O ASN C 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 101 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 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 211 through 220 Processing helix chain 'D' and resid 231 through 244 Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.827A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.649A pdb=" N GLN D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 365 Processing helix chain 'D' and resid 415 through 419 removed outlier: 4.116A pdb=" N GLY D 419 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.570A pdb=" N GLU D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 520 through 527 Processing helix chain 'D' and resid 563 through 581 Processing helix chain 'D' and resid 632 through 665 Processing helix chain 'D' and resid 670 through 677 removed outlier: 3.659A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 removed outlier: 3.832A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 712 removed outlier: 3.796A 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 749 Processing helix chain 'D' and resid 776 through 782 removed outlier: 3.591A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 796 Processing helix chain 'D' and resid 821 through 839 removed outlier: 4.068A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 839 " --> pdb=" O VAL D 835 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 6.168A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 83 removed outlier: 7.261A pdb=" N GLY A 39 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 6.584A 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: 6.480A pdb=" N VAL A 172 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR A 171 " --> pdb=" O HIS A 225 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE A 227 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N PHE A 279 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N PHE A 256 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 479 through 480 removed outlier: 3.863A pdb=" N VAL A 514 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA A 515 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY A 765 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU A 517 " --> pdb=" O GLY A 763 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLY A 763 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 536 " --> pdb=" O LYS A 762 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.666A pdb=" N LEU A 536 " --> pdb=" O LYS A 762 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.714A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AA8, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.699A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS B 129 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU B 149 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N GLN B 131 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ARG B 384 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N SER B 148 " --> pdb=" O ARG B 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 203 removed outlier: 4.613A pdb=" N HIS B 225 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 254 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N PHE B 279 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N PHE B 256 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 389 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR B 404 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 391 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.874A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 373 " --> pdb=" O GLY B 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 432 through 433 Processing sheet with id=AB3, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB4, first strand: chain 'B' and resid 682 through 683 removed outlier: 7.447A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 75 through 83 removed outlier: 5.704A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N ALA C 105 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ARG C 37 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE C 107 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY C 39 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS C 129 " --> pdb=" O VAL C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 198 through 203 removed outlier: 6.711A pdb=" N VAL C 172 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N HIS C 225 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N PHE C 279 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N PHE C 256 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N MET C 276 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU C 389 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR C 404 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AB8, first strand: chain 'C' and resid 433 through 435 Processing sheet with id=AB9, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC1, first strand: chain 'C' and resid 513 through 519 removed outlier: 7.189A pdb=" N ALA C 515 " --> pdb=" O GLY C 767 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLY C 767 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU C 517 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 765 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY