Starting phenix.real_space_refine on Sat Feb 7 00:36:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f59_31462/02_2026/7f59_31462_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f59_31462/02_2026/7f59_31462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f59_31462/02_2026/7f59_31462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f59_31462/02_2026/7f59_31462.map" model { file = "/net/cci-nas-00/data/ceres_data/7f59_31462/02_2026/7f59_31462_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f59_31462/02_2026/7f59_31462_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.101 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 171 5.16 5 C 18558 2.51 5 N 4806 2.21 5 O 5437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28972 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 6604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6604 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 801} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6572 Classifications: {'peptide': 831} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 797} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 6614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6614 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 33, 'TRANS': 801} Chain: "D" Number of atoms: 6471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6471 Classifications: {'peptide': 818} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 784} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 2441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2441 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGT:plan-1': 1, 'PGT:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.70, per 1000 atoms: 0.23 Number of scatterers: 28972 At special positions: 0 Unit cell: (125.12, 142.8, 220.32, 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 171 16.00 O 5437 8.00 N 4806 7.00 C 18558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.38 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.22 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.39 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.29 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS E 72 " distance=2.37 Simple disulfide: pdb=" SG CYS E 177 " - pdb=" SG CYS E 207 " distance=2.04 Simple disulfide: pdb=" SG CYS E 234 " - pdb=" SG CYS E 256 " distance=1.99 Simple disulfide: pdb=" SG CYS E 297 " - pdb=" SG CYS E 309 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 322 " distance=2.33 Simple disulfide: pdb=" SG CYS E 316 " - pdb=" SG CYS E 331 " 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=1, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " 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-ASN " NAG A1001 " - " ASN A 275 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 412 " " NAG B1003 " - " ASN B 546 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " " NAG D1003 " - " ASN D 546 " " NAG F 1 " - " ASN A 378 " " NAG G 1 " - " ASN B 378 " " NAG H 1 " - " ASN C 378 " " NAG I 1 " - " ASN D 378 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.1 seconds 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6768 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 48 sheets defined 43.4% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.983A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.128A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 210 through 222 removed outlier: 4.243A pdb=" N LEU A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 4.331A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.638A pdb=" N TYR A 271 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.701A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 317 through 335 removed outlier: 3.784A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 removed outlier: 3.996A pdb=" N PHE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 461 through 475 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.998A pdb=" N ASP A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 527 Processing helix chain 'A' and resid 560 through 582 removed outlier: 3.986A pdb=" N TRP A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 630 through 665 removed outlier: 4.217A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 Processing helix chain 'A' and resid 689 through 697 Processing helix chain 'A' and resid 699 through 713 Processing helix chain 'A' and resid 721 through 731 Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 773 through 789 removed outlier: 4.427A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 Processing helix chain 'A' and resid 824 through 851 removed outlier: 3.926A pdb=" N ALA A 828 " --> pdb=" O PHE A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 866 removed outlier: 3.742A pdb=" N ARG A 866 " --> pdb=" O VAL A 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 removed outlier: 4.396A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 102 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.940A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 168 removed outlier: 3.612A pdb=" N LEU B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 190 removed outlier: 3.985A pdb=" N ILE B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.621A pdb=" N ALA B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.954A pdb=" N GLY B 273 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.501A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.888A pdb=" N SER B 309 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 306 through 310' Processing helix chain 'B' and resid 317 through 335 removed outlier: 3.665A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 removed outlier: 3.581A pdb=" N LEU B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 removed outlier: 4.014A pdb=" N GLY B 419 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 475 Processing helix chain 'B' and resid 500 through 507 removed outlier: 4.145A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.646A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.816A pdb=" N TRP B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.618A pdb=" N MET B 620 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 660 removed outlier: 3.734A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 removed outlier: 3.660A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 695 Processing helix chain 'B' and resid 701 through 712 removed outlier: 3.754A pdb=" N MET B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 Processing helix chain 'B' and resid 738 through 747 Processing helix chain 'B' and resid 773 through 788 removed outlier: 4.606A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 798 Processing helix chain 'B' and resid 816 through 820 Processing helix chain 'B' and resid 821 through 850 removed outlier: 3.883A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 863 removed outlier: 3.787A pdb=" N SER B 859 " --> pdb=" O ARG B 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.624A pdb=" N VAL C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 125 removed outlier: 4.648A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 Processing helix chain 'C' and resid 180 through 190 removed outlier: 5.417A pdb=" N GLU C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 210 through 221 removed outlier: 4.573A pdb=" N LEU