Starting phenix.real_space_refine on Mon Aug 25 01:38:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f0o_28775/08_2025/8f0o_28775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0o_28775/08_2025/8f0o_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 { model { file = "/net/cci-nas-00/data/ceres_data/8f0o_28775/08_2025/8f0o_28775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0o_28775/08_2025/8f0o_28775.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f0o_28775/08_2025/8f0o_28775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0o_28775/08_2025/8f0o_28775.map" } 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-2.0-5787/lib/python3.9/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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.31, 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: 1.91 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.90 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: 3.37 Time building geometry restraints manager: 2.49 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 - 23.58: 13955 23.58 - 47.16: 939 47.16 - 70.74: 101 70.74 - 94.32: 67 94.32 - 117.89: 53 Dihedral angle restraints: 15115 sinusoidal: 6511 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 15112 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: 0.02 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: 4.550 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.590 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 17.633 117.895 9570 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 aren 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 covalent geometry : bond 0.00461 (24546) covalent geometry : angle 0.80268 (33238) SS BOND : bond 0.00140 ( 3) SS BOND : angle 0.68793 ( 6) hydrogen bonds : bond 0.14767 ( 1022) hydrogen bonds : angle 6.42485 ( 2994) link_ALPHA1-3 : bond 0.00977 ( 6) link_ALPHA1-3 : angle 3.33985 ( 18) link_ALPHA1-6 : bond 0.00588 ( 6) link_ALPHA1-6 : angle 4.38212 ( 18) link_BETA1-4 : bond 0.01453 ( 14) link_BETA1-4 : angle 4.30759 ( 42) link_NAG-ASN : bond 0.00757 ( 12) link_NAG-ASN : angle 4.11247 ( 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 : 1.006 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: 0.6569 time to fit residues: 97.8057 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 : 0.939 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3754 r_free = 0.3754 target = 0.043130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.032634 restraints weight = 222004.350| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 5.18 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24587 Z= 0.172 Angle : 0.623 10.542 33358 Z= 0.302 Chirality : 0.041 0.237 3870 Planarity : 0.004 0.055 4128 Dihedral : 13.271 110.219 3966 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.58 % Allowed : 5.73 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.15), residues: 2944 helix: 0.21 (0.14), residues: 1267 sheet: -0.42 (0.27), residues: 404 loop : -1.67 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 354 TYR 0.022 0.001 TYR D 571 PHE 0.025 0.001 PHE A 642 TRP 0.013 0.001 TRP D 564 HIS 0.004 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00367 (24546) covalent geometry : angle 0.60031 (33238) SS BOND : bond 0.00057 ( 3) SS BOND : angle 0.29646 ( 6) hydrogen bonds : bond 0.03729 ( 1022) hydrogen bonds : angle 4.57564 ( 2994) link_ALPHA1-3 : bond 0.01310 ( 6) link_ALPHA1-3 : angle 3.75229 ( 18) link_ALPHA1-6 : bond 0.00835 ( 6) link_ALPHA1-6 : angle 2.29818 ( 18) link_BETA1-4 : bond 0.00782 ( 14) link_BETA1-4 : angle 2.74069 ( 42) link_NAG-ASN : bond 0.00327 ( 12) link_NAG-ASN : angle 2.89511 ( 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 116 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7325 (mtp) cc_final: 0.6952 (mmt) REVERT: A 316 MET cc_start: 0.7907 (ttp) cc_final: 0.7257 (ttm) REVERT: A 501 MET cc_start: 0.9274 (mtt) cc_final: 0.9042 (mtt) REVERT: A 705 MET cc_start: 0.9232 (mtp) cc_final: 0.8980 (mtm) REVERT: A 709 MET cc_start: 0.9558 (mtm) cc_final: 0.9355 (mtp) REVERT: B 565 MET cc_start: 0.9010 (tpt) cc_final: 0.8697 (mpp) REVERT: B 691 MET cc_start: 0.8914 (tmm) cc_final: 0.8402 (tmm) REVERT: B 794 MET cc_start: 0.6095 (tpt) cc_final: 0.5516 (tpt) REVERT: C 50 MET cc_start: 0.7525 (mtm) cc_final: 0.7230 (mtp) REVERT: C 247 MET cc_start: 0.8590 (mtp) cc_final: 0.8254 (mtp) REVERT: C 298 MET cc_start: 0.9069 (mmm) cc_final: 0.8809 (mpm) REVERT: C 664 MET cc_start: 0.8881 (mmm) cc_final: 0.8435 (tmm) REVERT: C 737 MET cc_start: 0.8379 (ppp) cc_final: 0.8096 (tmm) REVERT: D 247 MET cc_start: 0.9274 (mmt) cc_final: 0.8799 (mmt) REVERT: D 501 MET cc_start: 0.7875 (mmp) cc_final: 0.7658 (mmp) REVERT: D 565 MET cc_start: 0.8167 (mpp) cc_final: 0.7935 (mmm) outliers start: 15 outliers final: 2 residues processed: 106 average time/residue: 0.6577 time to fit residues: 79.6951 Evaluate side-chains 102 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 208 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 242 optimal weight: 0.9980 chunk 276 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 200 optimal weight: 0.0980 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 336 GLN B 497 GLN C 81 GLN C 98 GLN C 196 ASN C 328 HIS D 367 HIS D 497 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.042111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.032176 restraints weight = 226468.636| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 4.65 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 24587 Z= 0.332 Angle : 0.769 8.920 33358 Z= 0.375 Chirality : 0.044 0.286 3870 Planarity : 0.004 0.047 4128 Dihedral : 11.597 99.896 3966 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.97 % Allowed : 10.87 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.16), residues: 2944 helix: 0.73 (0.14), residues: 1282 sheet: -0.38 (0.27), residues: 392 loop : -1.71 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 354 TYR 0.034 0.002 TYR A 774 PHE 0.029 0.002 PHE B 166 TRP 0.022 0.002 TRP D 296 HIS 0.008 0.002 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00704 (24546) covalent geometry : angle 0.74890 (33238) SS BOND : bond 0.00038 ( 3) SS BOND : angle 0.47463 ( 6) hydrogen bonds : bond 0.04267 ( 1022) hydrogen bonds : angle 4.77369 ( 2994) link_ALPHA1-3 : bond 0.01394 ( 6) link_ALPHA1-3 : angle 3.10118 ( 18) link_ALPHA1-6 : bond 0.01164 ( 6) link_ALPHA1-6 : angle 2.57808 ( 18) link_BETA1-4 : bond 0.00837 ( 14) link_BETA1-4 : angle 2.88500 ( 42) link_NAG-ASN : bond 0.00879 ( 12) link_NAG-ASN : angle 3.46553 ( 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 125 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.8942 (mmm) cc_final: 0.8691 (mmm) REVERT: A 501 MET cc_start: 0.8960 (mtt) cc_final: 0.8588 (mtt) REVERT: B 691 MET cc_start: 0.8756 (tmm) cc_final: 0.8204 (tmm) REVERT: B 794 MET cc_start: 0.6373 (tpt) cc_final: 0.5982 (tpt) REVERT: C 81 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8078 (mp10) REVERT: C 248 MET cc_start: 0.8479 (mmp) cc_final: 0.8262 (mmm) outliers start: 25 outliers final: 6 residues processed: 110 average time/residue: 0.6798 time to fit residues: 85.4829 Evaluate side-chains 105 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain D residue 245 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 38 optimal weight: 20.0000 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: 1.9990 chunk 117 optimal weight: 8.9990 chunk 294 optimal weight: 20.0000 chunk 206 optimal weight: 