Starting phenix.real_space_refine on Sat Jun 21 03:07:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f0o_28775/06_2025/8f0o_28775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0o_28775/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8f0o_28775/06_2025/8f0o_28775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0o_28775/06_2025/8f0o_28775.map" model { file = "/net/cci-nas-00/data/ceres_data/8f0o_28775/06_2025/8f0o_28775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0o_28775/06_2025/8f0o_28775.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.95, per 1000 atoms: 0.66 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: 6.30 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 2.89 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: 9.34 Time building geometry restraints manager: 7.20 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: 0.00 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: 4.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 57.230 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.000 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (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 TRP 0.020 0.002 TRP D 296 HIS 0.010 0.001 HIS A 253 PHE 0.038 0.002 PHE A 642 TYR 0.027 0.002 TYR D 251 ARG 0.005 0.000 ARG B 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00757 ( 12) link_NAG-ASN : angle 4.11247 ( 36) 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_ALPHA1-3 : bond 0.00977 ( 6) link_ALPHA1-3 : angle 3.33985 ( 18) hydrogen bonds : bond 0.14767 ( 1022) hydrogen bonds : angle 6.42485 ( 2994) SS BOND : bond 0.00140 ( 3) SS BOND : angle 0.68793 ( 6) covalent geometry : bond 0.00461 (24546) covalent geometry : angle 0.80268 (33238) *********************** 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 : 2.524 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: 1.4396 time to fit residues: 214.7645 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 : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 119 optimal weight: 40.0000 chunk 232 optimal weight: 6.9990 chunk 89 optimal weight: 0.3980 chunk 141 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- 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 C 81 GLN C 98 GLN C 196 ASN C 328 HIS D 81 GLN D 98 GLN D 203 GLN D 677 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.042862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.032947 restraints weight = 223607.840| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 4.67 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24587 Z= 0.238 Angle : 0.683 10.352 33358 Z= 0.332 Chirality : 0.042 0.225 3870 Planarity : 0.004 0.052 4128 Dihedral : 13.069 109.700 3966 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.66 % Allowed : 7.00 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 2944 helix: 0.26 (0.14), residues: 1275 sheet: -0.39 (0.27), residues: 396 loop : -1.69 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 296 HIS 0.006 0.001 HIS D 225 PHE 0.024 0.002 PHE A 642 TYR 0.023 0.001 TYR D 571 ARG 0.006 0.001 ARG D 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 12) link_NAG-ASN : angle 2.99059 ( 36) link_ALPHA1-6 : bond 0.00803 ( 6) link_ALPHA1-6 : angle 2.41325 ( 18) link_BETA1-4 : bond 0.00788 ( 14) link_BETA1-4 : angle 2.78532 ( 42) link_ALPHA1-3 : bond 0.01342 ( 6) link_ALPHA1-3 : angle 3.89214 ( 18) hydrogen bonds : bond 0.03863 ( 1022) hydrogen bonds : angle 4.63692 ( 2994) SS BOND : bond 0.00037 ( 3) SS BOND : angle 0.38148 ( 6) covalent geometry : bond 0.00505 (24546) covalent geometry : angle 0.66141 (33238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7662 (ttp) cc_final: 0.7289 (mtm) REVERT: A 433 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8603 (mm) REVERT: A 501 MET cc_start: 0.9040 (mtt) cc_final: 0.8787 (mtt) REVERT: B 691 MET cc_start: 0.8778 (tmm) cc_final: 0.8243 (tmm) REVERT: B 794 MET cc_start: 0.5943 (tpt) cc_final: 0.5344 (tpt) REVERT: C 298 MET cc_start: 0.8940 (mmm) cc_final: 0.8711 (mpm) REVERT: C 664 MET