C 763 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR C 768 " --> pdb=" O ASP C 528 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP C 528 " --> pdb=" O THR C 768 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 513 through 519 removed outlier: 7.189A pdb=" N ALA C 515 " --> pdb=" O GLY C 767 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLY C 767 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU C 517 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 765 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY C 763 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 540 through 543 Processing sheet with id=AC4, first strand: chain 'C' and resid 682 through 683 removed outlier: 3.585A pdb=" N GLY C 683 " --> pdb=" O ALA C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 75 through 83 removed outlier: 10.065A pdb=" N ALA D 105 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ARG D 37 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N PHE D 107 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY D 39 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS D 129 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU D 149 " --> pdb=" O HIS D 129 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N GLN D 131 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ARG D 384 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N SER D 148 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 198 through 203 removed outlier: 6.238A pdb=" N VAL D 172 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N HIS D 225 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL D 226 " --> pdb=" O HIS D 253 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N PHE D 279 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE D 256 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU D 389 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR D 404 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.641A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 432 through 437 removed outlier: 6.274A pdb=" N LEU D 433 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ARG D 481 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL D 435 " --> pdb=" O ARG D 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 513 through 517 removed outlier: 4.358A pdb=" N ALA D 515 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY D 765 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 681 through 683 removed outlier: 6.802A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TYR D 733 " --> pdb=" O ARG D 543 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ARG D 543 " --> pdb=" O TYR D 733 " (cutoff:3.500A) 1025 hydrogen bonds defined for protein. 2994 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: 4.63 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7382 1.34 - 1.46: 4689 1.46 - 1.58: 12254 1.58 - 1.69: 5 1.69 - 1.81: 216 Bond restraints: 24546 Sorted by residual: bond pdb=" C3 BMA I 3 " pdb=" O3 BMA I 3 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.591 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C1 BMA K 3 " pdb=" C2 BMA K 3 " ideal model delta sigma weight residual 1.519 1.585 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C3 BMA G 3 " pdb=" O3 BMA G 3 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" C5 MAN I 5 " pdb=" O5 MAN I 5 " ideal model delta sigma weight residual 1.418 1.479 -0.061 2.00e-02 2.50e+03 9.40e+00 ... (remaining 24541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 32108 1.91 - 3.83: 902 3.83 - 5.74: 149 5.74 - 7.66: 58 7.66 - 9.57: 21 Bond angle restraints: 33238 Sorted by residual: angle pdb=" C GLY D 547 " pdb=" N THR D 548 " pdb=" CA THR D 548 " ideal model delta sigma weight residual 121.54 131.11 -9.57 1.91e+00 2.74e-01 2.51e+01 angle pdb=" C LYS A 379 " pdb=" N THR A 380 " pdb=" CA THR A 380 " ideal model delta sigma weight residual 121.54 130.60 -9.06 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C PRO A 667 " pdb=" N ILE A 668 " pdb=" CA ILE A 668 " ideal model delta sigma weight residual 121.97 129.96 -7.99 1.80e+00 3.09e-01 1.97e+01 angle pdb=" C PRO B 561 " pdb=" N ASP B 562 " pdb=" CA ASP B 562 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C ALA B 707 " pdb=" N PHE B 708 " pdb=" CA PHE B 708 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 ... (remaining 33233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 12679 17.78 - 35.55: 1423 35.55 - 53.33: 188 53.33 - 71.10: 46 71.10 - 88.88: 17 Dihedral angle restraints: 14353 sinusoidal: 5749 harmonic: 8604 Sorted by residual: dihedral pdb=" CA PRO B 442 " pdb=" C PRO B 442 " pdb=" N TYR B 443 " pdb=" CA TYR B 443 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ALA A 191 " pdb=" C ALA A 191 " pdb=" N PRO A 192 " pdb=" CA PRO A 192 " ideal model delta harmonic sigma weight residual 180.00 154.22 25.78 0 5.00e+00 4.00e-02 2.66e+01 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 -154.63 -25.37 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 14350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3791 0.136 - 0.273: 74 0.273 - 0.409: 4 0.409 - 0.545: 0 0.545 - 0.682: 1 Chirality restraints: 3870 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" CB ILE B 519 " pdb=" CA ILE B 519 " pdb=" CG1 