C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.571A pdb=" N ALA C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 301 Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.559A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 366 removed outlier: 3.581A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 461 through 475 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 526 Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 562 through 583 Processing helix chain 'C' and resid 607 through 620 Processing helix chain 'C' and resid 630 through 664 Processing helix chain 'C' and resid 670 through 677 Processing helix chain 'C' and resid 689 through 696 Processing helix chain 'C' and resid 699 through 713 Processing helix chain 'C' and resid 720 through 731 Processing helix chain 'C' and resid 739 through 747 Processing helix chain 'C' and resid 773 through 788 removed outlier: 3.948A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 799 Processing helix chain 'C' and resid 824 through 848 Processing helix chain 'C' and resid 856 through 866 Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.959A pdb=" N ASN D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN D 67 " --> pdb=" O THR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 101 Processing helix chain 'D' and resid 111 through 124 Processing helix chain 'D' and resid 152 through 168 removed outlier: 3.502A pdb=" N LEU D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 190 removed outlier: 5.197A pdb=" N GLU D 187 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.651A pdb=" N ALA D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 266 through 270 Processing helix chain 'D' and resid 286 through 301 Processing helix chain 'D' and resid 317 through 335 removed outlier: 3.549A pdb=" N ALA D 321 " --> pdb=" O THR D 317 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 3.921A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 461 through 475 Processing helix chain 'D' and resid 500 through 507 removed outlier: 4.166A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.639A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 584 removed outlier: 4.242A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 620 Processing helix chain 'D' and resid 630 through 661 removed outlier: 3.789A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 675 removed outlier: 3.821A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 670 through 675' Processing helix chain 'D' and resid 688 through 695 Processing helix chain 'D' and resid 702 through 712 Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 739 through 749 Processing helix chain 'D' and resid 773 through 789 removed outlier: 4.183A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 800 removed outlier: 3.704A pdb=" N MET D 793 " --> pdb=" O GLY D 789 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP D 798 " --> pdb=" O MET D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 850 Processing helix chain 'E' and resid 347 through 372 removed outlier: 3.901A pdb=" N VAL E 368 " --> pdb=" O ILE E 364 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN E 369 " --> pdb=" O SER E 365 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 83 removed outlier: 5.392A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLY A 39 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 203 removed outlier: 7.066A pdb=" N VAL A 172 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR A 171 " --> pdb=" O HIS A 225 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE A 227 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 226 " --> pdb=" O HIS A 253 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 255 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE A 279 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 390 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N SER A 393 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS A 401 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 369 Processing sheet with id=AA4, first strand: chain 'A' and resid 432 through 437 Processing sheet with id=AA5, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA7, first strand: chain 'A' and resid 737 through 738 removed outlier: 3.817A pdb=" N MET A 737 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 539 " --> pdb=" O MET A 737 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 737 through 738 removed outlier: 3.817A pdb=" N MET A 737 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 539 " --> pdb=" O MET A 737 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 38 removed outlier: 5.822A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.357A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 172 through 176 removed outlier: 3.726A pdb=" N TYR B 176 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 226 through 228 removed outlier: 4.358A pdb=" N PHE B 279 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 394 " --> pdb=" O MET B 276 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 392 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 390 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 400 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AB5, first strand: chain 'B' and resid 403 through 406 removed outlier: 3.640A pdb=" N ASN B 412 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP B 406 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 436 through 437 Processing sheet with id=AB7, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB8, first strand: chain 'B' and resid 490 through 492 Processing sheet with id=AB9, first strand: chain 'B' and resid 513 through 518 removed outlier: 3.981A pdb=" N ALA B 515 " --> pdb=" O GLY B 765 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY B 765 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU B 517 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY B 763 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 540 through 543 removed outlier: 3.848A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 684 through 685 removed outlier: 6.632A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 39 through 41 removed outlier: 6.561A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 106 through 107 removed outlier: 6.485A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 171 through 176 removed outlier: 7.472A pdb=" N VAL C 172 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 225 through 228 removed outlier: 6.271A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AC8, first strand: chain 'C' and resid 392 through 395 Processing sheet with id=AC9, first strand: chain 'C' and resid 434 through 437 Processing sheet with id=AD1, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AD2, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AD3, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.842A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 737 through 738 removed outlier: 3.640A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AD6, first strand: chain 'D' and resid 39 through 40 removed outlier: 6.986A pdb=" N GLY D 39 " --> pdb=" O LEU D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 42 through 43 removed outlier: 6.213A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 173 through 176 removed outlier: 6.204A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 369 through 370 