cc_start: 0.8770 (mmm) cc_final: 0.8471 (tmm) REVERT: D 247 MET cc_start: 0.8937 (mmt) cc_final: 0.8660 (mmt) REVERT: D 534 MET cc_start: 0.6639 (pmm) cc_final: 0.6383 (pmm) REVERT: D 565 MET cc_start: 0.8100 (mpp) cc_final: 0.7849 (mmm) REVERT: D 709 MET cc_start: 0.8722 (ppp) cc_final: 0.8317 (ppp) outliers start: 17 outliers final: 2 residues processed: 107 average time/residue: 1.5869 time to fit residues: 194.2630 Evaluate side-chains 102 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU 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 142 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 270 optimal weight: 8.9990 chunk 246 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 242 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.043308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.032905 restraints weight = 213721.439| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 5.00 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24587 Z= 0.108 Angle : 0.566 9.468 33358 Z= 0.269 Chirality : 0.040 0.251 3870 Planarity : 0.003 0.046 4128 Dihedral : 11.031 101.692 3966 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.74 % Allowed : 9.06 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2944 helix: 0.93 (0.15), residues: 1273 sheet: -0.16 (0.27), residues: 391 loop : -1.51 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 564 HIS 0.003 0.001 HIS C 129 PHE 0.024 0.001 PHE A 642 TYR 0.018 0.001 TYR D 571 ARG 0.006 0.000 ARG B 58 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 12) link_NAG-ASN : angle 2.71915 ( 36) link_ALPHA1-6 : bond 0.01279 ( 6) link_ALPHA1-6 : angle 2.28567 ( 18) link_BETA1-4 : bond 0.00801 ( 14) link_BETA1-4 : angle 2.87563 ( 42) link_ALPHA1-3 : bond 0.01535 ( 6) link_ALPHA1-3 : angle 3.05450 ( 18) hydrogen bonds : bond 0.03246 ( 1022) hydrogen bonds : angle 4.27384 ( 2994) SS BOND : bond 0.00070 ( 3) SS BOND : angle 0.23909 ( 6) covalent geometry : bond 0.00227 (24546) covalent geometry : angle 0.54286 (33238) *********************** 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 119 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6970 (mtp) cc_final: 0.6517 (mmt) REVERT: A 234 MET cc_start: 0.9121 (tpp) cc_final: 0.8827 (tpp) REVERT: A 298 MET cc_start: 0.9421 (tmm) cc_final: 0.9220 (tmm) REVERT: A 316 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7154 (ttm) REVERT: A 360 MET cc_start: 0.9128 (mmm) cc_final: 0.8897 (mmm) REVERT: A 501 MET cc_start: 0.9315 (mtt) cc_final: 0.8915 (mtt) REVERT: A 534 MET cc_start: 0.8271 (mtm) cc_final: 0.7720 (mtm) REVERT: A 691 MET cc_start: 0.8596 (ptm) cc_final: 0.8253 (ptp) REVERT: A 793 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8658 (ppp) REVERT: A 794 MET cc_start: 0.8533 (mmm) cc_final: 0.8178 (mmm) REVERT: B 565 MET cc_start: 0.8938 (tpp) cc_final: 0.8621 (mpp) REVERT: B 691 MET cc_start: 0.8974 (tmm) cc_final: 0.8442 (tmm) REVERT: B 737 MET cc_start: 0.7606 (tpp) cc_final: 0.7301 (tpt) REVERT: B 793 MET cc_start: 0.9012 (tpp) cc_final: 0.8364 (pp-130) REVERT: B 794 MET cc_start: 0.6238 (tpt) cc_final: 0.4238 (tpt) REVERT: C 50 MET cc_start: 0.7278 (mtp) cc_final: 0.6986 (ttm) REVERT: C 248 MET cc_start: 0.9008 (mmp) cc_final: 0.8736 (mmm) REVERT: C 298 MET cc_start: 0.9092 (mmm) cc_final: 0.8741 (tpp) REVERT: C 664 MET cc_start: 0.8914 (mmm) cc_final: 0.8417 (tmm) REVERT: D 247 MET cc_start: 0.9317 (mmt) cc_final: 0.8951 (mmt) REVERT: D 248 MET cc_start: 0.9062 (mmm) cc_final: 0.8743 (mmp) REVERT: D 413 MET cc_start: 0.8394 (mmm) cc_final: 0.7942 (mmm) REVERT: D 534 MET cc_start: 0.7003 (pmm) cc_final: 0.6685 (pmm) outliers start: 19 outliers final: 4 residues processed: 105 average time/residue: 1.6328 time to fit residues: 196.4932 Evaluate side-chains 104 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 793 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 198 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 239 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 72 optimal weight: 0.0000 chunk 271 optimal weight: 