Starting phenix.real_space_refine on Fri Mar 6 04:03:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f56_31459/03_2026/7f56_31459_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f56_31459/03_2026/7f56_31459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f56_31459/03_2026/7f56_31459_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f56_31459/03_2026/7f56_31459_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f56_31459/03_2026/7f56_31459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f56_31459/03_2026/7f56_31459.map" } resolution = 4.1 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= 0.005 sd= 0.085 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 157 5.16 5 C 17826 2.51 5 N 4601 2.21 5 O 5250 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27834 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 6578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6578 Classifications: {'peptide': 831} Link IDs: {'PTRANS': 33, 'TRANS': 797} Chain: "B" Number of atoms: 6575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6575 Classifications: {'peptide': 831} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 797} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 6604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6604 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 801} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 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: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1226 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 142} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "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: "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: 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.23, per 1000 atoms: 0.22 Number of scatterers: 27834 At special positions: 0 Unit cell: (125.12, 161.84, 208.08, 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 157 16.00 O 5250 8.00 N 4601 7.00 C 17826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.40 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.21 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=2.31 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS E 72 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 430 " " NAG A1002 " - " ASN A 546 " " NAG A1003 " - " ASN A 412 " " NAG B1001 " - " ASN B 751 " " NAG B1002 " - " ASN B 546 " " NAG B1003 " - " ASN B 275 " " NAG B1004 " - " ASN B 412 " " NAG C1001 " - " ASN C 751 " " NAG C1002 " - " ASN C 546 " " NAG C1003 " - " ASN C 275 " " NAG C1004 " - " ASN C 378 " " NAG C1005 " - " ASN C 412 " " NAG D1001 " - " ASN D 751 " " NAG D1002 " - " ASN D 546 " " NAG D1003 " - " ASN D 275 " " NAG D1004 " - " ASN D 412 " " NAG F 1 " - " ASN A 275 " " NAG G 1 " - " ASN A 378 " " NAG H 1 " - " ASN B 378 " " NAG I 1 " - " ASN D 378 " Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.3 seconds 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 45 sheets defined 46.0% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 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: 3.745A 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: 4.127A 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: 4.330A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 removed outlier: 4.450A pdb=" N TYR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER A 272 " --> pdb=" O PRO A 268 " (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: 3.785A 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 461 through 474 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 560 through 584 Processing helix chain 'A' and resid 607 through 620 Processing helix chain 'A' and resid 631 through 665 removed outlier: 4.026A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 690 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 772 through 788 removed outlier: 4.441A pdb=" N ASP A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 4.350A 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 821 through 850 Processing helix chain 'A' and resid 855 through 863 removed outlier: 3.686A pdb=" N SER A 859 " --> pdb=" O ARG A 855 " (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: 3.732A 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: 3.620A 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: 3.666A 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 418 removed outlier: 3.505A pdb=" N LYS B 418 " --> pdb=" O GLU B 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 418' Processing helix chain 'B' and resid 424 through 429 removed outlier: 3.937A pdb=" N LEU B 428 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 454 removed outlier: 4.045A pdb=" N TYR B 454 " --> pdb=" O LYS