0.0870 chunk 258 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3771 r_free = 0.3771 target = 0.043047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.033131 restraints weight = 222227.658| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 4.69 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2050 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= 0.123 Angle : 0.598 9.879 33358 Z= 0.285 Chirality : 0.041 0.313 3870 Planarity : 0.003 0.039 4128 Dihedral : 10.348 97.933 3966 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.08 % Allowed : 12.73 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.16), residues: 2944 helix: 1.10 (0.15), residues: 1284 sheet: -0.29 (0.28), residues: 369 loop : -1.54 (0.17), residues: 1291 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 D 564 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00262 (24546) covalent geometry : angle 0.57799 (33238) SS BOND : bond 0.00093 ( 3) SS BOND : angle 0.24578 ( 6) hydrogen bonds : bond 0.03414 ( 1022) hydrogen bonds : angle 4.34753 ( 2994) link_ALPHA1-3 : bond 0.01477 ( 6) link_ALPHA1-3 : angle 3.03563 ( 18) link_ALPHA1-6 : bond 0.01162 ( 6) link_ALPHA1-6 : angle 1.68272 ( 18) link_BETA1-4 : bond 0.00762 ( 14) link_BETA1-4 : angle 2.83281 ( 42) link_NAG-ASN : bond 0.00419 ( 12) link_NAG-ASN : angle 2.83670 ( 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 127 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 316 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7304 (mtm) REVERT: A 360 MET cc_start: 0.8903 (mmm) cc_final: 0.8660 (mmm) REVERT: A 501 MET cc_start: 0.9003 (mtt) cc_final: 0.8780 (mtt) REVERT: B 360 MET cc_start: 0.9200 (tpt) cc_final: 0.8982 (ttm) REVERT: B 565 MET cc_start: 0.9064 (tpp) cc_final: 0.8679 (mpp) REVERT: B 691 MET cc_start: 0.8824 (tmm) cc_final: 0.8254 (tmm) REVERT: B 737 MET cc_start: 0.6495 (tpt) cc_final: 0.6256 (tpt) REVERT: B 794 MET cc_start: 0.6183 (tpt) cc_final: 0.5839 (tpt) REVERT: C 298 MET cc_start: 0.8358 (tpp) cc_final: 0.8012 (tmm) REVERT: D 438 ILE cc_start: 0.4640 (OUTLIER) cc_final: 0.4257 (tp) REVERT: D 565 MET cc_start: 0.7971 (mpp) cc_final: 0.7744 (mmm) REVERT: D 794 MET cc_start: 0.6781 (ptt) cc_final: 0.6485 (ptt) outliers start: 28 outliers final: 5 residues processed: 116 average time/residue: 0.7194 time to fit residues: 96.1409 Evaluate side-chains 104 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 47 SER Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain D residue 438 ILE 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: 4.9990 chunk 160 optimal weight: 9.9990 chunk 247 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 271 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 241 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN C 508 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.046970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.029901 restraints weight = 201705.560| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 7.01 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2605 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= 0.370 Angle : 0.788 10.907 33358 Z= 0.384 Chirality : 0.045 0.338 3870 Planarity : 0.004 0.047 4128 Dihedral : 10.318 99.752 3966 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.51 % Allowed : 15.13 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.16), residues: 2944 helix: 0.91 (0.14), residues: 1280 sheet: -0.55 (0.27), residues: 391 loop : -1.67 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 431 TYR 0.034 0.002 TYR A 774 PHE 0.024 0.002 PHE B 42 TRP 0.016 0.002 TRP D 564 HIS 0.009 0.002 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00784 (24546) covalent geometry : angle 0.77178 (33238) SS BOND : bond 0.00048 ( 3) SS BOND : angle 0.45607 ( 6) hydrogen bonds : bond 0.04126 ( 1022) hydrogen bonds : angle 4.81305 ( 2994) link_ALPHA1-3 : bond 0.01276 ( 6) link_ALPHA1-3 : angle 3.05447 ( 18) link_ALPHA1-6 : bond 0.01085 ( 6) link_ALPHA1-6 : angle 1.93816 ( 18) link_BETA1-4 : bond 0.00792 ( 14) link_BETA1-4 : angle 2.60238 ( 42) link_NAG-ASN : bond 0.00772 ( 12) link_NAG-ASN : angle 3.33096 ( 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 137 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.9083 (mmm) cc_final: 0.8781 (mmm) REVERT: B 360 MET cc_start: 0.9273 (tpt) cc_final: 0.8923 (tpp) REVERT: B 691 MET cc_start: 0.9140 (tmm) cc_final: 0.8607 (tmm) REVERT: B 737 MET cc_start: 0.6678 (tpt) cc_final: 0.6261 (tpt) REVERT: B 794 MET cc_start: 0.7062 (tpt) cc_final: 0.6831 (tpt) REVERT: C 81 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8108 (mp10) REVERT: C 664 MET cc_start: 0.9167 (tpt) cc_final: 0.8572 (tmm) REVERT: C 735 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8154 (t80) REVERT: D 145 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8290 (t80) REVERT: D 438 ILE cc_start: 0.4707 (OUTLIER) cc_final: 0.4345 (tp) REVERT: D 664 MET cc_start: 0.9270 (mmm) cc_final: 0.9059 (mmm) REVERT: D 770 MET cc_start: 0.6337 (mpm) cc_final: 0.6088 (mpp) outliers start: 39 outliers final: 8 residues processed: 127 average time/residue: 0.6443 time to fit residues: 94.4332 Evaluate side-chains 109 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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 D residue 145 PHE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 438 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 276 optimal weight: 30.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3749 r_free = 0.3749 target = 0.042446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.032537 restraints weight = 223494.335| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 4.62 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24587 Z= 0.170 Angle : 0.653 11.347 33358 Z= 0.309 Chirality : 0.042 0.337 3870 Planarity : 0.003 0.038 4128 Dihedral : 9.640 95.076 3966 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.12 % Allowed : 16.22 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.16), residues: 2944 helix: 1.18 (0.15), residues: 1278 sheet: -0.34 (0.29), residues: 350 loop : -1.53 (0.17), residues: 1316 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 0.026 0.001 PHE C 735 TRP 0.014 0.001 TRP D 706 HIS 0.003 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00365 (24546) covalent geometry : angle 0.63569 (33238) SS BOND : bond 0.00106 ( 3) SS BOND : angle 0.22132 ( 6) hydrogen bonds : bond 0.03547 ( 1022) hydrogen bonds : angle 4.44803 ( 2994) link_ALPHA1-3 : bond 0.01387 ( 6) link_ALPHA1-3 : angle 3.08943 ( 18) link_ALPHA1-6 : bond 0.01216 ( 6) link_ALPHA1-6 : angle 1.71931 ( 18) link_BETA1-4 : bond 0.00788 ( 14) link_BETA1-4 : angle 2.55839 ( 42) link_NAG-ASN : bond 0.00447 ( 12) link_NAG-ASN : angle 2.94375 ( 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 127 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7833 (ttm) cc_final: 0.7401 (mtm) REVERT: A 360 MET cc_start: 0.8902 (mmm) cc_final: 0.8652 (mmm) REVERT: A 691 MET cc_start: 0.8741 (ptm) cc_final: 0.8251 (ptt) REVERT: B 247 MET cc_start: 0.8629 (tpp) cc_final: 0.8415 (mmt) REVERT: B 360 MET cc_start: 0.9269 (tpt) cc_final: 0.9010 (tpt) REVERT: B 565 MET cc_start: 0.8982 (tpp) cc_final: 0.8586 (mpp) REVERT: B 691 MET cc_start: 0.8970 (tmm) cc_final: 0.8410 (tmm) REVERT: B 737 MET cc_start: 0.6820 (tpt) cc_final: 0.6599 (tpt) REVERT: B 794 MET cc_start: 0.6524 (tpt) cc_final: 0.6208 (tpt) REVERT: C 247 MET cc_start: 0.8620 (mmm) cc_final: 0.8325 (mmm) REVERT: C 298 MET cc_start: 