Processing sheet with id=AE1, first strand: chain 'D' and resid 389 through 390 removed outlier: 3.654A pdb=" N THR D 404 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 393 through 394 removed outlier: 3.605A pdb=" N GLU D 400 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 433 through 435 Processing sheet with id=AE4, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AE5, first strand: chain 'D' and resid 514 through 518 removed outlier: 8.348A pdb=" N ALA D 515 " --> pdb=" O GLY D 767 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY D 767 " --> pdb=" O ALA D 515 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU D 517 " --> pdb=" O GLY D 765 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 514 through 518 removed outlier: 8.348A pdb=" N ALA D 515 " --> pdb=" O GLY D 767 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY D 767 " --> pdb=" O ALA D 515 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU D 517 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 735 through 738 removed outlier: 3.503A pdb=" N MET D 737 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 684 through 685 removed outlier: 6.536A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 54 through 58 removed outlier: 3.739A pdb=" N ILE E 84 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER E 132 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU E 86 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE E 130 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 72 through 77 removed outlier: 3.608A pdb=" N PHE E 141 " --> pdb=" O CYS E 72 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET E 137 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS E 140 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP E 119 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP E 109 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU E 117 " --> pdb=" O ASP E 109 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 178 through 180 removed outlier: 7.026A pdb=" N PHE E 179 " --> pdb=" O THR E 210 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N LYS E 212 " --> pdb=" O PHE E 179 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 239 " --> pdb=" O PHE E 255 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 185 through 188 removed outlier: 3.614A pdb=" N GLY E 186 " --> pdb=" O PHE E 289 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET E 287 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG E 284 " --> pdb=" O TYR E 226 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR E 226 " --> pdb=" O ARG E 284 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG E 286 " --> pdb=" O LEU E 224 " (cutoff:3.500A) 1187 hydrogen bonds defined for protein. 3390 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: 5.60 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4729 1.30 - 1.43: 7896 1.43 - 1.56: 16714 1.56 - 1.69: 0 1.69 - 1.82: 285 Bond restraints: 29624 Sorted by residual: bond pdb=" C LEU A 445 " pdb=" O LEU A 445 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.51e-02 4.39e+03 1.76e+01 bond pdb=" CA ASP B 260 " pdb=" C ASP B 260 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" N ASN A 549 " pdb=" CA ASN A 549 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.14e-02 7.69e+03 1.16e+01 bond pdb=" C PRO E 295 " pdb=" O PRO E 295 " ideal model delta sigma weight residual 1.243 1.214 0.029 8.50e-03 1.38e+04 1.16e+01 bond pdb=" C GLU B 267 " pdb=" N PRO B 268 " ideal model delta sigma weight residual 1.337 1.305 0.032 9.80e-03 1.04e+04 1.05e+01 ... (remaining 29619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 38775 2.69 - 5.37: 1184 5.37 - 8.06: 125 8.06 - 10.74: 20 10.74 - 13.43: 3 Bond angle restraints: 40107 Sorted by residual: angle pdb=" N PRO E 295 " pdb=" CA PRO E 295 " pdb=" C PRO E 295 " ideal model delta sigma weight residual 110.58 123.04 -12.46 1.07e+00 8.73e-01 1.36e+02 angle pdb=" N CYS E 297 " pdb=" CA CYS E 297 " pdb=" C CYS E 297 " ideal model delta sigma weight residual 110.23 119.43 -9.20 1.45e+00 4.76e-01 4.03e+01 angle pdb=" N THR D 180 " pdb=" CA THR D 180 " pdb=" C THR D 180 " ideal model delta sigma weight residual 112.87 105.31 7.56 1.20e+00 6.94e-01 3.96e+01 angle pdb=" N THR E 298 " pdb=" CA THR E 298 " pdb=" C THR E 298 " ideal model delta sigma weight residual 109.14 100.06 9.08 1.49e+00 4.50e-01 3.71e+01 angle pdb=" C LYS E 198 " pdb=" CA LYS E 198 " pdb=" CB LYS E 198 " ideal model delta sigma weight residual 110.67 119.61 -8.94 1.52e+00 4.33e-01 3.46e+01 ... (remaining 40102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 16863 21.65 - 43.30: 965 43.30 - 64.95: 70 64.95 - 86.60: 50 86.60 - 108.25: 20 Dihedral angle restraints: 17968 sinusoidal: 7448 harmonic: 10520 Sorted by residual: dihedral pdb=" CB CYS E 45 " pdb=" SG CYS E 45 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual 93.00 36.82 56.18 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CA PHE B 694 " pdb=" C PHE B 694 " pdb=" N LYS B 695 " pdb=" CA LYS B 695 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA GLU E 328 " pdb=" C GLU E 328 " pdb=" N ASN E 329 " pdb=" CA ASN E 329 " ideal model delta harmonic sigma weight residual 180.00 -150.28 -29.72 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 17965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.976: 4514 0.976 - 1.952: 1 1.952 - 2.928: 0 2.928 - 3.905: 1 3.905 - 4.881: 1 Chirality restraints: 4517 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 0.77 -3.17 2.00e-02 2.50e+03 2.51e+04 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 378 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 2.48 -4.88 2.00e-01 2.50e+01 5.96e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.48e+01 ... (remaining 4514 not shown) Planarity restraints: 5083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1001 " -0.348 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG A1001 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1001 " -0.138 2.00e-02 2.50e+03 pdb=" N2 NAG A1001 " 0.534 2.00e-02 2.50e+03 pdb=" O7 NAG A1001 " -0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1001 " -0.323 2.00e-02 2.50e+03 2.80e-01 9.82e+02 pdb=" C7 NAG B1001 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG B1001 " -0.133 2.00e-02 2.50e+03 pdb=" N2 NAG B1001 " 0.501 2.00e-02 2.50e+03 pdb=" O7 NAG B1001 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.320 2.00e-02 2.50e+03 2.77e-01 9.60e+02 pdb=" C7 NAG F 1 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.030 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.484 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.204 2.00e-02 2.50e+03 ... (remaining 5080 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 37 2.24 - 2.91: 13852 2.91 - 3.57: 45201 3.57 - 4.24: 67228 4.24 - 4.90: 106583 Nonbonded interactions: 232901 Sorted by model distance: nonbonded pdb=" NH2 ARG C 220 " pdb=" CD1 PHE E 102 " model vdw 1.580 3.420 nonbonded pdb=" CZ ARG C 220 " pdb=" CE1 PHE E 102 " model vdw 1.652 2.856 nonbonded pdb=" NH2 ARG C 220 " pdb=" CE1 PHE E 102 " model vdw 1.842 3.420 nonbonded pdb=" O ILE D 699 " pdb=" OG SER D 700 " model vdw 2.157 3.040 nonbonded pdb=" N GLU D 233 " pdb=" OE1 GLU D 233 " model vdw 2.167 3.120 ... (remaining 232896 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 527 or (resid 528 and (name N or name CA or nam \ e C or name