ILE B 519 " pdb=" CG2 ILE B 519 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 381 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.71 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 3867 not shown) Planarity restraints: 4140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 275 " -0.034 2.00e-02 2.50e+03 3.28e-02 1.35e+01 pdb=" CG ASN A 275 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 275 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 275 " 0.030 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 191 " 0.058 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO D 192 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 192 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 192 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 441 " -0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO C 442 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 442 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 442 " -0.045 5.00e-02 4.00e+02 ... (remaining 4137 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6182 2.80 - 3.32: 20392 3.32 - 3.85: 40366 3.85 - 4.37: 43750 4.37 - 4.90: 75381 Nonbonded interactions: 186071 Sorted by model distance: nonbonded pdb=" O VAL C 716 " pdb=" OH TYR C 733 " model vdw 2.274 3.040 nonbonded pdb=" OE2 GLU C 738 " pdb=" OH TYR C 764 " model vdw 2.320 3.040 nonbonded pdb=" O ALA D 656 " pdb=" OG1 THR D 660 " model vdw 2.328 3.040 nonbonded pdb=" O ASP C 528 " pdb=" OG1 THR C 768 " model vdw 2.336 3.040 nonbonded pdb=" O VAL B 327 " pdb=" OG SER B 331 " model vdw 2.336 3.040 ... (remaining 186066 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 21.970 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 0.078 24587 Z= 0.234 Angle : 0.837 15.045 33358 Z= 0.416 Chirality : 0.053 0.682 3870 Planarity : 0.006 0.087 4128 Dihedral : 14.763 88.881 8808 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.13), residues: 2944 helix: -1.85 (0.11), residues: 1260 sheet: -0.52 (0.26), residues: 408 loop : -2.08 (0.15), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 712 TYR 0.027 0.002 TYR D 251 PHE 0.038 0.002 PHE A 642 TRP 0.020 0.002 TRP D 296 HIS 0.010 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.23 (24546) covalent geometry : angle 0.80268 / 0.41 (33238) SS BOND : bond 0.00140 / 0.07 ( 3) SS BOND : angle 0.68793 / 0.58 ( 6) hydrogen bonds : bond 0.14767 / 9.89 ( 1022) hydrogen bonds : angle 6.42485 / 4.46 ( 2994) link_ALPHA1-3 : bond 0.00977 / 0.60 ( 6) link_ALPHA1-3 : angle 3.33985 / 2.05 ( 18) link_ALPHA1-6 : bond 0.00588 / 0.36 ( 6) link_ALPHA1-6 : angle 4.38212 / 3.86 ( 18) link_BETA1-4 : bond 0.01453 / 1.06 ( 14) link_BETA1-4 : angle 4.30759 / 3.13 ( 42) link_NAG-ASN : bond 0.00757 / 0.46 ( 12) link_NAG-ASN : angle 4.11247 / 3.26 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.9082 (mtp) cc_final: 0.8813 (mtm) REVERT: A 709 MET cc_start: 0.9419 (mtt) cc_final: 0.9142 (mtm) REVERT: B 691 MET cc_start: 0.9035 (tmm) cc_final: 0.8537 (tmm) REVERT: C 50 MET cc_start: 0.7387 (mtm) cc_final: 0.7165 (mtp) REVERT: C 247 MET cc_start: 0.8334 (mtp) cc_final: 0.8042 (ttp) REVERT: C 501 MET cc_start: 0.9021 (mtm) cc_final: 0.8817 (mtt) REVERT: C 664 MET cc_start: 0.8777 (mmm) cc_final: 0.8479 (tmm) REVERT: C 705 MET cc_start: 0.9132 (mmt) cc_final: 0.8922 (mmt) REVERT: D 794 MET cc_start: 0.6711 (mtm) cc_final: 0.6355 (ptp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.6609 time to fit residues: 98.6537 Evaluate side-chains 100 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 98 GLN ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN D 81 GLN D 98 GLN D 677 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.043159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.032837 restraints weight = 217830.163| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 5.08 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24587 Z= 0.170 Angle : 0.594 9.720 33358 Z= 0.294 Chirality : 0.040 0.281 3870 Planarity : 0.004 0.056 4128 Dihedral : 4.650 24.283 3204 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.66 % Allowed : 5.61 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.15), residues: 2944 helix: 0.18 (0.14), residues: 1273 sheet: -0.41 (0.27), residues: 404 loop : -1.69 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 354 TYR 0.021 0.001 TYR D 571 PHE 0.025 0.001 PHE A 642 TRP 0.013 0.001 TRP A 368 HIS 0.004 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (24546) covalent geometry : angle 0.57573 / 0.29 (33238) SS BOND : bond 0.00067 / 0.03 ( 3) SS BOND : angle 0.31616 / 0.28 ( 6) hydrogen bonds : bond 0.03794 / 2.55 ( 1022) hydrogen bonds : angle 4.59735 / 3.22 ( 2994) link_ALPHA1-3 : bond 0.00849 / 0.61 ( 6) link_ALPHA1-3 : angle 2.80494 / 1.89 ( 18) link_ALPHA1-6 : bond 0.00596 / 0.36 ( 6) link_ALPHA1-6 : angle 1.61977 / 1.20 ( 18) link_BETA1-4 : bond 0.00819 / 0.56 ( 14) link_BETA1-4 : angle 2.46112 / 1.53 ( 42) link_NAG-ASN : bond 0.00294 / 0.23 ( 12) link_NAG-ASN : angle 2.85701 / 2.01 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7346 (mtp) cc_final: 0.6952 (mmt) REVERT: A 316 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7278 (ttm) REVERT: A 501 MET cc_start: 0.9237 (mtt) cc_final: 0.9036 (mtt) REVERT: A 534 MET cc_start: 0.8488 (mtp) cc_final: 