0.0970 chunk 282 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 241 GLN B 497 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.043216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.032791 restraints weight = 215905.095| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 5.12 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24587 Z= 0.119 Angle : 0.556 9.345 33358 Z= 0.265 Chirality : 0.040 0.318 3870 Planarity : 0.003 0.042 4128 Dihedral : 9.867 93.472 3966 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.01 % Allowed : 10.02 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2944 helix: 1.24 (0.15), residues: 1279 sheet: -0.01 (0.28), residues: 386 loop : -1.45 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 564 HIS 0.002 0.001 HIS B 225 PHE 0.025 0.001 PHE B 166 TYR 0.023 0.001 TYR D 571 ARG 0.013 0.000 ARG B 58 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 12) link_NAG-ASN : angle 2.66483 ( 36) link_ALPHA1-6 : bond 0.01168 ( 6) link_ALPHA1-6 : angle 1.73575 ( 18) link_BETA1-4 : bond 0.00750 ( 14) link_BETA1-4 : angle 2.83396 ( 42) link_ALPHA1-3 : bond 0.01510 ( 6) link_ALPHA1-3 : angle 2.97016 ( 18) hydrogen bonds : bond 0.03107 ( 1022) hydrogen bonds : angle 4.13613 ( 2994) SS BOND : bond 0.00059 ( 3) SS BOND : angle 0.19281 ( 6) covalent geometry : bond 0.00256 (24546) covalent geometry : angle 0.53480 (33238) *********************** 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 125 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7049 (mtp) cc_final: 0.6607 (mmt) REVERT: A 234 MET cc_start: 0.9121 (tpp) cc_final: 0.8811 (tpp) REVERT: A 316 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7370 (ttm) REVERT: A 360 MET cc_start: 0.9120 (mmm) cc_final: 0.8898 (mmm) REVERT: A 501 MET cc_start: 0.9342 (mtt) cc_final: 0.9126 (mtt) REVERT: A 534 MET cc_start: 0.8256 (mtm) cc_final: 0.7727 (mtm) REVERT: A 691 MET cc_start: 0.8653 (ptm) cc_final: 0.8404 (ptp) REVERT: A 793 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8641 (ppp) REVERT: A 794 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8217 (mmm) REVERT: B 565 MET cc_start: 0.9062 (tpp) cc_final: 0.8750 (mpp) REVERT: B 691 MET cc_start: 0.8998 (tmm) cc_final: 0.8456 (tmm) REVERT: B 737 MET cc_start: 0.7647 (tpp) cc_final: 0.7350 (tpt) REVERT: B 794 MET cc_start: 0.6323 (tpt) cc_final: 0.5851 (tpt) REVERT: C 298 MET cc_start: 0.9081 (mmm) cc_final: 0.8781 (tpp) REVERT: C 360 MET cc_start: 0.9191 (mmm) cc_final: 0.8983 (mmm) REVERT: C 664 MET cc_start: 0.8969 (mmm) cc_final: 0.8465 (tmm) REVERT: D 247 MET cc_start: 0.9287 (mmt) cc_final: 0.8999 (mmt) REVERT: D 248 MET cc_start: 0.9072 (mmm) cc_final: 0.8789 (mmp) REVERT: D 360 MET cc_start: 0.9176 (mtt) cc_final: 0.8945 (ttt) REVERT: D 413 MET cc_start: 0.8459 (mmm) cc_final: 0.8039 (mmm) REVERT: D 438 ILE cc_start: 0.4736 (OUTLIER) cc_final: 0.4322 (tp) REVERT: D 565 MET cc_start: 0.7921 (mpp) cc_final: 0.7709 (mmm) REVERT: D 664 MET cc_start: 0.9155 (mmm) cc_final: 0.8945 (mmm) REVERT: D 709 MET cc_start: 0.8722 (ppp) cc_final: 0.8508 (ppp) outliers start: 26 outliers final: 5 residues processed: 109 average time/residue: 1.5744 time to fit residues: 196.6440 Evaluate side-chains 107 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 794 MET 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 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 224 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 79 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 290 optimal weight: 30.0000 chunk 110 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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** D 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.042915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.032957 restraints weight = 223535.028| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 4.70 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24587 Z= 0.198 Angle : 0.606 10.457 33358 Z= 0.292 Chirality : 0.041 0.347 3870 Planarity : 0.003 0.038 4128 Dihedral : 9.197 