O or name CB )) or resid 529 through 663 or (resid 664 and (name N o \ r name CA or name C or name O or name CB )) or resid 665 through 850)) selection = (chain 'B' and (resid 33 through 269 or (resid 270 and (name N or name CA or nam \ e C or name O or name CB )) or resid 271 through 471 or (resid 472 and (name N o \ r name CA or name C or name O or name CB )) or resid 473 through 691 or (resid 6 \ 92 and (name N or name CA or name C or name O or name CB )) or resid 693 through \ 850)) selection = (chain 'C' and (resid 33 through 269 or (resid 270 and (name N or name CA or nam \ e C or name O or name CB )) or resid 271 through 471 or (resid 472 and (name N o \ r name CA or name C or name O or name CB )) or resid 473 through 527 or (resid 5 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 529 through \ 663 or (resid 664 and (name N or name CA or name C or name O or name CB )) or r \ esid 665 through 691 or (resid 692 and (name N or name CA or name C or name O or \ name CB )) or resid 693 through 850)) selection = (chain 'D' and (resid 33 through 269 or (resid 270 and (name N or name CA or nam \ e C or name O or name CB )) or resid 271 through 471 or (resid 472 and (name N o \ r name CA or name C or name O or name CB )) or resid 473 through 527 or (resid 5 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 529 through \ 691 or (resid 692 and (name N or name CA or name C or name O or name CB )) or r \ esid 693 through 850)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.920 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.010 0.363 29654 Z= 0.501 Angle : 1.126 20.167 40184 Z= 0.654 Chirality : 0.108 4.881 4517 Planarity : 0.012 0.300 5072 Dihedral : 14.054 108.252 11170 Min Nonbonded Distance : 1.580 Molprobity Statistics. All-atom Clashscore : 29.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.51 % Favored : 88.43 % Rotamer: Outliers : 0.19 % Allowed : 1.05 % Favored : 98.76 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.13), residues: 3614 helix: -0.54 (0.13), residues: 1378 sheet: -2.21 (0.26), residues: 386 loop : -2.53 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 634 TYR 0.043 0.003 TYR A 44 PHE 0.042 0.003 PHE A 42 TRP 0.053 0.003 TRP B 706 HIS 0.012 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00846 (29624) covalent geometry : angle 1.08791 (40107) SS BOND : bond 0.23757 ( 10) SS BOND : angle 7.23279 ( 20) hydrogen bonds : bond 0.20230 ( 1186) hydrogen bonds : angle 8.12981 ( 3390) Misc. bond : bond 0.19143 ( 1) link_BETA1-4 : bond 0.01636 ( 8) link_BETA1-4 : angle 4.28375 ( 24) link_NAG-ASN : bond 0.01629 ( 11) link_NAG-ASN : angle 7.70276 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 180 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 664 MET cc_start: 0.8573 (tmm) cc_final: 0.8263 (tmm) REVERT: A 691 MET cc_start: 0.8782 (ppp) cc_final: 0.8450 (ppp) REVERT: A 709 MET cc_start: 0.8126 (pmm) cc_final: 0.7882 (pmm) REVERT: A 737 MET cc_start: 0.7995 (ttp) cc_final: 0.7626 (ttp) REVERT: A 793 MET cc_start: 0.9297 (mpp) cc_final: 0.8908 (mpp) REVERT: A 794 MET cc_start: 0.9366 (mpp) cc_final: 0.8744 (mpp) REVERT: B 316 MET cc_start: 0.8260 (mmt) cc_final: 0.8015 (mmt) REVERT: B 705 MET cc_start: 0.9096 (ttt) cc_final: 0.8865 (ttt) REVERT: B 770 MET cc_start: 0.8203 (mmt) cc_final: 0.7692 (mmt) REVERT: C 664 MET cc_start: 0.9080 (ppp) cc_final: 0.8604 (tmm) REVERT: D 534 MET cc_start: 0.9025 (ppp) cc_final: 0.8659 (ppp) REVERT: D 737 MET cc_start: 0.8883 (ptp) cc_final: 0.8509 (ptp) REVERT: E 137 MET cc_start: 0.8403 (mmt) cc_final: 0.8115 (mmp) REVERT: E 308 MET cc_start: 0.8699 (mmp) cc_final: 0.7988 (mmm) outliers start: 6 outliers final: 3 residues processed: 186 average time/residue: 0.1826 time to fit residues: 56.0601 Evaluate side-chains 147 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN A 604 ASN A 622 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 111 HIS B 129 HIS B 350 HIS ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN C 430 ASN C 610 ASN D 98 GLN D 253 HIS D 591 ASN ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.061490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.047882 restraints weight = 225980.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.048710 restraints weight = 134474.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.048888 restraints weight = 106716.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.048744 restraints weight = 96913.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.048926 restraints weight = 90930.338| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29654 Z= 0.173 Angle : 0.748 11.746 40184 Z= 0.376 Chirality : 0.046 0.346 4517 Planarity : 0.005 0.081 5072 Dihedral : 8.590 68.368 4317 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.22 % Allowed : 5.24 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.14), residues: 3614 helix: 0.36 (0.13), residues: 1406 sheet: -1.96 (0.25), residues: 425 loop : -2.09 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 220 TYR 0.017 0.002 TYR A 44 PHE 0.043 0.002 PHE E 112 TRP 0.026 0.002 TRP B 706 HIS 0.008 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00366 (29624) covalent geometry : angle 0.73054 (40107) SS BOND : bond 0.00550 ( 10) SS BOND : angle 1.47307 ( 20) hydrogen bonds : bond 0.05055 ( 1186) hydrogen bonds : angle 5.89217 ( 3390) Misc. bond : bond 0.00346 ( 1) link_BETA1-4 : bond 0.00622 ( 8) link_BETA1-4 : angle 2.98301 ( 24) link_NAG-ASN : bond 0.01325 ( 11) link_NAG-ASN : angle 5.00486 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 MET cc_start: 0.9067 (ptp) cc_final: 0.8821 (ppp) REVERT: A 555 PHE cc_start: 0.6548 (m-80) cc_final: 0.6173 (t80) REVERT: A 664 MET cc_start: 0.8661 (tmm) cc_final: 0.8382 (tmm) REVERT: A 691 MET cc_start: 0.8650 (ppp) cc_final: 0.8222 (ppp) REVERT: A 709 MET cc_start: 0.8334 (pmm) cc_final: 0.8038 (pmm) REVERT: A 794 MET cc_start: 0.9030 (mpp) cc_final: 0.8515 (mpp) REVERT: B 770 MET cc_start: 0.7986 (mmt) cc_final: 0.7417 (mmt) REVERT: B 861 MET cc_start: 0.7877 (mpp) cc_final: 0.7578 (mpp) REVERT: C 247 MET cc_start: 0.8179 (tpp) cc_final: 0.7829 (tpp) REVERT: C 276 MET cc_start: 0.8734 (mpp) cc_final: 0.8456 (mpp) REVERT: C 569 LEU cc_start: 0.9219 (pp) cc_final: 0.8402 (mm) REVERT: C 644 THR cc_start: 0.8574 (p) cc_final: 0.8367 (t) REVERT: C 664 MET cc_start: 0.9085 (ppp) cc_final: 0.8652 (tmm) REVERT: D 248 MET cc_start: 0.8499 (mmm) cc_final: 0.8297 (mmm) REVERT: D 534 MET cc_start: 0.8942 (ppp) cc_final: 0.8517 (ppp) REVERT: D 565 MET cc_start: 0.8654 (ppp) cc_final: 0.8341 (ppp) REVERT: D 737 MET cc_start: 0.8677 (ptp) cc_final: 0.8037 (ptm) REVERT: D 770 MET cc_start: 0.7960 (mmm) cc_final: 0.7164 (mmp) REVERT: D 793 MET cc_start: 0.8881 (ppp) cc_final: 0.8619 (ppp) REVERT: D 794 MET cc_start: 0.8589 (ttt) cc_final: 0.8218 (ttt) REVERT: E 137 MET cc_start: 0.8959 (mmt) cc_final: 0.8538 (mmm) REVERT: E 308 MET cc_start: 0.8644 (mmp) cc_final: 0.7992 (mmm) outliers start: 7 outliers final: 0 residues processed: 187 average time/residue: 0.1539 time to fit residues: 50.0163 Evaluate side-chains 148 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 240 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 320 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 355 optimal weight: 20.0000 chunk 145 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 348 optimal weight: 0.0670 chunk 67 optimal weight: 20.0000 chunk 328 optimal weight: 6.