0.8262 (tpp) cc_final: 0.7966 (tmm) REVERT: C 664 MET cc_start: 0.8768 (tpt) cc_final: 0.8456 (tmm) REVERT: C 735 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8270 (t80) REVERT: C 793 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8456 (pp-130) REVERT: C 794 MET cc_start: 0.8658 (mmm) cc_final: 0.8197 (mmm) REVERT: D 145 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8129 (t80) REVERT: D 438 ILE cc_start: 0.4505 (OUTLIER) cc_final: 0.4015 (tp) REVERT: D 770 MET cc_start: 0.5952 (mpm) cc_final: 0.5615 (mpp) outliers start: 29 outliers final: 8 residues processed: 119 average time/residue: 0.6586 time to fit residues: 90.2353 Evaluate side-chains 109 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 533 PHE Chi-restraints excluded: chain C residue 86 TYR 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 823 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 438 ILE 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: 3.9990 chunk 125 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 182 optimal weight: 0.0970 chunk 238 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 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 = 0.3755 r_free = 0.3755 target = 0.042586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.032673 restraints weight = 223748.371| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 4.64 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2615 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= 0.157 Angle : 0.646 12.835 33358 Z= 0.302 Chirality : 0.041 0.340 3870 Planarity : 0.003 0.037 4128 Dihedral : 9.081 90.669 3966 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.16 % Allowed : 17.03 % Favored : 81.81 % 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 aren not related in a simple way. whole: -0.11 (0.16), residues: 2944 helix: 1.34 (0.15), residues: 1282 sheet: -0.25 (0.29), residues: 350 loop : -1.49 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 431 TYR 0.019 0.001 TYR D 571 PHE 0.022 0.001 PHE C 735 TRP 0.021 0.001 TRP A 640 HIS 0.003 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00341 (24546) covalent geometry : angle 0.62939 (33238) SS BOND : bond 0.00089 ( 3) SS BOND : angle 0.22165 ( 6) hydrogen bonds : bond 0.03395 ( 1022) hydrogen bonds : angle 4.32058 ( 2994) link_ALPHA1-3 : bond 0.01301 ( 6) link_ALPHA1-3 : angle 3.08354 ( 18) link_ALPHA1-6 : bond 0.01112 ( 6) link_ALPHA1-6 : angle 1.66106 ( 18) link_BETA1-4 : bond 0.00766 ( 14) link_BETA1-4 : angle 2.42581 ( 42) link_NAG-ASN : bond 0.00362 ( 12) link_NAG-ASN : angle 2.83262 ( 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 128 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7802 (ttm) cc_final: 0.7420 (mtm) REVERT: A 691 MET cc_start: 0.8751 (ptm) cc_final: 0.8271 (ptt) REVERT: B 247 MET cc_start: 0.8619 (tpp) cc_final: 0.8405 (tpp) REVERT: B 360 MET cc_start: 0.9249 (tpt) cc_final: 0.8942 (tpt) REVERT: B 565 MET cc_start: 0.9012 (tpp) cc_final: 0.8562 (mpp) REVERT: B 691 MET cc_start: 0.8959 (tmm) cc_final: 0.8410 (tmm) REVERT: B 737 MET cc_start: 0.6972 (tpt) cc_final: 0.6735 (tpt) REVERT: B 794 MET cc_start: 0.6531 (tpt) cc_final: 0.6194 (tpt) REVERT: C 298 MET cc_start: 0.8323 (tpp) cc_final: 0.8011 (tmm) REVERT: C 664 MET cc_start: 0.8755 (tpt) cc_final: 0.8348 (tmm) REVERT: C 735 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8240 (t80) REVERT: C 793 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8473 (pp-130) REVERT: C 794 MET cc_start: 0.8588 (mmm) cc_final: 0.8119 (mmm) REVERT: D 145 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8489 (t80) REVERT: D 438 ILE cc_start: 0.4563 (OUTLIER) cc_final: 0.3992 (tp) REVERT: D 770 MET cc_start: 0.5773 (mpm) cc_final: 0.5429 (mpp) outliers start: 30 