92.529 3966 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.12 % Allowed : 11.96 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2944 helix: 1.38 (0.15), residues: 1287 sheet: 0.03 (0.28), residues: 386 loop : -1.47 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 564 HIS 0.005 0.001 HIS D 225 PHE 0.021 0.001 PHE B 166 TYR 0.023 0.001 TYR D 571 ARG 0.010 0.000 ARG B 58 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 12) link_NAG-ASN : angle 2.78684 ( 36) link_ALPHA1-6 : bond 0.01116 ( 6) link_ALPHA1-6 : angle 1.79401 ( 18) link_BETA1-4 : bond 0.00776 ( 14) link_BETA1-4 : angle 2.54192 ( 42) link_ALPHA1-3 : bond 0.01358 ( 6) link_ALPHA1-3 : angle 3.01794 ( 18) hydrogen bonds : bond 0.03323 ( 1022) hydrogen bonds : angle 4.23108 ( 2994) SS BOND : bond 0.00042 ( 3) SS BOND : angle 0.25997 ( 6) covalent geometry : bond 0.00423 (24546) covalent geometry : angle 0.58787 (33238) *********************** 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 128 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 2.491 Fit side-chains revert: symmetry clash REVERT: A 234 MET cc_start: 0.8741 (tpp) cc_final: 0.8486 (tpp) REVERT: A 316 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7348 (mtm) REVERT: A 534 MET cc_start: 0.7813 (mtm) cc_final: 0.7409 (mtm) REVERT: B 691 MET cc_start: 0.8781 (tmm) cc_final: 0.8221 (tmm) REVERT: B 794 MET cc_start: 0.6162 (tpt) cc_final: 0.5748 (tpt) REVERT: C 81 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: C 664 MET cc_start: 0.8716 (mmm) cc_final: 0.8453 (tmm) REVERT: C 794 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8368 (mmm) REVERT: D 413 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8101 (mmm) REVERT: D 438 ILE cc_start: 0.4666 (OUTLIER) cc_final: 0.4126 (tp) REVERT: D 534 MET cc_start: 0.6679 (pmm) cc_final: 0.6369 (pmm) REVERT: D 737 MET cc_start: 0.8239 (ppp) cc_final: 0.7189 (ppp) outliers start: 29 outliers final: 6 residues processed: 115 average time/residue: 1.4703 time to fit residues: 194.4032 Evaluate side-chains 108 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 794 MET Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 244 optimal weight: 6.9990 chunk 233 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 23 optimal weight: 0.0030 chunk 250 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 257 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- 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** ** A 714 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 = 0.3753 r_free = 0.3753 target = 0.043129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.032713 restraints weight = 213082.898| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 5.08 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24587 Z= 0.113 Angle : 0.591 11.130 33358 Z= 0.276 Chirality : 0.041 0.347 3870 Planarity : 0.003 0.039 4128 Dihedral : 8.571 87.850 3966 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.04 % Allowed : 13.43 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2944 helix: 1.49 (0.15), residues: 1289 sheet: 0.07 (0.28), residues: 381 loop : -1.38 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 296 HIS 0.002 0.001 HIS B 225 PHE 0.018 0.001 PHE A 642 TYR 0.023 0.001 TYR D 571 ARG 0.004 0.000 ARG B 58 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 12) link_NAG-ASN : angle 2.56570 ( 36) link_ALPHA1-6 : bond 0.01222 ( 6) link_ALPHA1-6 : angle 1.65010 ( 18) link_BETA1-4 : bond 0.00738 ( 14) link_BETA1-4 : angle 2.49535 ( 42) link_ALPHA1-3 : bond 0.01551 ( 6) link_ALPHA1-3 : angle 3.19438 ( 18) hydrogen bonds : bond 0.03077 ( 1022) hydrogen bonds : angle 4.07122 ( 2994) SS BOND : bond 0.00075 ( 3) SS BOND : angle 0.19162 ( 6) covalent geometry : bond 0.00246 (24546) covalent geometry : angle 0.57294 (33238) *********************** 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 125 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.9138 (tpp) cc_final: 0.8772 (tpp) REVERT: A 316 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7289 (mtm) REVERT: A 534 MET cc_start: 0.8335 (mtm) cc_final: 0.7779 (mtm) REVERT: A 737 MET cc_start: 0.8750 (pmm) cc_final: 0.8340 (pmm) REVERT: B 565 MET cc_start: 0.8874 (tpp) cc_final: 0.8588 (mpp) REVERT: B 691 MET cc_start: 0.9027 (tmm) cc_final: 0.8428 (tmm) REVERT: B 793 MET cc_start: 0.9064 (tpp) cc_final: 0.8418 (pp-130) REVERT: B 794 MET cc_start: 0.6408 (tpt) cc_final: 0.4510 (tpt) REVERT: C 298 MET cc_start: 0.8473 (tpp) cc_final: 0.8140 (tmm) REVERT: C 360 MET cc_start: 0.9185 (mmm) cc_final: 0.8943 (mmm) REVERT: C 664 MET cc_start: 0.8947 (mmm) cc_final: 0.8413 (tmm) REVERT: C 793 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8671 (pp-130) REVERT: C 794 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8549 (mmm) REVERT: D 50 MET cc_start: 0.8167 (ttp) cc_final: 0.7725 (tmm) REVERT: D 248 MET cc_start: 0.9006 (mmm) cc_final: 0.8740 (mmp) REVERT: D 413 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8087 (mmm) REVERT: D 438 ILE cc_start: 0.4613 (OUTLIER) cc_final: 0.4136 (tp) REVERT: D 534 MET cc_start: 0.6847 (pmm) cc_final: 0.6561 (pmm) REVERT: D 664 MET cc_start: 0.9163 (mmm) cc_final: 0.8841 (mmt) REVERT: D 709 MET cc_start: 0.8723 (ppp) cc_final: 0.8424 (ppp) REVERT: D 737 MET cc_start: 0.7933 (ppp) cc_final: 0.6533 (ppp) REVERT: D 794 MET cc_start: 0.6775 (ptp) cc_final: 0.6536 (ptt) outliers start: 27 outliers final: 5 residues processed: 116 average time/residue: 1.6064 time to fit residues: 213.8841 Evaluate side-chains 107 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 2.797 ------------------------------------------------------------------------------- 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 329 VAL Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 794 MET Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 796 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 118 optimal weight: 0.0060 chunk 150 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 282 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 78 optimal weight: 0.0570 chunk 290 optimal weight: 20.0000 chunk 274 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 overall best weight: 1.1516 ------------------------------------------------------------------------------- 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** ** A 714 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 = 0.3764 r_free = 0.3764 target = 0.043183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.032830 restraints weight = 214718.253| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 5.04 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24587 Z= 0.111 Angle : 0.587 11.818 33358 Z= 0.273 Chirality : 0.040 0.348 3870 Planarity : 0.003 0.038 4128 Dihedral : 7.975 83.022 3966 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.85 % Allowed : 14.36 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2944 helix: 1.58 (0.15), residues: 1289 sheet: 0.13 (0.28), residues: 383 loop : -1.34 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 564 HIS 0.002 0.001 HIS D 328 PHE 0.025 0.001 PHE C 735 TYR 0.019 0.001 TYR D 571 ARG 0.004 0.000 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 12) link_NAG-ASN : angle 2.48094 ( 36) link_ALPHA1-6 : bond 0.01295 ( 6) link_ALPHA1-6 : angle 1.64579 ( 18) link_BETA1-4 : bond 0.00757 ( 14) link_BETA1-4 : angle 2.37231 ( 42) link_ALPHA1-3 : bond 0.01582 ( 6) link_ALPHA1-3 : angle 3.36656 ( 18) hydrogen bonds : bond 0.02992 ( 1022) hydrogen bonds : angle 3.99103 ( 2994) SS BOND : bond 0.00082 ( 3) SS BOND : angle 0.22260 ( 6) covalent geometry : bond 0.00241 (24546) covalent geometry : angle 0.56963 (33238) *********************** 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 120 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.9101 (tpp) cc_final: 0.8819 (mmt) REVERT: A 316 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7305 (mtm) REVERT: A 534 MET cc_start: 0.8297 (mtm) cc_final: 0.7733 (mtm) REVERT: A 691 MET cc_start: 0.8795 (ptm) cc_final: 0.8234 (ptt) REVERT: A 737 MET cc_start: 0.8762 (pmm) cc_final: 0.8290 (pmm) REVERT: A 793 MET cc_start: 0.9053 (ptt) cc_final: 0.8767 (pp-130) REVERT: B 565 MET cc_start: 0.8865 (tpp) cc_final: 0.8555 (mpp) REVERT: B 691 MET cc_start: 0.9019 (tmm) cc_final: 0.8446 (tmm) REVERT: B 794 MET cc_start: 0.6417 (tpt) cc_final: 0.6046 (tpt) REVERT: C 664 MET cc_start: 0.8943 (mmm) cc_final: 0.8438 (tmm) REVERT: C 735 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8034 (t80) REVERT: C 793 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8738 (ppp) REVERT: D 248 MET cc_start: 0.8999 (mmm) cc_final: 0.8608 (mmm) REVERT: D 413 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8123 (mmm) REVERT: D 438 ILE cc_start: 0.4686 (OUTLIER) cc_final: 0.4156 (tp) REVERT: D 737 MET cc_start: 0.7923 (ppp) cc_final: 0.6998 (ppp) REVERT: D 794 MET cc_start: 0.6778 (ptp) cc_final: 0.6563 (ptt) outliers start: 22 outliers final: 8 residues processed: 111 average time/residue: 2.0220 time to fit residues: 260.3398 Evaluate side-chains 110 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 3.378 ------------------------------------------------------------------------------- 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 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 645 LEU Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Chi-restraints excluded: chain D residue 796 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 291 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 266 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.042606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.032666 restraints weight = 224544.218| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 4.64 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24587 Z= 0.235 Angle : 0.696 13.309 33358 Z= 0.327 Chirality : 0.042 0.331 3870 Planarity : 0.003 0.037 4128 Dihedral : 7.922 80.582 3966 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.81 % Allowed : 15.13 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2944 helix: 1.50 (0.15), residues: 1290 sheet: 0.08 (0.28), residues: 385 loop : -1.42 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 564 HIS 0.006 0.001 HIS D 225 PHE 0.025 0.001 PHE C 735 TYR 0.021 0.001 TYR A 774 ARG 0.005 0.000 ARG A 431 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 12) link_NAG-ASN : angle 2.78507 ( 36) link_ALPHA1-6 : bond 0.01053 ( 6) link_ALPHA1-6 : angle 1.85190 ( 18) link_BETA1-4 : bond 0.00791 ( 14) link_BETA1-4 : angle 2.31180 ( 42) link_ALPHA1-3 : bond 0.01389 ( 6) link_ALPHA1-3 : angle 3.45532 ( 18) hydrogen bonds : bond 0.03419 ( 1022) hydrogen bonds : angle 4.26342 ( 2994) SS BOND : bond 0.00066 ( 3) SS BOND : angle 0.39877 ( 6) covalent geometry : bond 0.00505 (24546) covalent geometry : angle 0.68041 (33238) *********************** 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 119 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7423 (mtm) REVERT: A 534 MET cc_start: 0.7947 (mtm) cc_final: 0.7505 (mtm) REVERT: B 323 MET cc_start: 0.8963 (mmm) cc_final: 0.8699 (tpt) REVERT: B 565 MET cc_start: 0.8907 (tpp) cc_final: 0.8516 (mpp) REVERT: B 691 MET cc_start: 0.8903 (tmm) cc_final: 0.8376 (tmm) REVERT: B 794 MET cc_start: 0.6436 (tpt) cc_final: 0.6112 (tpt) REVERT: C 81 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: C 316 MET cc_start: 0.8654 (mmm) cc_final: 0.8443 (mpp) REVERT: C 664 MET cc_start: 0.8732 (mmm) cc_final: 0.8414 (tmm) REVERT: C 735 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8255 (t80) REVERT: C 793 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8532 (pp-130) REVERT: D 413 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8135 (mmm) REVERT: D 438 ILE cc_start: 0.4612 (OUTLIER) cc_final: 0.4137 (tp) REVERT: D 664 MET cc_start: 0.8972 (mmm) cc_final: 0.8696 (mmt) outliers start: 21 outliers final: 3 residues processed: 110 average time/residue: 1.8985 time to fit residues: 237.7966 Evaluate side-chains 106 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 3.084 ------------------------------------------------------------------------------- 