B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 500 through 507 removed outlier: 3.786A pdb=" N ASP B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 560 through 584 removed outlier: 4.250A pdb=" N TRP B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 619 Processing helix chain 'B' and resid 631 through 662 removed outlier: 4.012A pdb=" N ILE B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 Processing helix chain 'B' and resid 688 through 695 Processing helix chain 'B' and resid 701 through 712 Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.551A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 747 Processing helix chain 'B' and resid 773 through 788 removed outlier: 3.955A pdb=" N LYS B 777 " --> pdb=" O PRO B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 Processing helix chain 'B' and resid 816 through 821 Processing helix chain 'B' and resid 821 through 850 removed outlier: 3.912A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 863 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 179 through 185 removed outlier: 3.624A pdb=" N ILE C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 210 through 222 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: 3.821A 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: 3.640A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.885A 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 461 through 475 removed outlier: 3.755A pdb=" N ASP C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 563 through 584 removed outlier: 4.018A pdb=" N PHE C 584 " --> pdb=" O VAL C 580 " (cutoff:3.500A) 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 697 removed outlier: 3.665A pdb=" N PHE C 693 " --> pdb=" O ALA C 689 " (cutoff:3.500A) 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 748 Processing helix chain 'C' and resid 773 through 789 removed outlier: 4.073A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 800 removed outlier: 3.569A pdb=" N MET C 793 " --> pdb=" O GLY C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 848 removed outlier: 3.531A pdb=" N ALA C 828 " --> pdb=" O PHE C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 867 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: 3.933A 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: 3.650A 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: 3.920A 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 413 through 417 removed outlier: 3.976A pdb=" N GLN D 417 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 461 through 475 Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.511A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP D 507 " --> pdb=" O ARG D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.760A pdb=" N LYS D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 584 removed outlier: 3.825A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.580A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 619 " --> pdb=" O GLY D 615 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET D 620 " --> pdb=" O VAL D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 665 removed outlier: 4.370A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 695 Processing helix chain 'D' and resid 701 through 712 removed outlier: 3.570A pdb=" N MET D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 739 through 749 Processing helix chain 'D' and resid 772 through 789 removed outlier: 4.367A pdb=" N ASP D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 800 removed outlier: 3.628A pdb=" N MET D 793 " --> pdb=" O GLY D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 820 Processing helix chain 'D' and resid 821 through 850 removed outlier: 3.943A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 354 through 382 removed outlier: 3.804A pdb=" N VAL E 358 " --> pdb=" O THR E 354 " (cutoff:3.500A) Proline residue: E 373 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.681A pdb=" N LEU A 36 " --> pdb=" O THR A 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, 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: 6.031A 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=AA3, first strand: chain 'A' and resid 198 through 203 removed outlier: 7.067A 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: 3.591A 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: 4.703A pdb=" N PHE A 279 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 394 " --> pdb=" O MET A 276 " (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: 5.271A pdb=" N LYS A 401 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 369 Processing sheet with id=AA5, first strand: chain 'A' and resid 477 through 482 removed outlier: 6.257A pdb=" N LEU A 433 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ARG