0.8238 (mtm) REVERT: A 705 MET cc_start: 0.9249 (mtp) cc_final: 0.8991 (mtm) REVERT: A 709 MET cc_start: 0.9570 (mtt) cc_final: 0.9359 (mtp) REVERT: A 770 MET cc_start: 0.8273 (tpp) cc_final: 0.7983 (tpp) REVERT: B 565 MET cc_start: 0.9010 (tpt) cc_final: 0.8699 (mpp) REVERT: B 691 MET cc_start: 0.8956 (tmm) cc_final: 0.8456 (tmm) REVERT: B 793 MET cc_start: 0.8992 (tpt) cc_final: 0.8314 (pp-130) REVERT: B 794 MET cc_start: 0.6086 (tpt) cc_final: 0.3850 (tpt) REVERT: C 50 MET cc_start: 0.7530 (mtm) cc_final: 0.7262 (mtp) REVERT: C 247 MET cc_start: 0.8713 (mtp) cc_final: 0.8178 (ttp) REVERT: C 298 MET cc_start: 0.9058 (mmm) cc_final: 0.8809 (mpm) REVERT: C 664 MET cc_start: 0.8894 (mmm) cc_final: 0.8440 (tmm) REVERT: C 737 MET cc_start: 0.8382 (ppp) cc_final: 0.8103 (tmm) REVERT: D 247 MET cc_start: 0.9306 (mmt) cc_final: 0.8770 (mmt) REVERT: D 565 MET cc_start: 0.8161 (mpp) cc_final: 0.7930 (mmm) REVERT: D 709 MET cc_start: 0.8736 (ppp) cc_final: 0.8390 (ppp) outliers start: 17 outliers final: 2 residues processed: 106 average time/residue: 0.7336 time to fit residues: 88.8133 Evaluate side-chains 103 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 534 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 144 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 253 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 242 optimal weight: 1.9990 chunk 276 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 336 GLN B 497 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN C 98 GLN C 196 ASN C 328 HIS D 203 GLN D 367 HIS D 497 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.041896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.032008 restraints weight = 227491.455| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 4.58 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 24587 Z= 0.374 Angle : 0.799 8.768 33358 Z= 0.396 Chirality : 0.045 0.256 3870 Planarity : 0.005 0.049 4128 Dihedral : 5.016 27.778 3204 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.97 % Allowed : 11.22 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.15), residues: 2944 helix: 0.61 (0.14), residues: 1282 sheet: -0.43 (0.27), residues: 392 loop : -1.74 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 354 TYR 0.038 0.002 TYR A 774 PHE 0.032 0.002 PHE B 42 TRP 0.025 0.002 TRP D 296 HIS 0.010 0.002 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.37 (24546) covalent geometry : angle 0.78465 / 0.39 (33238) SS BOND : bond 0.00043 / 0.02 ( 3) SS BOND : angle 0.48049 / 0.37 ( 6) hydrogen bonds : bond 0.04402 / 2.92 ( 1022) hydrogen bonds : angle 4.90613 / 3.45 ( 2994) link_ALPHA1-3 : bond 0.00867 / 0.65 ( 6) link_ALPHA1-3 : angle 2.69725 / 1.88 ( 18) link_ALPHA1-6 : bond 0.00490 / 0.27 ( 6) link_ALPHA1-6 : angle 1.91025 / 1.31 ( 18) link_BETA1-4 : bond 0.00886 / 0.57 ( 14) link_BETA1-4 : angle 2.29201 / 1.44 ( 42) link_NAG-ASN : bond 0.00832 / 0.63 ( 12) link_NAG-ASN : angle 3.38565 / 2.31 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8959 (tpp) cc_final: 0.8729 (mmt) REVERT: A 316 MET cc_start: 0.8132 (ttp) cc_final: 0.7512 (mtm) REVERT: A 360 MET cc_start: 0.9025 (mmm) cc_final: 0.8823 (mmm) REVERT: A 501 MET cc_start: 0.9118 (mtt) cc_final: 0.8915 (mtt) REVERT: B 691 MET cc_start: 0.8874 (tmm) cc_final: 0.8308 (tmm) REVERT: B 794 MET cc_start: 0.6574 (tpt) cc_final: 0.6150 (tpt) REVERT: C 81 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8182 (mp10) REVERT: C 247 MET cc_start: 0.8159 (mtp) cc_final: 0.7819 (mtp) REVERT: C 298 MET cc_start: 0.8973 (mmm) cc_final: 0.8743 (tpp) REVERT: C 737 MET cc_start: 0.8535 (ppp) cc_final: 0.8310 (pp-130) REVERT: D 323 MET cc_start: 0.8833 (tpp) cc_final: 0.8587 (tpt) REVERT: D 413 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8290 (mmm) REVERT: D 501 MET cc_start: 0.7835 (mmm) cc_final: 0.7556 (mpt) outliers start: 25 outliers final: 6 residues processed: 110 average time/residue: 0.7578 time to fit residues: 95.1505 Evaluate side-chains 106 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 796 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 287 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 294 optimal weight: 0.0000 chunk 206 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.043044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.033100 restraints weight = 222444.953| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 4.71 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24587 Z= 0.117 Angle : 0.578 10.572 33358 Z= 0.281 Chirality : 0.040 0.266 3870 Planarity : 0.003 0.040 4128 Dihedral : 4.593 24.872 3204 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.93 % Allowed : 13.04 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2944 helix: 1.09 (0.15), residues: 1282 sheet: -0.29 (0.28), residues: 369 loop : -1.55 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 354 TYR 0.023 0.001 TYR D 571 PHE 0.020 0.001 PHE A 642 TRP 0.013 0.001 TRP C 296 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (24546) covalent geometry : angle 0.56316 / 0.28 (33238) SS BOND : bond 0.00095 / 0.05 ( 3) SS BOND : angle 0.26007 / 0.24 ( 6) hydrogen bonds : bond 0.03440 / 2.30 ( 1022) hydrogen bonds : angle 4.36819 / 3.06 ( 2994) link_ALPHA1-3 : bond 0.00850 / 0.61 ( 6) link_ALPHA1-3 : angle 2.53955 / 