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 774 TYR 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 413 MET Chi-restraints excluded: chain D residue 438 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 205 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 294 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 244 optimal weight: 0.3980 chunk 221 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- 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 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.047720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.030656 restraints weight = 202055.956| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 7.07 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 24587 Z= 0.225 Angle : 0.703 13.369 33358 Z= 0.331 Chirality : 0.042 0.328 3870 Planarity : 0.003 0.035 4128 Dihedral : 7.845 77.301 3966 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.66 % Allowed : 15.75 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2944 helix: 1.43 (0.15), residues: 1288 sheet: -0.00 (0.28), residues: 388 loop : -1.44 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 564 HIS 0.005 0.001 HIS D 225 PHE 0.022 0.001 PHE C 735 TYR 0.020 0.001 TYR A 774 ARG 0.005 0.000 ARG A 431 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 12) link_NAG-ASN : angle 2.82607 ( 36) link_ALPHA1-6 : bond 0.01008 ( 6) link_ALPHA1-6 : angle 1.65080 ( 18) link_BETA1-4 : bond 0.00776 ( 14) link_BETA1-4 : angle 2.28564 ( 42) link_ALPHA1-3 : bond 0.01293 ( 6) link_ALPHA1-3 : angle 3.53099 ( 18) hydrogen bonds : bond 0.03505 ( 1022) hydrogen bonds : angle 4.35059 ( 2994) SS BOND : bond 0.00059 ( 3) SS BOND : angle 0.38987 ( 6) covalent geometry : bond 0.00483 (24546) covalent geometry : angle 0.68688 (33238) *********************** 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 115 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7186 (mtm) REVERT: A 534 MET cc_start: 0.8208 (mtm) cc_final: 0.7678 (mtm) REVERT: A 691 MET cc_start: 0.8832 (ptm) cc_final: 0.8231 (ptt) REVERT: B 565 MET cc_start: 0.8899 (tpp) cc_final: 0.8567 (mpp) REVERT: B 691 MET cc_start: 0.9156 (tmm) cc_final: 0.8593 (tmm) REVERT: B 794 MET cc_start: 0.7001 (tpt) cc_final: 0.6759 (tpt) REVERT: C 50 MET cc_start: 0.7304 (tmm) cc_final: 0.7050 (tmm) REVERT: C 81 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7866 (mp10) REVERT: C 316 MET cc_start: 0.8957 (mmm) cc_final: 0.8701 (mpp) REVERT: C 664 MET cc_start: 0.9024 (mmm) cc_final: 0.8476 (tmm) REVERT: C 793 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8799 (pp-130) REVERT: C 794 MET cc_start: 0.9160 (tpp) cc_final: 0.8934 (tpt) REVERT: D 50 MET cc_start: 0.8327 (ttp) cc_final: 0.7786 (tmm) REVERT: D 413 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8145 (mmm) REVERT: D 438 ILE cc_start: 0.4722 (OUTLIER) cc_final: 0.4261 (tp) REVERT: D 664 MET cc_start: 0.9221 (mmm) cc_final: 0.8821 (mmt) outliers start: 17 outliers final: 4 residues processed: 108 average time/residue: 1.6910 time to fit residues: 210.5891 Evaluate side-chains 107 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 2.882 ------------------------------------------------------------------------------- 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 774 TYR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 55 optimal weight: 8.9990 chunk 192 optimal weight: 5.9990 chunk 257 optimal weight: 0.3980 chunk 133 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 276 optimal weight: 30.0000 chunk 146 optimal weight: 6.9990 chunk 288 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.042412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.032554 restraints weight = 224119.373| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 4.69 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24587 Z= 0.194 Angle : 0.707 13.509 33358 Z= 0.329 Chirality : 0.041 0.330 3870 Planarity : 0.003 0.036 4128 Dihedral : 7.757 74.783 3966 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.66 % Allowed : 15.75 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2944 helix: 1.44 (0.15), residues: 1289 sheet: -0.08 (0.29), residues: 359 loop : -1.40 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 564 HIS 0.004 0.001 HIS D 225 PHE 0.029 0.001 PHE D 145 TYR 0.019 0.001 TYR C 252 ARG 0.004 0.000 ARG A 431 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 12) link_NAG-ASN : angle 2.81051 ( 36) link_ALPHA1-6 : bond 0.00948 ( 6) link_ALPHA1-6 : angle 1.64092 ( 18) link_BETA1-4 : bond 0.00792 ( 14) link_BETA1-4 : angle 2.30708 ( 42) link_ALPHA1-3 : bond 0.01317 ( 6) link_ALPHA1-3 : angle 3.53924 ( 18) hydrogen bonds : bond 0.03439 ( 1022) hydrogen bonds : angle 4.28109 ( 2994) SS BOND : bond 0.00050 ( 3) SS BOND : angle 0.32580 ( 6) covalent geometry : bond 0.00418 (24546) covalent geometry : angle 0.69197 (33238) ********************** 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 115 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 3.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7397 (mtm) REVERT: A 501 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8501 (mtt) REVERT: A 534 MET cc_start: 0.8002 (mtm) cc_final: 0.7558 (mtm) REVERT: A 691 MET cc_start: 0.8733 (ptm) cc_final: 0.8206 (ptt) REVERT: B 565 MET cc_start: 0.8996 (tpp) cc_final: 0.8544 (mpp) REVERT: B 691 MET cc_start: 0.8914 (tmm) cc_final: 0.8362 (tmm) REVERT: B 793 MET cc_start: 0.9034 (tpp) cc_final: 0.8328 (pp-130) REVERT: B 794 MET cc_start: 0.6369 (tpt) cc_final: 0.4420 (tpt) REVERT: C 81 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7952 (mp10) REVERT: C 664 MET cc_start: 0.8705 (mmm) cc_final: 0.8420 (tmm) REVERT: C 735 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8224 (t80) REVERT: C 793 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8482 (pp-130) REVERT: D 413 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8146 (mmm) REVERT: D 438 ILE cc_start: 0.4763 (OUTLIER) cc_final: 0.4251 (tp) REVERT: D 664 MET cc_start: 0.9003 (mmm) cc_final: 0.8675 (mmt) REVERT: D 770 MET cc_start: 0.5894 (mpm) cc_final: 0.5436 (mpp) outliers start: 17 outliers final: 4 residues processed: 110 average time/residue: 2.1748 time to fit residues: 275.4258 Evaluate side-chains 109 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 774 TYR 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 413 MET 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 77 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 244 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 278 optimal weight: 1.9990 chunk 122 optimal weight: 30.0000 chunk 142 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.042556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.032685 restraints weight = 220624.537| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 4.69 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24587 Z= 0.171 Angle : 0.697 13.598 33358 Z= 0.323 Chirality : 0.041 0.330 3870 Planarity : 0.003 0.036 4128 Dihedral : 7.591 71.377 3966 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.66 % Allowed : 16.06 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2944 helix: 1.51 (0.15), residues: 1286 sheet: 0.00 (0.28), residues: 376 loop : -1.37 (0.18), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 564 HIS 0.004 0.001 HIS D 225 PHE 0.036 0.001 PHE D 145 TYR 0.020 0.001 TYR C 252 ARG 0.004 0.000 ARG A 431 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 12) link_NAG-ASN : angle 2.75496 ( 36) link_ALPHA1-6 : bond 0.00933 ( 6) link_ALPHA1-6 : angle 1.57641 ( 18) link_BETA1-4 : bond 0.00800 ( 14) link_BETA1-4 : angle 2.29351 ( 42) link_ALPHA1-3 : bond 0.01255 ( 6) link_ALPHA1-3 : angle 3.51970 ( 18) hydrogen bonds : bond 0.03356 ( 1022) hydrogen bonds : angle 4.23452 ( 2994) SS BOND : bond 0.00057 ( 3) SS BOND : angle 0.29422 ( 6) covalent geometry : bond 0.00371 (24546) covalent geometry : angle 0.68174 (33238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13543.16 seconds wall clock time: 241 minutes 32.39 seconds (14492.39 seconds total)