outliers final: 9 residues processed: 123 average time/residue: 0.6684 time to fit residues: 94.7124 Evaluate side-chains 111 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 396 GLU 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 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: 0.0570 chunk 100 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 196 optimal weight: 9.9990 chunk 113 optimal weight: 30.0000 chunk 145 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3912 r_free = 0.3912 target = 0.047596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.030400 restraints weight = 199030.653| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 5.80 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24587 Z= 0.146 Angle : 0.666 13.554 33358 Z= 0.308 Chirality : 0.041 0.337 3870 Planarity : 0.003 0.039 4128 Dihedral : 8.647 86.827 3966 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.28 % Allowed : 17.41 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.16), residues: 2944 helix: 1.45 (0.15), residues: 1284 sheet: -0.19 (0.29), residues: 345 loop : -1.45 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 458 TYR 0.018 0.001 TYR D 571 PHE 0.020 0.001 PHE A 642 TRP 0.054 0.001 TRP A 640 HIS 0.003 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00319 (24546) covalent geometry : angle 0.64989 (33238) SS BOND : bond 0.00095 ( 3) SS BOND : angle 0.20993 ( 6) hydrogen bonds : bond 0.03325 ( 1022) hydrogen bonds : angle 4.23381 ( 2994) link_ALPHA1-3 : bond 0.01273 ( 6) link_ALPHA1-3 : angle 3.11431 ( 18) link_ALPHA1-6 : bond 0.01077 ( 6) link_ALPHA1-6 : angle 1.65588 ( 18) link_BETA1-4 : bond 0.00763 ( 14) link_BETA1-4 : angle 2.38059 ( 42) link_NAG-ASN : bond 0.00366 ( 12) link_NAG-ASN : angle 2.76677 ( 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 131 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8093 (ttm) cc_final: 0.7371 (mtm) REVERT: A 685 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.8965 (m) REVERT: A 691 MET cc_start: 0.8794 (ptm) cc_final: 0.8239 (ptt) REVERT: A 792 HIS cc_start: 0.9150 (OUTLIER) cc_final: 0.8884 (t-170) REVERT: B 360 MET cc_start: 0.9243 (tpt) cc_final: 0.8757 (tpp) REVERT: B 691 MET cc_start: 0.9101 (tmm) cc_final: 0.8523 (tmm) REVERT: B 737 MET cc_start: 0.7014 (tpt) cc_final: 0.6556 (tpt) REVERT: B 794 MET cc_start: 0.7009 (tpt) cc_final: 0.6751 (tpt) REVERT: C 298 MET cc_start: 0.8536 (tpp) cc_final: 0.8238 (tmm) REVERT: C 664 MET cc_start: 0.9061 (tpt) cc_final: 0.8279 (tmm) REVERT: C 735 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8175 (t80) REVERT: C 793 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8722 (pp-130) REVERT: D 145 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8437 (t80) REVERT: D 360 MET cc_start: 0.9209 (mtm) cc_final: 0.8754 (mtm) REVERT: D 438 ILE cc_start: 0.4516 (OUTLIER) cc_final: 0.4089 (tp) REVERT: D 664 MET cc_start: 0.9062 (mmm) cc_final: 0.8781 (mmt) REVERT: D 737 MET cc_start: 0.7945 (ppp) cc_final: 0.7421 (ppp) REVERT: D 770 MET cc_start: 0.6206 (mpm) cc_final: 0.5922 (mpp) outliers start: 33 outliers final: 12 residues processed: 126 average time/residue: 0.6743 time to fit residues: 98.7415 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 : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL 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 329 VAL 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 367 HIS Chi-restraints excluded: chain C residue 396 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 6 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 158 optimal weight: 0.4980 chunk 142 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3742 r_free = 0.3742 target = 0.042179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.032349 