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.062437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.048548 restraints weight = 226385.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.049091 restraints weight = 138042.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.049248 restraints weight = 107568.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.049429 restraints weight = 93200.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.049586 restraints weight = 86037.575| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29654 Z= 0.130 Angle : 0.658 12.356 40184 Z= 0.331 Chirality : 0.045 0.417 4517 Planarity : 0.004 0.073 5072 Dihedral : 7.123 56.448 4317 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.14), residues: 3614 helix: 0.82 (0.14), residues: 1407 sheet: -1.72 (0.26), residues: 433 loop : -1.93 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 748 TYR 0.023 0.001 TYR C 44 PHE 0.028 0.002 PHE E 112 TRP 0.023 0.001 TRP B 296 HIS 0.015 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00283 (29624) covalent geometry : angle 0.64298 (40107) SS BOND : bond 0.00401 ( 10) SS BOND : angle 0.99739 ( 20) hydrogen bonds : bond 0.04250 ( 1186) hydrogen bonds : angle 5.35736 ( 3390) Misc. bond : bond 0.00308 ( 1) link_BETA1-4 : bond 0.00707 ( 8) link_BETA1-4 : angle 2.57238 ( 24) link_NAG-ASN : bond 0.00849 ( 11) link_NAG-ASN : angle 4.40724 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8817 (mmt) cc_final: 0.8452 (mmm) REVERT: A 664 MET cc_start: 0.8570 (tmm) cc_final: 0.8156 (tmm) REVERT: A 691 MET cc_start: 0.8683 (ppp) cc_final: 0.8238 (ppp) REVERT: A 709 MET cc_start: 0.8402 (pmm) cc_final: 0.8086 (pmm) REVERT: B 323 MET cc_start: 0.8334 (ppp) cc_final: 0.7990 (ppp) REVERT: B 565 MET cc_start: 0.8638 (mtt) cc_final: 0.8381 (mmp) REVERT: B 641 TRP cc_start: 0.8072 (m-10) cc_final: 0.7679 (m-10) REVERT: B 770 MET cc_start: 0.8051 (mmt) cc_final: 0.7530 (mmt) REVERT: C 97 ASP cc_start: 0.7759 (m-30) cc_final: 0.7504 (m-30) REVERT: C 247 MET cc_start: 0.8380 (tpp) cc_final: 0.8137 (tpp) REVERT: C 569 LEU cc_start: 0.9211 (pp) cc_final: 0.8799 (mm) REVERT: C 620 MET cc_start: 0.8530 (mmm) cc_final: 0.7370 (mmm) REVERT: C 644 THR cc_start: 0.8616 (p) cc_final: 0.8407 (t) REVERT: C 664 MET cc_start: 0.9156 (ppp) cc_final: 0.8832 (tmm) REVERT: D 248 MET cc_start: 0.8435 (mmm) cc_final: 0.7880 (mmp) REVERT: D 565 MET cc_start: 0.8686 (ppp) cc_final: 0.8335 (ppp) REVERT: D 737 MET cc_start: 0.8682 (ptp) cc_final: 0.8085 (ptm) REVERT: D 794 MET cc_start: 0.8657 (ttt) cc_final: 0.8251 (ttt) REVERT: E 137 MET cc_start: 0.8967 (mmt) cc_final: 0.8467 (mmm) REVERT: E 308 MET cc_start: 0.8563 (mmp) cc_final: 0.7999 (mmm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1526 time to fit residues: 46.0162 Evaluate side-chains 149 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 184 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 105 optimal weight: 0.0070 chunk 107 optimal weight: 0.9990 chunk 306 optimal weight: 20.0000 chunk 284 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 193 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN C 98 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.062985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.049108 restraints weight = 224541.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.049577 restraints weight = 130003.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.049933 restraints weight = 102757.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.050027 restraints weight = 91328.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.050146 restraints weight = 85286.632| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29654 Z= 0.117 Angle : 0.620 11.152 40184 Z= 0.310 Chirality : 0.043 0.344 4517 Planarity : 0.004 0.044 5072 Dihedral : 6.229 54.755 4317 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.14), residues: 3614 helix: 1.05 (0.14), residues: 1420 sheet: -1.48 (0.25), residues: 439 loop : -1.90 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 800 TYR 0.020 0.001 TYR A 44 PHE 0.039 0.001 PHE D 642 TRP 0.022 0.001 TRP B 296 HIS 0.009 0.001 HIS E 230 Details of bonding type rmsd covalent geometry : bond 0.00252 (29624) covalent geometry : angle 0.60633 (40107) SS BOND : bond 0.00387 ( 10) SS BOND : angle 1.23494 ( 20) hydrogen bonds : bond 0.03789 ( 1186) hydrogen bonds : angle 5.05862 ( 3390) Misc. bond : bond 0.00176 ( 1) link_BETA1-4 : bond 0.00768 ( 8) link_BETA1-4 : angle 2.37080 ( 24) link_NAG-ASN : bond 0.00751 ( 11) link_NAG-ASN : angle 4.11580 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 MET cc_start: 0.8243 (tmm) cc_final: 0.8010 (tmm) REVERT: A 534 MET cc_start: 0.7691 (ppp) cc_final: 0.6934 (ppp) REVERT: A 565 MET cc_start: 0.8905 (mmt) cc_final: 0.8542 (mmm) REVERT: A 664 MET cc_start: 0.8848 (tmm) cc_final: 0.8325 (tmm) REVERT: A 691 MET cc_start: 0.8655 (ppp) cc_final: 0.8258 (ppp) REVERT: A 705 MET cc_start: 0.9080 (ppp) cc_final: 0.8410 (tmm) REVERT: A 709 MET cc_start: 0.8501 (pmm) cc_final: 0.7951 (pmm) REVERT: A 794 MET cc_start: 0.9138 (mpp) cc_final: 0.8618 (mpp) REVERT: B 247 MET cc_start: 0.8344 (tpp) cc_final: 0.7931 (tpt) REVERT: B 360 MET cc_start: 0.9122 (tpt) cc_final: 0.8672 (tpp) REVERT: B 641 TRP cc_start: 0.8032 (m-10) cc_final: 0.7690 (m-10) REVERT: B 644 THR cc_start: 0.7783 (m) cc_final: 0.7572 (t) REVERT: B 691 MET cc_start: 0.8731 (ptt) cc_final: 0.8256 (ptt) REVERT: B 770 MET cc_start: 0.8116 (mmt) cc_final: 0.7602 (mmt) REVERT: B 861 MET cc_start: 0.7683 (mpp) cc_final: 0.7346 (mpp) REVERT: C 97 ASP cc_start: 0.7927 (m-30) cc_final: 0.7616 (m-30) REVERT: C 247 MET cc_start: 0.8451 (tpp) cc_final: 0.8189 (tpp) REVERT: C 569 LEU cc_start: 0.9215 (pp) cc_final: 0.8798 (mm) REVERT: C 620 MET cc_start: 0.8726 (mmm) cc_final: 0.7736 (mmm) REVERT: C 664 MET cc_start: 0.9289 (ppp) cc_final: 0.9027 (tmm) REVERT: C 794 MET cc_start: 0.9106 (pmm) cc_final: 0.8505 (pmm) REVERT: D 248 MET cc_start: 0.8396 (mmm) cc_final: 0.7811 (mmp) REVERT: D 534 MET cc_start: 0.8979 (ppp) cc_final: 0.8706 (ppp) REVERT: D 565 MET cc_start: 0.8687 (ppp) cc_final: 0.8368 (ppp) REVERT: D 737 MET cc_start: 0.8578 (ptp) cc_final: 0.8180 (ptm) REVERT: D 770 MET cc_start: 0.7619 (mmp) cc_final: 0.6908 (mmp) REVERT: D 794 MET cc_start: 0.8921 (ttt) cc_final: 0.8555 (ttt) REVERT: E 137 MET cc_start: 0.9175 (mmt) cc_final: 0.8697 (mmm) REVERT: E 264 MET cc_start: 0.8362 (mmm) cc_final: 0.7799 (tpp) REVERT: E 308 MET cc_start: 0.8572 (mmp) cc_final: 0.8090 (mmm) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.1615 time to fit residues: 51.3772 Evaluate side-chains 148 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 354 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 198 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 352 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** 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 = 0.3602 r_free = 0.3602 target = 0.060369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.046316 restraints weight = 225354.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.046543 restraints weight = 146729.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.046796 restraints weight = 131808.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.046787 restraints weight = 110044.