A 481 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 512 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 436 " --> pdb=" O LEU A 512 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA7, first strand: chain 'A' and resid 490 through 492 Processing sheet with id=AA8, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA9, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.874A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 737 through 738 removed outlier: 3.710A pdb=" N MET A 737 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 539 " --> pdb=" O MET A 737 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 38 removed outlier: 5.821A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, 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=AB4, 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=AB5, first strand: chain 'B' and resid 226 through 228 removed outlier: 4.359A pdb=" N PHE B 279 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 4.279A 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: 3.588A pdb=" N GLU B 400 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AB7, first strand: chain 'B' and resid 403 through 405 removed outlier: 3.546A pdb=" N ASN B 412 " --> pdb=" O THR B 404 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 436 through 437 Processing sheet with id=AB9, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AC1, first strand: chain 'B' and resid 528 through 529 Processing sheet with id=AC2, first strand: chain 'B' and resid 534 through 535 removed outlier: 4.233A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 717 through 718 removed outlier: 7.866A pdb=" N VAL B 718 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEU B 736 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 9.126A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N VAL B 685 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N TYR B 733 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG B 543 " --> pdb=" O TYR B 733 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET B 737 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 755 " --> pdb=" O ILE B 540 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 39 through 41 removed outlier: 6.562A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 106 through 107 removed outlier: 6.484A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 171 through 176 removed outlier: 7.473A 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=AC6 Processing sheet with id=AC7, 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=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AC9, first strand: chain 'C' and resid 392 through 395 Processing sheet with id=AD1, first strand: chain 'C' and resid 435 through 437 Processing sheet with id=AD2, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AD3, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AD4, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.744A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 737 through 738 removed outlier: 3.501A pdb=" N MET C 737 " --> pdb=" O SER C 539 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AD7, first strand: chain 'D' and resid 39 through 40 removed outlier: 6.985A pdb=" N GLY D 39 " --> pdb=" O LEU D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 42 through 43 removed outlier: 6.214A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, 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=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 369 through 370 Processing sheet with id=AE2, first strand: chain 'D' and resid 389 through 390 Processing sheet with id=AE3, 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=AE4, first strand: chain 'D' and resid 433 through 437 removed outlier: 6.302A pdb=" N LEU D 433 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG D 481 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL D 435 " --> pdb=" O ARG D 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AE6, first strand: chain 'D' and resid 528 through 529 removed outlier: 3.833A pdb=" N ASP D 528 " --> pdb=" O THR D 768 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 717 through 718 removed outlier: 6.659A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N VAL D 685 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR D 542 " --> pdb=" O THR D 753 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 54 through 58 removed outlier: 3.613A pdb=" N ARG E 153 " --> pdb=" O ASP E 89 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER E 132 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 72 through 77 removed outlier: 3.506A pdb=" N TRP E 138 " --> pdb=" O ARG E 108 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS E 140 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU E 105 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ARG E 120 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL E 107 " --> pdb=" O ILE E 118 " (cutoff:3.500A) 1144 hydrogen bonds defined for protein. 