1.74 ( 18) link_ALPHA1-6 : bond 0.00578 / 0.34 ( 6) link_ALPHA1-6 : angle 1.49132 / 1.08 ( 18) link_BETA1-4 : bond 0.00753 / 0.52 ( 14) link_BETA1-4 : angle 2.18777 / 1.37 ( 42) link_NAG-ASN : bond 0.00284 / 0.21 ( 12) link_NAG-ASN : angle 2.68966 / 1.81 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8863 (tpp) cc_final: 0.8553 (tpp) REVERT: A 316 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7286 (mtm) REVERT: A 360 MET cc_start: 0.8893 (mmm) cc_final: 0.8656 (mmm) REVERT: A 501 MET cc_start: 0.9049 (mtt) cc_final: 0.8812 (mtt) REVERT: B 360 MET cc_start: 0.9242 (tpt) cc_final: 0.9024 (ttm) REVERT: B 691 MET cc_start: 0.8866 (tmm) cc_final: 0.8283 (tmm) REVERT: B 737 MET cc_start: 0.6348 (tpt) cc_final: 0.6136 (tpt) REVERT: B 794 MET cc_start: 0.6282 (tpt) cc_final: 0.5861 (tpt) REVERT: C 247 MET cc_start: 0.8059 (mtp) cc_final: 0.7660 (ttp) REVERT: C 248 MET cc_start: 0.8698 (mmm) cc_final: 0.8469 (mmm) REVERT: D 323 MET cc_start: 0.8722 (tpp) cc_final: 0.8484 (tpt) REVERT: D 413 MET cc_start: 0.8544 (mmm) cc_final: 0.8289 (mmm) REVERT: D 565 MET cc_start: 0.7862 (mpp) cc_final: 0.7627 (mmm) REVERT: D 737 MET cc_start: 0.8170 (ppp) cc_final: 0.7319 (ppp) outliers start: 24 outliers final: 4 residues processed: 110 average time/residue: 0.7231 time to fit residues: 91.3820 Evaluate side-chains 102 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 86 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 133 optimal weight: 8.9990 chunk 116 optimal weight: 20.0000 chunk 241 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 81 GLN C 367 HIS C 508 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.046936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.029830 restraints weight = 201637.833| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 7.00 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 24587 Z= 0.364 Angle : 0.791 10.613 33358 Z= 0.387 Chirality : 0.044 0.255 3870 Planarity : 0.004 0.052 4128 Dihedral : 4.970 27.390 3204 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.70 % Allowed : 15.25 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2944 helix: 0.86 (0.14), residues: 1278 sheet: -0.57 (0.28), residues: 367 loop : -1.70 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 431 TYR 0.036 0.002 TYR A 774 PHE 0.029 0.002 PHE C 735 TRP 0.017 0.002 TRP D 564 HIS 0.009 0.002 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00773 / 0.36 (24546) covalent geometry : angle 0.77785 / 0.38 (33238) SS BOND : bond 0.00052 / 0.03 ( 3) SS BOND : angle 0.43878 / 0.33 ( 6) hydrogen bonds : bond 0.04226 / 2.81 ( 1022) hydrogen bonds : angle 4.86091 / 3.43 ( 2994) link_ALPHA1-3 : bond 0.00867 / 0.64 ( 6) link_ALPHA1-3 : angle 2.62793 / 1.84 ( 18) link_ALPHA1-6 : bond 0.00448 / 0.24 ( 6) link_ALPHA1-6 : angle 1.91859 / 1.33 ( 18) link_BETA1-4 : bond 0.00879 / 0.57 ( 14) link_BETA1-4 : angle 2.22300 / 1.40 ( 42) link_NAG-ASN : bond 0.00733 / 0.56 ( 12) link_NAG-ASN : angle 3.23012 / 2.21 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 98 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8965 (tpp) cc_final: 0.8690 (tpp) REVERT: A 360 MET cc_start: 0.9066 (mmm) cc_final: 0.8797 (mmm) REVERT: A 793 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8753 (ppp) REVERT: A 794 MET cc_start: 0.9006 (mmm) cc_final: 0.8552 (mmm) REVERT: B 691 MET cc_start: 0.9152 (tmm) cc_final: 0.8602 (tmm) REVERT: B 737 MET cc_start: 0.6784 (tpt) cc_final: 0.6413 (tpt) REVERT: B 794 MET cc_start: 0.7149 (tpt) cc_final: 0.6934 (tpt) REVERT: C 81 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: C 664 MET cc_start: 0.9182 (tpt) cc_final: 0.8583 (tmm) REVERT: C 735 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8296 (t80) REVERT: C 794 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.9075 (mmm) REVERT: D 145 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8337 (t80) REVERT: D 413 MET cc_start: 0.8595 (mmm) cc_final: 0.8206 (mmm) REVERT: D 438 ILE cc_start: 0.4592 (OUTLIER) cc_final: 0.4299 (tp) REVERT: D 541 LEU cc_start: 0.9699 (OUTLIER) cc_final: 0.9481 (tm) REVERT: D 664 MET cc_start: 0.9278 (mmm) cc_final: 0.9062 (mmm) REVERT: D 737 MET cc_start: 0.7910 (ppp) cc_final: 0.6693 (ppp) outliers start: 44 outliers final: 9 residues processed: 131 average time/residue: 0.6774 time to fit residues: 102.4365 Evaluate side-chains 114 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 794 MET Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 541 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 258 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 276 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.047352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.030468 restraints weight = 201153.252| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 7.03 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24587 Z= 0.183 Angle : 0.650 11.252 33358 Z= 0.311 Chirality : 0.041 0.262 3870 Planarity : 0.003 0.040 4128 Dihedral : 4.728 23.881 3204 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.47 % Allowed : 16.80 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 2944 helix: 1.14 (0.15), residues: 1281 sheet: -0.44 (0.28), residues: 356 loop : -1.59 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 431 TYR 0.020 0.001 TYR D 571 PHE 