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.046847 restraints weight = 102466.010| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29654 Z= 0.212 Angle : 0.689 10.290 40184 Z= 0.348 Chirality : 0.044 0.350 4517 Planarity : 0.004 0.043 5072 Dihedral : 6.215 54.587 4317 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3614 helix: 1.06 (0.14), residues: 1420 sheet: -1.64 (0.24), residues: 471 loop : -1.94 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 300 TYR 0.015 0.002 TYR A 44 PHE 0.016 0.002 PHE B 42 TRP 0.022 0.002 TRP B 296 HIS 0.010 0.002 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00457 (29624) covalent geometry : angle 0.67660 (40107) SS BOND : bond 0.00486 ( 10) SS BOND : angle 1.16523 ( 20) hydrogen bonds : bond 0.03964 ( 1186) hydrogen bonds : angle 5.20290 ( 3390) Misc. bond : bond 0.00097 ( 1) link_BETA1-4 : bond 0.00642 ( 8) link_BETA1-4 : angle 2.42978 ( 24) link_NAG-ASN : bond 0.00740 ( 11) link_NAG-ASN : angle 4.04404 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8853 (mmt) cc_final: 0.8491 (mmm) REVERT: A 664 MET cc_start: 0.8619 (tmm) cc_final: 0.8198 (tmm) REVERT: A 691 MET cc_start: 0.8761 (ppp) cc_final: 0.8324 (ppp) REVERT: A 709 MET cc_start: 0.8252 (pmm) cc_final: 0.7938 (pmm) REVERT: A 794 MET cc_start: 0.8973 (mpp) cc_final: 0.8467 (mpp) REVERT: B 247 MET cc_start: 0.8266 (tpp) cc_final: 0.7799 (tpt) REVERT: B 360 MET cc_start: 0.9058 (tpt) cc_final: 0.8736 (tpp) REVERT: B 641 TRP cc_start: 0.7840 (m-10) cc_final: 0.7553 (m-10) REVERT: B 770 MET cc_start: 0.8073 (mmt) cc_final: 0.7518 (mmt) REVERT: C 97 ASP cc_start: 0.7758 (m-30) cc_final: 0.7514 (m-30) REVERT: C 664 MET cc_start: 0.9132 (ppp) cc_final: 0.8823 (tmm) REVERT: C 794 MET cc_start: 0.8786 (pmm) cc_final: 0.8268 (pmm) REVERT: D 248 MET cc_start: 0.8561 (mmm) cc_final: 0.8298 (mmm) REVERT: D 360 MET cc_start: 0.8159 (mmt) cc_final: 0.7763 (mmp) REVERT: D 413 MET cc_start: 0.8399 (ptp) cc_final: 0.8069 (ptp) REVERT: D 565 MET cc_start: 0.8785 (ppp) cc_final: 0.8423 (ppp) REVERT: D 737 MET cc_start: 0.8530 (ptp) cc_final: 0.8023 (ptm) REVERT: D 770 MET cc_start: 0.8264 (mmp) cc_final: 0.7728 (mmp) REVERT: D 794 MET cc_start: 0.8850 (ttt) cc_final: 0.8570 (ttt) REVERT: E 137 MET cc_start: 0.9160 (mmt) cc_final: 0.8894 (mmm) REVERT: E 308 MET cc_start: 0.8658 (mmp) cc_final: 0.8152 (mmm) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1611 time to fit residues: 47.1510 Evaluate side-chains 144 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 185 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 320 optimal weight: 6.9990 chunk 246 optimal weight: 30.0000 chunk 120 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 HIS ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.059246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.045299 restraints weight = 226806.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.045496 restraints weight = 151935.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.045653 restraints weight = 144970.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.045785 restraints weight = 113449.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.046140 restraints weight = 106211.668| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 29654 Z= 0.300 Angle : 0.782 11.389 40184 Z= 0.399 Chirality : 0.047 0.355 4517 Planarity : 0.005 0.064 5072 Dihedral : 6.695 58.323 4317 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3614 helix: 0.77 (0.14), residues: 1416 sheet: -1.81 (0.24), residues: 459 loop : -2.13 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 358 TYR 0.020 0.002 TYR C 254 PHE 0.025 0.002 PHE A 42 TRP 0.021 0.002 TRP D 368 HIS 0.013 0.002 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00639 (29624) covalent geometry : angle 0.77136 (40107) SS BOND : bond 0.00584 ( 10) SS BOND : angle 1.20740 ( 20) hydrogen bonds : bond 0.04351 ( 1186) hydrogen bonds : angle 5.51821 ( 3390) Misc. bond : bond 0.00074 ( 1) link_BETA1-4 : bond 0.00592 ( 8) link_BETA1-4 : angle 2.40617 ( 24) link_NAG-ASN : bond 0.00793 ( 11) link_NAG-ASN : angle 3.98953 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8080 (mmp) cc_final: 0.7849 (mmm) REVERT: A 323 MET cc_start: 0.8292 (ppp) cc_final: 0.7881 (ppp) REVERT: A 534 MET cc_start: 0.7894 (ppp) cc_final: 0.7151 (ppp) REVERT: A 565 MET cc_start: 0.8859 (mmt) cc_final: 0.8544 (mmm) REVERT: A 620 MET cc_start: 0.8763 (ttm) cc_final: 0.8558 (ttm) REVERT: A 664 MET cc_start: 0.8545 (tmm) cc_final: 0.8145 (tmm) REVERT: A 691 MET cc_start: 0.8778 (ppp) cc_final: 0.8302 (ppp) REVERT: A 709 MET cc_start: 0.8250 (pmm) cc_final: 0.8007 (pmm) REVERT: A 794 MET cc_start: 0.8943 (mpp) cc_final: 0.8440 (mpp) REVERT: B 323 MET cc_start: 0.8570 (ptm) cc_final: 0.8037 (ppp) REVERT: B 360 MET cc_start: 0.9139 (tpt) cc_final: 0.8815 (tpp) REVERT: B 565 MET cc_start: 0.8829 (mmm) cc_final: 0.8353 (mmp) REVERT: B 691 MET cc_start: 0.8390 (ptt) cc_final: 0.7845 (ptt) REVERT: B 770 MET cc_start: 0.8156 (mmt) cc_final: 0.7584 (mmt) REVERT: C 97 ASP cc_start: 0.7760 (m-30) cc_final: 0.7523 (m-30) REVERT: C 316 MET cc_start: 0.8578 (mmm) cc_final: 0.8308 (mmm) REVERT: C 501 MET cc_start: 0.8075 (mpp) cc_final: 0.7718 (mpp) REVERT: C 569 LEU cc_start: 0.9145 (pp) cc_final: 0.8691 (pp) REVERT: C 620 MET cc_start: 0.8650 (mmp) cc_final: 0.7752 (mmm) REVERT: C 664 MET cc_start: 0.9055 (ppp) cc_final: 0.8649 (tmm) REVERT: C 794 MET cc_start: 0.8930 (pmm) cc_final: 0.8415 (pmm) REVERT: C 861 MET cc_start: 0.1023 (tpt) cc_final: 0.0761 (tpp) REVERT: D 248 MET cc_start: 0.8498 (mmm) cc_final: 0.8297 (mmm) REVERT: D 534 MET cc_start: 0.8958 (ppp) cc_final: 0.8597 (ppp) REVERT: D 565 MET cc_start: 0.8822 (ppp) cc_final: 0.8416 (ppp) REVERT: D 642 PHE cc_start: 0.8976 (t80) cc_final: 0.8581 (t80) REVERT: D 705 MET cc_start: 0.8721 (mmm) cc_final: 0.8423 (tpp) REVERT: D 737 MET cc_start: 0.8589 (ptp) cc_final: 0.8118 (ptp) REVERT: D 770 MET cc_start: 0.8429 (mmp) cc_final: 0.7800 (mmp) REVERT: D 794 MET cc_start: 0.8880 (ttt) cc_final: 0.8587 (ttt) REVERT: E 137 MET cc_start: 0.9170 (mmt) cc_final: 0.8909 (mmm) REVERT: E 264 MET cc_start: 0.8278 (mmm) cc_final: 0.7955 (mmm) REVERT: E 308 MET cc_start: 0.8715 (mmp) cc_final: 0.8209 (mmm) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1619 time to fit residues: 44.6905 Evaluate side-chains 140 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 279 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 354 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 288 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 243 optimal weight: 0.0000 chunk 276 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.061554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.047962 restraints weight = 224205.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.048191 restraints weight = 137592.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.048505 restraints weight = 121441.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.048539 restraints weight = 100058.