restraints weight = 222508.730| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 4.69 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24587 Z= 0.189 Angle : 0.701 13.342 33358 Z= 0.325 Chirality : 0.042 0.334 3870 Planarity : 0.003 0.041 4128 Dihedral : 8.321 83.474 3966 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.12 % Allowed : 18.03 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.16), residues: 2944 helix: 1.40 (0.15), residues: 1290 sheet: -0.16 (0.29), residues: 352 loop : -1.46 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 775 TYR 0.018 0.001 TYR D 571 PHE 0.028 0.001 PHE B 166 TRP 0.040 0.001 TRP A 640 HIS 0.005 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00409 (24546) covalent geometry : angle 0.68601 (33238) SS BOND : bond 0.00075 ( 3) SS BOND : angle 0.25110 ( 6) hydrogen bonds : bond 0.03409 ( 1022) hydrogen bonds : angle 4.28718 ( 2994) link_ALPHA1-3 : bond 0.01170 ( 6) link_ALPHA1-3 : angle 3.15623 ( 18) link_ALPHA1-6 : bond 0.01016 ( 6) link_ALPHA1-6 : angle 1.76389 ( 18) link_BETA1-4 : bond 0.00792 ( 14) link_BETA1-4 : angle 2.34966 ( 42) link_NAG-ASN : bond 0.00484 ( 12) link_NAG-ASN : angle 2.89385 ( 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 126 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7455 (mtm) REVERT: A 534 MET cc_start: 0.7894 (mtm) cc_final: 0.7564 (mtm) REVERT: A 691 MET cc_start: 0.8718 (ptm) cc_final: 0.8198 (ptt) REVERT: B 360 MET cc_start: 0.9217 (tpt) cc_final: 0.8932 (tpt) REVERT: B 565 MET cc_start: 0.9038 (tpp) cc_final: 0.8646 (mpp) REVERT: B 691 MET cc_start: 0.8886 (tmm) cc_final: 0.8361 (tmm) REVERT: B 794 MET cc_start: 0.6430 (tpt) cc_final: 0.6125 (tpt) REVERT: C 247 MET cc_start: 0.8686 (mmm) cc_final: 0.8396 (tpp) REVERT: C 664 MET cc_start: 0.8693 (tpt) cc_final: 0.8224 (tmm) REVERT: C 735 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8201 (t80) REVERT: C 793 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8452 (pp-130) REVERT: C 794 MET cc_start: 0.8614 (tpp) cc_final: 0.8175 (mmm) REVERT: D 145 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8501 (t80) REVERT: D 360 MET cc_start: 0.9166 (mtm) cc_final: 0.8799 (mtm) REVERT: D 438 ILE cc_start: 0.4674 (OUTLIER) cc_final: 0.4133 (tp) REVERT: D 737 MET cc_start: 0.8040 (ppp) cc_final: 0.7211 (ppp) REVERT: D 770 MET cc_start: 0.5665 (mpm) cc_final: 0.5316 (mpp) outliers start: 29 outliers final: 17 residues processed: 123 average time/residue: 0.7067 time to fit residues: 100.3048 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 : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 514 VAL 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 329 VAL 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 367 HIS Chi-restraints excluded: chain C residue 396 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 213 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 200 optimal weight: 20.0000 chunk 129 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN D 98 GLN D 677 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.042691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.032863 restraints weight = 221167.339| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 4.67 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24587 Z= 0.125 Angle : 0.687 14.547 33358 Z= 0.314 Chirality : 0.041 0.338 3870 Planarity : 0.003 0.039 4128 Dihedral : 7.817 78.911 3966 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.93 % Allowed : 18.27 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.16), residues: 2944 helix: 1.51 (0.15), residues: 1289 sheet: -0.03 (0.30), residues: 346 loop : -1.39 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 220 TYR 0.017 0.001 TYR D 571 PHE 0.027 0.001 PHE B 166 