0.028 0.001 PHE C 735 TRP 0.014 0.001 TRP D 564 HIS 0.004 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (24546) covalent geometry : angle 0.63603 / 0.31 (33238) SS BOND : bond 0.00097 / 0.05 ( 3) SS BOND : angle 0.23485 / 0.20 ( 6) hydrogen bonds : bond 0.03597 / 2.41 ( 1022) hydrogen bonds : angle 4.49076 / 3.15 ( 2994) link_ALPHA1-3 : bond 0.00860 / 0.61 ( 6) link_ALPHA1-3 : angle 2.55258 / 1.75 ( 18) link_ALPHA1-6 : bond 0.00498 / 0.29 ( 6) link_ALPHA1-6 : angle 1.61225 / 1.16 ( 18) link_BETA1-4 : bond 0.00784 / 0.53 ( 14) link_BETA1-4 : angle 2.16861 / 1.36 ( 42) link_NAG-ASN : bond 0.00370 / 0.27 ( 12) link_NAG-ASN : angle 2.82084 / 1.89 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 98 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8889 (tpp) cc_final: 0.8599 (tpp) REVERT: A 316 MET cc_start: 0.8069 (ttm) cc_final: 0.7168 (mtm) REVERT: A 360 MET cc_start: 0.9021 (mmm) cc_final: 0.8765 (mmm) REVERT: A 501 MET cc_start: 0.9232 (mtt) cc_final: 0.9031 (mtt) REVERT: A 691 MET cc_start: 0.8761 (ptm) cc_final: 0.8181 (ptt) REVERT: B 360 MET cc_start: 0.9121 (tpt) cc_final: 0.8897 (ttm) REVERT: B 691 MET cc_start: 0.9137 (tmm) cc_final: 0.8590 (tmm) REVERT: B 737 MET cc_start: 0.6745 (tpt) cc_final: 0.6329 (tpt) REVERT: B 794 MET cc_start: 0.7072 (tpt) cc_final: 0.6849 (tpt) REVERT: C 664 MET cc_start: 0.9178 (tpt) cc_final: 0.8583 (tmm) REVERT: C 735 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8237 (t80) REVERT: C 794 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.9025 (mmm) REVERT: D 145 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8300 (t80) REVERT: D 413 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8208 (mmm) REVERT: D 438 ILE cc_start: 0.4672 (OUTLIER) cc_final: 0.4243 (tp) REVERT: D 541 LEU cc_start: 0.9748 (OUTLIER) cc_final: 0.9542 (tm) REVERT: D 737 MET cc_start: 0.7901 (ppp) cc_final: 0.6481 (ppp) outliers start: 38 outliers final: 14 residues processed: 128 average time/residue: 0.6518 time to fit residues: 97.0680 Evaluate side-chains 117 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 794 MET Chi-restraints excluded: chain C residue 819 ASN Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 244 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 238 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 241 GLN C 81 GLN ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.042595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.032621 restraints weight = 221336.280| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 4.68 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24587 Z= 0.131 Angle : 0.610 12.084 33358 Z= 0.289 Chirality : 0.040 0.260 3870 Planarity : 0.003 0.038 4128 Dihedral : 4.485 21.285 3204 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.39 % Allowed : 17.38 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2944 helix: 1.37 (0.15), residues: 1281 sheet: -0.30 (0.29), residues: 348 loop : -1.48 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 354 TYR 0.031 0.001 TYR D 571 PHE 0.020 0.001 PHE C 735 TRP 0.019 0.001 TRP D 564 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (24546) covalent geometry : angle 0.59679 / 0.29 (33238) SS BOND : bond 0.00110 / 0.05 ( 3) SS BOND : angle 0.23466 / 0.21 ( 6) hydrogen bonds : bond 0.03317 / 2.21 ( 1022) hydrogen bonds : angle 4.26491 / 2.99 ( 2994) link_ALPHA1-3 : bond 0.00860 / 0.61 ( 6) link_ALPHA1-3 : angle 2.43092 / 1.65 ( 18) link_ALPHA1-6 : bond 0.00484 / 0.29 ( 6) link_ALPHA1-6 : angle 1.51797 / 1.11 ( 18) link_BETA1-4 : bond 0.00731 / 0.50 ( 14) link_BETA1-4 : angle 2.10795 / 1.32 ( 42) link_NAG-ASN : bond 0.00246 / 0.19 ( 12) link_NAG-ASN : angle 2.64132 / 1.81 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8707 (tpp) cc_final: 0.8443 (tpp) REVERT: A 316 MET cc_start: 0.7677 (ttm) cc_final: 0.7373 (mtm) REVERT: A 691 MET cc_start: 0.8664 (ptm) cc_final: 0.8189 (ptt) REVERT: A 793 MET cc_start: 0.8841 (ptt) cc_final: 0.8600 (pp-130) REVERT: B 565 MET cc_start: 0.9042 (tpp) cc_final: 0.8650 (mpp) REVERT: B 691 MET cc_start: 0.8827 (tmm) cc_final: 0.8309 (tmm) REVERT: B 794 MET cc_start: 0.6493 (tpt) cc_final: 0.6211 (tpt) REVERT: C 81 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8193 (mp10) REVERT: C 664 MET cc_start: 0.8713 (tpt) cc_final: 0.8273 (tmm) REVERT: C 735 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8319 (t80) REVERT: C 793 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8398 (ppp) REVERT: D 145 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8058 (t80) REVERT: D 413 MET cc_start: 0.8395 (mmm) cc_final: 0.8121 (mmm) REVERT: D 438 ILE cc_start: 0.4644 (OUTLIER) cc_final: 0.4162 (tp) REVERT: D 737 MET cc_start: 0.8242 (ppp) cc_final: 0.6719 (ppp) outliers start: 36 outliers final: 13 residues processed: 127 average time/residue: 0.6217 time to fit residues: 91.3688 Evaluate side-chains 115 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 819 ASN Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 35 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 196 optimal weight: 7.9990 chunk 113 optimal weight: 30.0000 chunk 145 optimal weight: 10.0000 chunk 189 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 81 GLN ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.047200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.030232 