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.048603 restraints weight = 93638.232| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29654 Z= 0.134 Angle : 0.651 10.690 40184 Z= 0.327 Chirality : 0.044 0.339 4517 Planarity : 0.004 0.043 5072 Dihedral : 6.313 59.776 4317 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3614 helix: 1.11 (0.14), residues: 1417 sheet: -1.56 (0.24), residues: 457 loop : -1.97 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 358 TYR 0.033 0.001 TYR C 566 PHE 0.049 0.002 PHE E 112 TRP 0.026 0.002 TRP B 296 HIS 0.008 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00297 (29624) covalent geometry : angle 0.64075 (40107) SS BOND : bond 0.00426 ( 10) SS BOND : angle 0.98415 ( 20) hydrogen bonds : bond 0.03811 ( 1186) hydrogen bonds : angle 5.08021 ( 3390) Misc. bond : bond 0.00108 ( 1) link_BETA1-4 : bond 0.00610 ( 8) link_BETA1-4 : angle 2.18313 ( 24) link_NAG-ASN : bond 0.00538 ( 11) link_NAG-ASN : angle 3.69858 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.7429 (tmm) cc_final: 0.7191 (tmm) REVERT: A 565 MET cc_start: 0.8811 (mmt) cc_final: 0.8453 (mmm) REVERT: A 664 MET cc_start: 0.8560 (tmm) cc_final: 0.8133 (tmm) REVERT: A 691 MET cc_start: 0.8742 (ppp) cc_final: 0.8269 (ppp) REVERT: A 709 MET cc_start: 0.7817 (pmm) cc_final: 0.7417 (mmt) REVERT: A 794 MET cc_start: 0.8952 (mpp) cc_final: 0.8454 (mpp) REVERT: B 248 MET cc_start: 0.8424 (tpt) cc_final: 0.8045 (tpp) REVERT: B 360 MET cc_start: 0.9069 (tpt) cc_final: 0.8732 (tpp) REVERT: B 565 MET cc_start: 0.8767 (mmm) cc_final: 0.8256 (mmp) REVERT: B 691 MET cc_start: 0.8586 (ptt) cc_final: 0.8304 (ptt) REVERT: B 770 MET cc_start: 0.8139 (mmt) cc_final: 0.7621 (mmt) REVERT: B 861 MET cc_start: 0.7644 (mpp) cc_final: 0.7243 (mpp) REVERT: C 97 ASP cc_start: 0.7545 (m-30) cc_final: 0.7317 (m-30) REVERT: C 316 MET cc_start: 0.8302 (mmm) cc_final: 0.7983 (mmm) REVERT: C 340 MET cc_start: 0.6067 (mtt) cc_final: 0.5810 (mtt) REVERT: C 569 LEU cc_start: 0.9252 (pp) cc_final: 0.8754 (mm) REVERT: C 664 MET cc_start: 0.9109 (ppp) cc_final: 0.8767 (tmm) REVERT: C 737 MET cc_start: 0.8625 (pmm) cc_final: 0.8225 (pmm) REVERT: D 360 MET cc_start: 0.7915 (mmt) cc_final: 0.7509 (mmp) REVERT: D 534 MET cc_start: 0.8948 (ppp) cc_final: 0.8527 (ppp) REVERT: D 565 MET cc_start: 0.8716 (ppp) cc_final: 0.8326 (ppp) REVERT: D 737 MET cc_start: 0.8568 (ptp) cc_final: 0.8237 (ptm) REVERT: D 770 MET cc_start: 0.8452 (mmp) cc_final: 0.7360 (mmp) REVERT: D 794 MET cc_start: 0.8836 (ttt) cc_final: 0.8623 (ttt) REVERT: E 137 MET cc_start: 0.9094 (mmt) cc_final: 0.8823 (mmm) REVERT: E 264 MET cc_start: 0.8210 (mmm) cc_final: 0.7887 (mmm) REVERT: E 308 MET cc_start: 0.8624 (mmp) cc_final: 0.8173 (mmm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1577 time to fit residues: 45.7895 Evaluate side-chains 143 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 104 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 chunk 258 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 265 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 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 = 0.3642 r_free = 0.3642 target = 0.060810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.047238 restraints weight = 227111.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.047615 restraints weight = 141474.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.047749 restraints weight = 126886.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.047819 restraints weight = 103226.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.048189 restraints weight = 96897.526| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29654 Z= 0.210 Angle : 0.700 11.784 40184 Z= 0.354 Chirality : 0.045 0.346 4517 Planarity : 0.004 0.043 5072 Dihedral : 6.372 56.883 4317 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.14), residues: 3614 helix: 1.04 (0.14), residues: 1411 sheet: -1.81 (0.24), residues: 480 loop : -1.99 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 300 TYR 0.016 0.002 TYR C 44 PHE 0.037 0.002 PHE E 112 TRP 0.025 0.002 TRP B 296 HIS 0.009 0.002 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00455 (29624) covalent geometry : angle 0.68985 (40107) SS BOND : bond 0.00479 ( 10) SS BOND : angle 0.98688 ( 20) hydrogen bonds : bond 0.03894 ( 1186) hydrogen bonds : angle 5.20381 ( 3390) Misc. bond : bond 0.00090 ( 1) link_BETA1-4 : bond 0.00545 ( 8) link_BETA1-4 : angle 2.21416 ( 24) link_NAG-ASN : bond 0.00636 ( 11) link_NAG-ASN : angle 3.71708 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.8285 (ppp) cc_final: 0.7701 (ppp) REVERT: A 565 MET cc_start: 0.8813 (mmt) cc_final: 0.8462 (mmm) REVERT: A 620 MET cc_start: 0.8765 (ttm) cc_final: 0.8533 (ttm) REVERT: A 664 MET cc_start: 0.8484 (tmm) cc_final: 0.8068 (tmm) REVERT: A 691 MET cc_start: 0.8739 (ppp) cc_final: 0.8263 (ppp) REVERT: A 709 MET cc_start: 0.7860 (pmm) cc_final: 0.7527 (pmm) REVERT: A 794 MET cc_start: 0.8961 (mpp) cc_final: 0.8452 (mpp) REVERT: B 248 MET cc_start: 0.8143 (tpt) cc_final: 0.7842 (tpp) REVERT: B 323 MET cc_start: 0.8351 (ppp) cc_final: 0.7992 (ppp) REVERT: B 565 MET cc_start: 0.8779 (mmm) cc_final: 0.8279 (mmp) REVERT: B 770 MET cc_start: 0.8183 (mmt) cc_final: 0.7678 (mmt) REVERT: B 861 MET cc_start: 0.7595 (mpp) cc_final: 0.7244 (mpp) REVERT: C 97 ASP cc_start: 0.7535 (m-30) cc_final: 0.7324 (m-30) REVERT: C 569 LEU cc_start: 0.9209 (pp) cc_final: 0.8970 (mm) REVERT: C 664 MET cc_start: 0.9070 (ppp) cc_final: 0.8667 (tmm) REVERT: C 737 MET cc_start: 0.8670 (pmm) cc_final: 0.8301 (pmm) REVERT: C 861 MET cc_start: 0.1053 (tpp) cc_final: 0.0487 (tpt) REVERT: D 360 MET cc_start: 0.8017 (mmt) cc_final: 0.7610 (mmp) REVERT: D 565 MET cc_start: 0.8729 (ppp) cc_final: 0.8332 (ppp) REVERT: D 737 MET cc_start: 0.8568 (ptp) cc_final: 0.8076 (ptm) REVERT: D 770 MET cc_start: 0.8466 (mmp) cc_final: 0.7459 (mmp) REVERT: E 308 MET cc_start: 0.8700 (mmp) cc_final: 0.8223 (mmm) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1561 time to fit residues: 43.7687 Evaluate side-chains 146 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 170 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 320 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 329 optimal weight: 0.9980 chunk 290 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 297 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.061696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.048036 restraints weight = 224274.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.048533 restraints weight = 132862.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.048667 restraints weight = 117318.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.048645 restraints weight = 100858.