TRP 0.038 0.001 TRP A 640 HIS 0.002 0.001 HIS D 129 Details of bonding type rmsd covalent geometry : bond 0.00276 (24546) covalent geometry : angle 0.67214 (33238) SS BOND : bond 0.00109 ( 3) SS BOND : angle 0.24369 ( 6) hydrogen bonds : bond 0.03205 ( 1022) hydrogen bonds : angle 4.14239 ( 2994) link_ALPHA1-3 : bond 0.01315 ( 6) link_ALPHA1-3 : angle 3.24685 ( 18) link_ALPHA1-6 : bond 0.01043 ( 6) link_ALPHA1-6 : angle 1.45667 ( 18) link_BETA1-4 : bond 0.00766 ( 14) link_BETA1-4 : angle 2.32835 ( 42) link_NAG-ASN : bond 0.00272 ( 12) link_NAG-ASN : angle 2.68657 ( 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 121 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7425 (mtm) REVERT: A 501 MET cc_start: 0.8757 (mtt) cc_final: 0.8301 (mtt) REVERT: A 534 MET cc_start: 0.7778 (mtm) cc_final: 0.7450 (mtm) REVERT: A 691 MET cc_start: 0.8707 (ptm) cc_final: 0.8204 (ptt) REVERT: B 360 MET cc_start: 0.9184 (tpt) cc_final: 0.8672 (tpp) REVERT: B 691 MET cc_start: 0.8847 (tmm) cc_final: 0.8330 (tmm) REVERT: B 793 MET cc_start: 0.9072 (tpp) cc_final: 0.8363 (pp-130) REVERT: B 794 MET cc_start: 0.6181 (tpt) cc_final: 0.4407 (tpt) REVERT: C 735 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8199 (t80) REVERT: C 793 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8520 (pp-130) REVERT: D 145 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8436 (t80) REVERT: D 360 MET cc_start: 0.9113 (mtm) cc_final: 0.8791 (mtm) REVERT: D 438 ILE cc_start: 0.4573 (OUTLIER) cc_final: 0.4061 (tp) REVERT: D 737 MET cc_start: 0.8017 (ppp) cc_final: 0.7161 (ppp) REVERT: D 770 MET cc_start: 0.5596 (mpm) cc_final: 0.5155 (mpp) outliers start: 24 outliers final: 13 residues processed: 118 average time/residue: 0.7643 time to fit residues: 103.3839 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 : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 514 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 329 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 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 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: 9.9990 chunk 153 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 245 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3754 r_free = 0.3754 target = 0.042525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.032719 restraints weight = 221146.672| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.61 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2887 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= 0.146 Angle : 0.695 13.399 33358 Z= 0.318 Chirality : 0.041 0.337 3870 Planarity : 0.003 0.039 4128 Dihedral : 7.600 75.854 3966 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.89 % Allowed : 18.50 % Favored : 80.61 % 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 aren not related in a simple way. whole: 0.18 (0.16), residues: 2944 helix: 1.56 (0.15), residues: 1288 sheet: 0.07 (0.30), residues: 346 loop : -1.38 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 431 TYR 0.030 0.001 TYR D 571 PHE 0.026 0.001 PHE B 166 TRP 0.040 0.001 TRP A 640 HIS 0.003 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00321 (24546) covalent geometry : angle 0.68057 (33238) SS BOND : bond 0.00083 ( 3) SS BOND : angle 0.22646 ( 6) hydrogen bonds : bond 0.03240 ( 1022) hydrogen bonds : angle 4.14803 ( 2994) link_ALPHA1-3 : bond 0.01351 ( 6) link_ALPHA1-3 : angle 3.38150 ( 18) link_ALPHA1-6 : bond 0.00985 ( 6) link_ALPHA1-6 : angle 1.52803 ( 18) link_BETA1-4 : bond 0.00818 ( 14) link_BETA1-4 : angle 2.33862 ( 42) link_NAG-ASN : bond 0.00381 ( 12) link_NAG-ASN : angle 2.65091 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5984.66 seconds wall clock time: 103 minutes 35.06 seconds (6215.06 seconds total)