restraints weight = 201527.444| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 7.04 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24587 Z= 0.253 Angle : 0.724 13.053 33358 Z= 0.343 Chirality : 0.042 0.253 3870 Planarity : 0.003 0.044 4128 Dihedral : 4.626 22.998 3204 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.35 % Allowed : 18.34 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2944 helix: 1.26 (0.15), residues: 1281 sheet: -0.48 (0.28), residues: 369 loop : -1.52 (0.18), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 431 TYR 0.026 0.001 TYR D 571 PHE 0.023 0.002 PHE B 166 TRP 0.022 0.002 TRP A 640 HIS 0.006 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 (24546) covalent geometry : angle 0.71115 / 0.34 (33238) SS BOND : bond 0.00083 / 0.04 ( 3) SS BOND : angle 0.33050 / 0.26 ( 6) hydrogen bonds : bond 0.03649 / 2.42 ( 1022) hydrogen bonds : angle 4.47242 / 3.15 ( 2994) link_ALPHA1-3 : bond 0.00813 / 0.59 ( 6) link_ALPHA1-3 : angle 2.47252 / 1.70 ( 18) link_ALPHA1-6 : bond 0.00433 / 0.25 ( 6) link_ALPHA1-6 : angle 1.70836 / 1.22 ( 18) link_BETA1-4 : bond 0.00796 / 0.52 ( 14) link_BETA1-4 : angle 2.13472 / 1.34 ( 42) link_NAG-ASN : bond 0.00519 / 0.39 ( 12) link_NAG-ASN : angle 2.91608 / 2.00 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8904 (tpp) cc_final: 0.8632 (tpp) REVERT: A 316 MET cc_start: 0.8172 (ttm) cc_final: 0.7157 (mtm) REVERT: A 685 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8696 (m) REVERT: A 691 MET cc_start: 0.8834 (ptm) cc_final: 0.8241 (ptt) REVERT: B 691 MET cc_start: 0.9149 (tmm) cc_final: 0.8600 (tmm) REVERT: B 794 MET cc_start: 0.7038 (tpt) cc_final: 0.6814 (tpt) REVERT: C 316 MET cc_start: 0.8950 (mmm) cc_final: 0.8640 (mpp) REVERT: C 664 MET cc_start: 0.9163 (tpt) cc_final: 0.8467 (tmm) REVERT: C 792 HIS cc_start: 0.9260 (OUTLIER) cc_final: 0.9034 (t-170) REVERT: C 793 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8754 (pp-130) REVERT: C 794 MET cc_start: 0.9040 (mmm) cc_final: 0.8582 (mmm) REVERT: D 145 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8664 (t80) REVERT: D 413 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8191 (mmm) REVERT: D 438 ILE cc_start: 0.4598 (OUTLIER) cc_final: 0.4121 (tp) REVERT: D 737 MET cc_start: 0.7882 (ppp) cc_final: 0.6952 (ppp) outliers start: 35 outliers final: 17 residues processed: 125 average time/residue: 0.6685 time to fit residues: 96.6730 Evaluate side-chains 119 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 340 MET Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 792 HIS Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 819 ASN Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 6 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 204 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 151 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 GLN D 98 GLN ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.042524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.032605 restraints weight = 221579.619| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 4.66 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24587 Z= 0.142 Angle : 0.664 13.199 33358 Z= 0.310 Chirality : 0.041 0.258 3870 Planarity : 0.003 0.038 4128 Dihedral : 4.514 20.434 3204 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.85 % Allowed : 19.04 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.16), residues: 2944 helix: 1.38 (0.15), residues: 1287 sheet: -0.16 (0.29), residues: 347 loop : -1.48 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 300 TYR 0.027 0.001 TYR D 571 PHE 0.029 0.001 PHE B 166 TRP 0.024 0.001 TRP A 640 HIS 0.003 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (24546) covalent geometry : angle 0.65136 / 0.31 (33238) SS BOND : bond 0.00120 / 0.06 ( 3) SS BOND : angle 0.23304 / 0.21 ( 6) hydrogen bonds : bond 0.03333 / 2.22 ( 1022) hydrogen bonds : angle 4.25642 / 2.98 ( 2994) link_ALPHA1-3 : bond 0.00768 / 0.53 ( 6) link_ALPHA1-3 : angle 2.38566 / 1.61 ( 18) link_ALPHA1-6 : bond 0.00473 / 0.28 ( 6) link_ALPHA1-6 : angle 1.53209 / 1.13 ( 18) link_BETA1-4 : bond 0.00766 / 0.53 ( 14) link_BETA1-4 : angle 2.10432 / 1.33 ( 42) link_NAG-ASN : bond 0.00314 / 0.22 ( 12) link_NAG-ASN : angle 2.67600 / 1.82 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8755 (tpp) cc_final: 0.8469 (tpp) REVERT: A 316 MET cc_start: 0.7809 (ttm) cc_final: 0.7416 (mtm) REVERT: A 685 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8763 (m) REVERT: A 691 MET cc_start: 0.8732 (ptm) cc_final: 0.8215 (ptt) REVERT: A 792 HIS cc_start: 0.8814 (OUTLIER) cc_final: 0.8606 (t-170) REVERT: A 793 MET cc_start: 0.8849 (ptt) cc_final: 0.8619 (pp-130) REVERT: B 565 MET cc_start: 0.9034 (tpp) cc_final: 0.8697 (mpp) REVERT: B 691 MET cc_start: 0.8871 (tmm) cc_final: 0.8347 (tmm) REVERT: B 794 MET cc_start: 0.6455 (tpt) cc_final: 0.6208 (tpt) REVERT: C 316 MET cc_start: 0.8666 (mmm) cc_final: 0.8462 (mpp) REVERT: C 664 MET cc_start: 0.8692 (tpt) cc_final: 0.8190 (tmm) REVERT: C 793 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8378 (pp-130) REVERT: C 794 MET cc_start: 0.8390 (mmm) cc_final: 0.7920 (mmm) REVERT: D 50 MET cc_start: 0.7913 (ttp) cc_final: 0.7537 (tmm) REVERT: D 145 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8385 (t80) REVERT: D 360 MET cc_start: 0.9126 (mtt) cc_final: 0.8642 (mtt) REVERT: D 413 MET cc_start: 0.8433 (mmm) cc_final: 0.8150 (mmm) REVERT: D 438 ILE cc_start: 0.4704 (OUTLIER) cc_final: 0.4194 (tp) REVERT: D 664 MET cc_start: 0.8857 (mmm) cc_final: 0.8602 (mmt) outliers start: 22 outliers final: 13 residues processed: 116 average time/residue: 0.7113 time to fit residues: 94.4971 Evaluate side-chains 114 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 819 ASN Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 213 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 chunk 118 optimal weight: 0.1980 chunk 68 optimal weight: 4.