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.048854 restraints weight = 93206.298| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29654 Z= 0.138 Angle : 0.654 12.511 40184 Z= 0.328 Chirality : 0.043 0.339 4517 Planarity : 0.004 0.043 5072 Dihedral : 6.073 55.249 4317 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3614 helix: 1.20 (0.14), residues: 1421 sheet: -1.65 (0.24), residues: 460 loop : -1.93 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 184 TYR 0.017 0.001 TYR C 44 PHE 0.028 0.002 PHE D 642 TRP 0.033 0.002 TRP B 296 HIS 0.008 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00305 (29624) covalent geometry : angle 0.64486 (40107) SS BOND : bond 0.00407 ( 10) SS BOND : angle 0.89734 ( 20) hydrogen bonds : bond 0.03674 ( 1186) hydrogen bonds : angle 4.99929 ( 3390) Misc. bond : bond 0.00103 ( 1) link_BETA1-4 : bond 0.00630 ( 8) link_BETA1-4 : angle 2.15815 ( 24) link_NAG-ASN : bond 0.00548 ( 11) link_NAG-ASN : angle 3.51205 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 323 MET cc_start: 0.8178 (ppp) cc_final: 0.7536 (ppp) REVERT: A 565 MET cc_start: 0.8827 (mmt) cc_final: 0.8464 (mmm) REVERT: A 664 MET cc_start: 0.8514 (tmm) cc_final: 0.8028 (tmm) REVERT: A 691 MET cc_start: 0.8736 (ppp) cc_final: 0.8280 (ppp) REVERT: A 709 MET cc_start: 0.7819 (pmm) cc_final: 0.7475 (mmt) REVERT: A 794 MET cc_start: 0.8956 (mpp) cc_final: 0.8422 (mpp) REVERT: B 323 MET cc_start: 0.8354 (ppp) cc_final: 0.8040 (ppp) REVERT: B 565 MET cc_start: 0.8759 (mmm) cc_final: 0.8241 (mmp) REVERT: B 641 TRP cc_start: 0.8131 (m-10) cc_final: 0.7857 (m-10) REVERT: B 691 MET cc_start: 0.8043 (ptt) cc_final: 0.7543 (ptt) REVERT: B 705 MET cc_start: 0.9075 (ttt) cc_final: 0.8872 (ttm) REVERT: B 770 MET cc_start: 0.8218 (mmt) cc_final: 0.7750 (mmt) REVERT: B 861 MET cc_start: 0.7685 (mpp) cc_final: 0.7330 (mpp) REVERT: C 247 MET cc_start: 0.7642 (tpp) cc_final: 0.6681 (tpp) REVERT: C 569 LEU cc_start: 0.9353 (pp) cc_final: 0.9026 (mm) REVERT: C 664 MET cc_start: 0.9140 (ppp) cc_final: 0.8788 (tmm) REVERT: C 737 MET cc_start: 0.8814 (pmm) cc_final: 0.8417 (pmm) REVERT: C 861 MET cc_start: 0.0965 (tpp) cc_final: 0.0380 (tpt) REVERT: D 360 MET cc_start: 0.8049 (mmt) cc_final: 0.7615 (mmp) REVERT: D 534 MET cc_start: 0.9002 (ppp) cc_final: 0.8598 (ppp) REVERT: D 565 MET cc_start: 0.8712 (ppp) cc_final: 0.8302 (ppp) REVERT: D 737 MET cc_start: 0.8567 (ptp) cc_final: 0.8115 (ptm) REVERT: D 770 MET cc_start: 0.8520 (mmp) cc_final: 0.7720 (mmp) REVERT: E 228 MET cc_start: 0.7137 (mmp) cc_final: 0.6863 (mmp) REVERT: E 264 MET cc_start: 0.8197 (mmm) cc_final: 0.7779 (tpp) REVERT: E 308 MET cc_start: 0.8651 (mmp) cc_final: 0.8199 (mmm) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1645 time to fit residues: 46.5735 Evaluate side-chains 145 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 131 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 200 optimal weight: 0.4980 chunk 58 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 331 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 27 optimal weight: 50.0000 chunk 204 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 ASN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 HIS D 784 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.062261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.048401 restraints weight = 222387.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.048749 restraints weight = 128856.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.049022 restraints weight = 107917.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.049131 restraints weight = 95014.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.049275 restraints weight = 89536.582| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29654 Z= 0.119 Angle : 0.660 16.022 40184 Z= 0.327 Chirality : 0.044 0.347 4517 Planarity : 0.004 0.043 5072 Dihedral : 5.842 53.715 4317 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3614 helix: 1.28 (0.14), residues: 1420 sheet: -1.41 (0.25), residues: 459 loop : -1.83 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 184 TYR 0.037 0.001 TYR A 44 PHE 0.038 0.001 PHE D 642 TRP 0.030 0.002 TRP B 296 HIS 0.011 0.001 HIS C 792 Details of bonding type rmsd covalent geometry : bond 0.00265 (29624) covalent geometry : angle 0.65073 (40107) SS BOND : bond 0.00365 ( 10) SS BOND : angle 0.80445 ( 20) hydrogen bonds : bond 0.03593 ( 1186) hydrogen bonds : angle 4.91018 ( 3390) Misc. bond : bond 0.00104 ( 1) link_BETA1-4 : bond 0.00682 ( 8) link_BETA1-4 : angle 2.11630 ( 24) link_NAG-ASN : bond 0.00562 ( 11) link_NAG-ASN : angle 3.44221 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7228 Ramachandran restraints generated. 3614 Oldfield, 0 Emsley, 3614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8319 (tpp) cc_final: 0.8107 (tpp) REVERT: A 323 MET cc_start: 0.8101 (ppp) cc_final: 0.7497 (ppp) REVERT: A 565 MET cc_start: 0.8825 (mmt) cc_final: 0.8482 (mmm) REVERT: A 620 MET cc_start: 0.8688 (ttm) cc_final: 0.8470 (ttm) REVERT: A 664 MET cc_start: 0.8457 (tmm) cc_final: 0.7957 (tmm) REVERT: A 691 MET cc_start: 0.8724 (ppp) cc_final: 0.8270 (ppp) REVERT: A 709 MET cc_start: 0.7839 (pmm) cc_final: 0.7318 (mmt) REVERT: B 565 MET cc_start: 0.8794 (mmm) cc_final: 0.8283 (mmp) REVERT: B 691 MET cc_start: 0.8055 (ptt) cc_final: 0.7571 (ptt) REVERT: B 705 MET cc_start: 0.9077 (ttt) cc_final: 0.8749 (ttm) REVERT: B 770 MET cc_start: 0.8217 (mmt) cc_final: 0.7755 (mmt) REVERT: B 861 MET cc_start: 0.7664 (mpp) cc_final: 0.7312 (mpp) REVERT: C 247 MET cc_start: 0.8107 (tpp) cc_final: 0.6989 (tpp) REVERT: C 316 MET cc_start: 0.7770 (mmm) cc_final: 0.7509 (mmm) REVERT: C 569 LEU cc_start: 0.9343 (pp) cc_final: 0.9016 (mm) REVERT: C 664 MET cc_start: 0.9130 (ppp) cc_final: 0.8767 (tmm) REVERT: C 737 MET cc_start: 0.8667 (pmm) cc_final: 0.8268 (pmm) REVERT: C 861 MET cc_start: 0.1306 (tpp) cc_final: 0.0707 (tpt) REVERT: D 360 MET cc_start: 0.7809 (mmt) cc_final: 0.7342 (mmp) REVERT: D 534 MET cc_start: 0.9011 (ppp) cc_final: 0.8612 (ppp) REVERT: D 565 MET cc_start: 0.8715 (ppp) cc_final: 0.8324 (ppp) REVERT: D 737 MET cc_start: 0.8530 (ptp) cc_final: 0.8121 (ptm) REVERT: D 770 MET cc_start: 0.8511 (mmp) cc_final: 0.7690 (mmp) REVERT: E 264 MET cc_start: 0.8201 (mmm) cc_final: 0.7791 (tpp) REVERT: E 308 MET cc_start: 0.8697 (mmp) cc_final: 0.8214 (mmm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1566 time to fit residues: 45.4830 Evaluate side-chains 148 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 235 optimal weight: 9.9990 chunk 188 optimal weight: 0.9980 chunk 299 optimal weight: 2.9990 chunk 205 optimal weight: 0.0870 chunk 228 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 275 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 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 = 0.3689 r_free = 0.3689 target = 0.062515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.048899 restraints weight = 224878.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.049574 restraints weight = 133747.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.049591 restraints weight = 118827.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.049783 restraints weight = 94341.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.049933 restraints weight = 88157.607| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29654 Z= 0.116 Angle : 0.642 12.636 40184 Z= 0.317 Chirality : 0.043 0.347 4517 Planarity : 0.004 0.044 5072 Dihedral : 5.607 53.449 4317 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3614 helix: 1.35 (0.14), residues: 1425 sheet: -1.34 (0.25), residues: 464 loop : -1.76 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 300 TYR 0.020 0.001 TYR D 682 PHE 0.037 0.001 PHE D 642 TRP 0.026 0.002 TRP B 296 HIS 0.007 0.001 HIS C 792 Details of bonding type rmsd covalent geometry : bond 0.00261 (29624) covalent geometry : angle 0.63350 (40107) SS BOND : bond 0.00351 ( 10) SS BOND : angle 0.73638 ( 20) hydrogen bonds : bond 0.03483 ( 1186) hydrogen bonds : angle 4.80840 ( 3390) Misc. bond : bond 0.00096 ( 1) link_BETA1-4 : bond 0.00669 ( 8) link_BETA1-4 : angle 2.07705 ( 24) link_NAG-ASN : bond 0.00565 ( 11) link_NAG-ASN : angle 3.37109 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3905.58 seconds wall clock time: 69 minutes 0.14 seconds (4140.14 seconds total)