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 328 HIS D 677 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.042436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.032482 restraints weight = 221917.304| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 4.72 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24587 Z= 0.158 Angle : 0.691 13.434 33358 Z= 0.321 Chirality : 0.041 0.256 3870 Planarity : 0.003 0.038 4128 Dihedral : 4.503 20.355 3204 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.85 % Allowed : 19.12 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.16), residues: 2944 helix: 1.43 (0.15), residues: 1287 sheet: -0.25 (0.29), residues: 359 loop : -1.46 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 431 TYR 0.028 0.001 TYR D 571 PHE 0.028 0.001 PHE B 166 TRP 0.050 0.001 TRP D 706 HIS 0.004 0.001 HIS D 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (24546) covalent geometry : angle 0.67926 / 0.32 (33238) SS BOND : bond 0.00088 / 0.04 ( 3) SS BOND : angle 0.22105 / 0.19 ( 6) hydrogen bonds : bond 0.03346 / 2.23 ( 1022) hydrogen bonds : angle 4.25781 / 2.99 ( 2994) link_ALPHA1-3 : bond 0.00811 / 0.58 ( 6) link_ALPHA1-3 : angle 2.37071 / 1.61 ( 18) link_ALPHA1-6 : bond 0.00456 / 0.27 ( 6) link_ALPHA1-6 : angle 1.55383 / 1.14 ( 18) link_BETA1-4 : bond 0.00748 / 0.51 ( 14) link_BETA1-4 : angle 2.10591 / 1.32 ( 42) link_NAG-ASN : bond 0.00382 / 0.25 ( 12) link_NAG-ASN : angle 2.63154 / 1.82 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8848 (tpp) cc_final: 0.8537 (tpp) REVERT: A 316 MET cc_start: 0.7989 (ttm) cc_final: 0.7506 (mtm) REVERT: A 534 MET cc_start: 0.7992 (mtm) cc_final: 0.7653 (mtm) REVERT: A 685 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8641 (m) REVERT: A 691 MET cc_start: 0.8778 (ptm) cc_final: 0.8206 (ptt) REVERT: A 793 MET cc_start: 0.8923 (ptt) cc_final: 0.8675 (pp-130) REVERT: B 565 MET cc_start: 0.9024 (tpp) cc_final: 0.8703 (mpp) REVERT: B 691 MET cc_start: 0.8954 (tmm) cc_final: 0.8423 (tmm) REVERT: B 794 MET cc_start: 0.6512 (tpt) cc_final: 0.6276 (tpt) REVERT: C 664 MET cc_start: 0.8799 (tpt) cc_final: 0.8239 (tmm) REVERT: C 793 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8543 (pp-130) REVERT: D 50 MET cc_start: 0.7952 (ttp) cc_final: 0.7588 (tmm) REVERT: D 145 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8593 (t80) REVERT: D 360 MET cc_start: 0.9249 (mtt) cc_final: 0.8843 (mtt) REVERT: D 413 MET cc_start: 0.8469 (mmm) cc_final: 0.8174 (mmm) REVERT: D 438 ILE cc_start: 0.4662 (OUTLIER) cc_final: 0.4139 (tp) REVERT: D 770 MET cc_start: 0.5352 (mpp) cc_final: 0.4661 (pmm) outliers start: 22 outliers final: 14 residues processed: 117 average time/residue: 0.7265 time to fit residues: 97.4087 Evaluate side-chains 114 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 820 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 819 ASN Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 64 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 278 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 168 optimal weight: 0.0470 chunk 169 optimal weight: 4.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.042909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.033086 restraints weight = 221986.749| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 4.62 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 24587 Z= 0.106 Angle : 0.658 13.178 33358 Z= 0.305 Chirality : 0.040 0.256 3870 Planarity : 0.003 0.039 4128 Dihedral : 4.365 19.792 3204 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.93 % Allowed : 19.08 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2944 helix: 1.57 (0.15), residues: 1284 sheet: 0.02 (0.29), residues: 359 loop : -1.39 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 220 TYR 0.028 0.001 TYR D 571 PHE 0.023 0.001 PHE B 166 TRP 0.052 0.001 TRP A 640 HIS 0.006 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (24546) covalent geometry : angle 0.64675 / 0.30 (33238) SS BOND : bond 0.00129 / 0.06 ( 3) SS BOND : angle 0.28016 / 0.26 ( 6) hydrogen bonds : bond 0.03105 / 2.07 ( 1022) hydrogen bonds : angle 4.10038 / 2.87 ( 2994) link_ALPHA1-3 : bond 0.00889 / 0.63 ( 6) link_ALPHA1-3 : angle 2.29982 / 1.56 ( 18) link_ALPHA1-6 : bond 0.00523 / 0.32 ( 6) link_ALPHA1-6 : angle 1.43951 / 1.08 ( 18) link_BETA1-4 : bond 0.00682 / 0.49 ( 14) link_BETA1-4 : angle 2.10149 / 1.33 ( 42) link_NAG-ASN : bond 0.00262 / 0.21 ( 12) link_NAG-ASN : angle 2.37305 / 1.69 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6052.88 seconds wall clock time: 104 minutes 48.59 seconds (6288.59 seconds total)