3291 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: 5.22 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5990 1.33 - 1.45: 6880 1.45 - 1.57: 15324 1.57 - 1.70: 0 1.70 - 1.82: 266 Bond restraints: 28460 Sorted by residual: 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=" CA SER C 179 " pdb=" CB SER C 179 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.64e-02 3.72e+03 1.29e+01 bond pdb=" N VAL A 266 " pdb=" CA VAL A 266 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.16e+01 bond pdb=" N ILE B 473 " pdb=" CA ILE B 473 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.09e-02 8.42e+03 1.10e+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 1.04e+01 ... (remaining 28455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 35709 2.00 - 4.00: 2405 4.00 - 6.00: 341 6.00 - 7.99: 75 7.99 - 9.99: 12 Bond angle restraints: 38542 Sorted by residual: angle pdb=" N LEU A 619 " pdb=" CA LEU A 619 " pdb=" C LEU A 619 " ideal model delta sigma weight residual 111.28 102.65 8.63 1.09e+00 8.42e-01 6.26e+01 angle pdb=" N ASN C 546 " pdb=" CA ASN C 546 " pdb=" C ASN C 546 " ideal model delta sigma weight residual 111.33 102.21 9.12 1.21e+00 6.83e-01 5.67e+01 angle pdb=" N LEU C 261 " pdb=" CA LEU C 261 " pdb=" C LEU C 261 " ideal model delta sigma weight residual 113.23 104.76 8.47 1.24e+00 6.50e-01 4.66e+01 angle pdb=" N THR D 180 " pdb=" CA THR D 180 " pdb=" C THR D 180 " ideal model delta sigma weight residual 112.87 105.32 7.55 1.20e+00 6.94e-01 3.96e+01 angle pdb=" N ILE A 820 " pdb=" CA ILE A 820 " pdb=" C ILE A 820 " ideal model delta sigma weight residual 111.88 105.28 6.60 1.06e+00 8.90e-01 3.88e+01 ... (remaining 38537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 16406 23.20 - 46.40: 775 46.40 - 69.60: 92 69.60 - 92.81: 49 92.81 - 116.01: 42 Dihedral angle restraints: 17364 sinusoidal: 7312 harmonic: 10052 Sorted by residual: dihedral pdb=" CA ILE D 363 " pdb=" C ILE D 363 " pdb=" N LYS D 364 " pdb=" CA LYS D 364 " ideal model delta harmonic sigma weight residual -180.00 -151.31 -28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA LYS E 125 " pdb=" C LYS E 125 " pdb=" N SER E 126 " pdb=" CA SER E 126 " ideal model delta harmonic sigma weight residual 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA LEU A 197 " pdb=" C LEU A 197 " pdb=" N ARG A 198 " pdb=" CA ARG A 198 " ideal model delta harmonic sigma weight residual 180.00 153.12 26.88 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 17361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.893: 4373 0.893 - 1.786: 0 1.786 - 2.680: 1 2.680 - 3.573: 0 3.573 - 4.466: 1 Chirality restraints: 4375 Sorted by residual: chirality pdb=" C1 NAG D1003 " pdb=" ND2 ASN D 275 " pdb=" C2 NAG D1003 " pdb=" O5 NAG D1003 " both_signs ideal model delta sigma weight residual False -2.40 2.07 -4.47 2.00e-01 2.50e+01 4.99e+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 -2.01 -0.39 2.00e-02 2.50e+03 3.75e+02 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 4372 not shown) Planarity restraints: 4879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.359 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C7 NAG H 2 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.548 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 275 " 0.263 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" CG ASN D 275 " -0.100 2.00e-02 2.50e+03 pdb=" OD1 ASN D 275 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN D 275 " -0.510 2.00e-02 2.50e+03 pdb=" C1 NAG D1003 " 0.343 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG F 1 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.120 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.535 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.149 2.00e-02 2.50e+03 ... (remaining 4876 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 208 2.44 - 3.06: 21268 3.06 - 3.67: 44145 3.67 - 4.29: 62537 4.29 - 4.90: 96312 Nonbonded interactions: 224470 Sorted by model distance: nonbonded pdb=" CG ASN A 378 " pdb=" C8 NAG G 1 " model vdw 1.831 3.690 nonbonded pdb=" OD1 ASN A 378 " pdb=" C8 NAG G 1 " model vdw 1.928 3.460 nonbonded pdb=" OD1 ASN D 275 " pdb=" O7 NAG D1003 " model vdw 2.145 3.040 nonbonded pdb=" N GLU D 233 " pdb=" OE1 GLU D 233 " model vdw 2.166 3.120 nonbonded pdb=" NH2 ARG A 481 " pdb=" OE2 GLU A 484 " model vdw 2.197 3.120 ... (remaining 224465 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 663 or (resid 664 and (name N or name CA or nam \ e C or name O or name CB )) or resid 665 through 681 or (resid 682 and (name N o \ r name CA or name C or name O or name CB )) or resid 683 through 814 or (resid 8 \ 15 and (name N or name CA or name C or name O or name CB )) or resid 816 through \ 850 or resid 1001 through 1003)) selection = (chain 'B' and (resid 33 through 681 or (resid 682 and (name N or name CA or nam \ e C or name O or name CB )) or resid 683 through 814 or (resid 815 and (name N o \ r name CA or name C or name O or name CB )) or resid 816 through 850 or resid 10 \ 01 through 1003)) selection = (chain 'C' and (resid 33 through 663 or (resid 664 and (name N or name CA or nam \ e C or name O or name CB )) or resid 665 through 850 or resid 1003 through 1005) \ ) selection = (chain 'D' and (resid 33 through 681 or (resid 682 and (name N or name CA or nam \ e C or name O or name CB )) or resid 683 through 814 or (resid 815 and (name N o \ r name CA or name C or name O or name CB )) or resid 816 through 850 or resid 10 \ 02 through 1004)) } 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.620 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 0.376 28493 Z= 0.517 Angle : 1.167 23.965 38636 Z= 0.697 Chirality : 0.097 4.466 4375 Planarity : 0.014 0.309 4859 Dihedral : 15.308 116.007 10885 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 27.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 0.50 % Allowed : 1.56 % Favored : 97.94 % Cbeta Deviations : 0.09 % 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: -2.66 (0.13), residues: 3456 helix: -0.82 (0.13), residues: 1398 sheet: -2.41 (0.27), residues: 383 loop : -2.44 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 431 TYR 0.043 0.003 TYR A 44 PHE 0.042 0.003 PHE A 42 TRP 0.061 0.003 TRP E 138 HIS 0.012 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00851 (28460) covalent geometry : angle 1.11645 (38542) SS BOND : bond 0.27438 ( 5) SS BOND : angle 7.59456 ( 10) hydrogen bonds : bond 0.19470 ( 1144) hydrogen bonds : angle 7.61870 ( 3291) link_BETA1-4 : bond 0.00525 ( 8) link_BETA1-4 : angle 3.54396 ( 24) link_NAG-ASN : bond 0.10383 ( 20) link_NAG-ASN : angle 7.81010 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.700 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: symmetry clash REVERT: A 247 MET cc_start: 0.7700 (tpp) cc_final: 0.6945 (tpp) REVERT: A 394 LEU cc_start: 0.8096 (tp) cc_final: 0.7445 (tp) REVERT: B 360 MET cc_start: 0.8930 (tpt) cc_final: 0.8300 (tpp) REVERT: B 420 LYS cc_start: -0.3847 (OUTLIER) cc_final: -0.4617 (ptpt) REVERT: B 565 MET cc_start: 0.9322 (mpp) cc_final: 0.9068 (mpp) REVERT: B 691 MET cc_start: 0.9069 (tmm) cc_final: 0.8847 (tmm) REVERT: B 794 MET cc_start: 0.8012 (ppp) cc_final: 0.7568 (ppp) REVERT: C 276 MET cc_start: 0.8413 (mpp) cc_final: 0.8143 (mmm) REVERT: C 737 MET cc_start: 0.8977 (ptp) cc_final: 0.8550 (ptp) REVERT: C 793 MET cc_start: 0.9123 (mpp) cc_final: 0.8835 (mpp) REVERT: D 565 MET cc_start: 0.8365 (mtt) cc_final: 0.7610 (mmt) REVERT: D 620 MET cc_start: 0.8813 (mpp) cc_final: 0.8422 (mpp) REVERT: D 737 MET cc_start: 0.8092 (ppp) cc_final: 0.7619 (ppp) outliers start: 15 outliers final: 4 residues processed: 209 average time/residue: 0.1713 time to fit residues: 58.2068 Evaluate side-chains 140 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 10.0000 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 65 ASN A 137 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 GLN B 34 HIS B 111 HIS B 129 HIS B 350 HIS ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 253 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.050711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.037425 restraints weight = 262847.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.038392 restraints weight = 145384.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.038681 restraints weight = 95406.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.038798 restraints weight = 84348.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.038855 restraints weight = 77438.460| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 28493 Z= 0.201 Angle : 0.772 16.078 38636 Z= 0.389 Chirality : 0.047 0.477 4375 Planarity : 0.005 0.059 4859 Dihedral : 11.004 102.923 4323 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.17 % Allowed : 4.98 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.69 (0.14), residues: 3456 helix: 0.17 (0.13), residues: 1430 sheet: -1.98 (0.27), residues: 408 loop : -2.09 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 523 TYR 0.016 0.002 TYR D 682 PHE 0.046 0.002 PHE C 337 TRP 0.026 0.002 TRP E 138 HIS 0.008 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00422 (28460) covalent geometry : angle 0.75027 (38542) SS BOND : bond 0.00146 ( 5) SS BOND : angle 0.72532 ( 10) hydrogen bonds : bond 0.04978 ( 1144) hydrogen bonds : angle 5.52635 ( 3291) link_BETA1-4 : bond 0.01159 ( 8) link_BETA1-4 : angle 3.93220 ( 24) link_NAG-ASN : bond 0.00679 ( 20) link_NAG-ASN : angle 3.98698 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 0.818 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8256 (tpp) cc_final: 0.7645 (tpp) REVERT: B 565 MET cc_start: 0.9414 (mpp) cc_final: 0.9109 (mpp) REVERT: B 691 MET cc_start: 0.8908 (tmm) cc_final: 0.8552 (tmm) REVERT: B 794 MET cc_start: 0.8023 (ppp) cc_final: 0.7563 (ppp) REVERT: C 247 MET cc_start: 0.8170 (tpp) cc_final: 0.7570 (tpp) REVERT: C 276 MET cc_start: 0.8321 (mpp) cc_final: 0.7901 (mmm) REVERT: C 559 LEU cc_start: 0.8542 (tp) cc_final: 0.8208 (tt) REVERT: C 605 ASN cc_start: 0.9418 (t0) cc_final: 0.9121 (t0) REVERT: C 620 MET cc_start: 0.8939 (tpp) cc_final: 0.8550 (tpp) REVERT: C 664 MET cc_start: 0.9312 (ppp) cc_final: 0.8835 (ppp) REVERT: C 737 MET cc_start: 0.8852 (ptp) cc_final: 0.8639 (ptp) REVERT: C 793 MET cc_start: 0.9068 (mpp) cc_final: 0.8745 (mpp) REVERT: C 794 MET cc_start: 0.9152 (ttm) cc_final: 0.8937 (ptm) REVERT: D 234 MET cc_start: 0.8326 (tpp) cc_final: 0.8112 (tpp) REVERT: D 413 MET cc_start: 0.8331 (ptp) cc_final: 0.8018 (ptp) REVERT: D 565 MET cc_start: 0.8404 (mtt) cc_final: 0.7817 (mmt) REVERT: D 620 MET cc_start: 0.8949 (mpp) cc_final: 0.8679 (mpp) REVERT: D 691 MET cc_start: 0.8335 (pmm) cc_final: 0.8013 (pmm) outliers start: 5 outliers final: 1 residues processed: 159 average time/residue: 0.1528 time to fit residues: 41.5083 Evaluate side-chains 136 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 103 optimal weight: 2.9990 chunk 149 optimal weight: 0.1980 chunk 129 optimal weight: 30.0000 chunk 296 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 281 optimal weight: 9.9990 chunk 231 optimal weight: 0.0980 chunk 270 optimal weight: 0.1980 chunk 269 optimal weight: 0.9990 chunk 187 optimal weight: 0.1980 chunk 154 optimal weight: 6.9990 overall best weight: 0.3382 ------------------------------------------------------------------------------- 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** B 111 HIS B 116 ASN B 136 HIS B 302 GLN C 34 HIS ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS C 232 HIS D 610 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.051319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.038134 restraints weight = 262209.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.039097 restraints weight = 150742.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.039500 restraints weight = 98022.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.039614 restraints weight = 85404.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.039658 restraints weight = 76495.369| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28493 Z= 0.129 Angle : 0.667 15.593 38636 Z= 0.333 Chirality : 0.044 0.488 4375 Planarity : 0.004 0.064 4859 Dihedral : 8.988 95.999 4323 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.07 % Allowed : 3.49 % Favored : 96.45 % 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: -1.16 (0.14), residues: 3456 helix: 0.70 (0.13), residues: 1434 sheet: -1.64 (0.27), residues: 403 loop : -1.92 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 503 TYR 0.023 0.001 TYR C 44 PHE 0.035 0.002 PHE C 836 TRP 0.047 0.002 TRP A 706 HIS 0.017 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00277 (28460) covalent geometry : angle 0.64750 (38542) SS BOND : bond 0.00104 ( 5) SS BOND : angle 0.56396 ( 10) hydrogen bonds : bond 0.04245 ( 1144) hydrogen bonds : angle 4.99109 ( 3291) link_BETA1-4 : bond 0.01077 ( 8) link_BETA1-4 : angle 3.77585 ( 24) link_NAG-ASN : bond 0.00739 ( 20) link_NAG-ASN : angle 3.33690 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8126 (tpp) cc_final: 0.7913 (tpp) REVERT: B 248 MET cc_start: 0.9008 (tpp) cc_final: 0.8765 (tpp) REVERT: B 534 MET cc_start: 0.7759 (tmm) cc_final: 0.7280 (tmm) REVERT: B 565 MET cc_start: 0.9409 (mpp) cc_final: 0.9078 (mpp) REVERT: B 691 MET cc_start: 0.8779 (tmm) cc_final: 0.8484 (tmm) REVERT: B 794 MET cc_start: 0.8446 (ppp) cc_final: 0.7985 (ppp) REVERT: C 247 MET cc_start: 0.7910 (tpp) cc_final: 0.7512 (tpp) REVERT: C 248 MET cc_start: 0.8657 (tpp) cc_final: 0.8403 (tpp) REVERT: C 276 MET cc_start: 0.8538 (mpp) cc_final: 0.8037 (mmm) REVERT: C 534 MET cc_start: 0.8630 (mmp) cc_final: 0.8410 (mmp) REVERT: C 605 ASN cc_start: 0.9417 (t0) cc_final: 0.9103 (t0) REVERT: C 620 MET cc_start: 0.8931 (tpp) cc_final: 0.8227 (tpp) REVERT: C 664 MET cc_start: 0.9272 (ppp) cc_final: 0.8725 (ppp) REVERT: C 793 MET cc_start: 0.9147 (mpp) cc_final: 0.8854 (mpp) REVERT: D 248 MET cc_start: 0.8961 (mmm) cc_final: 0.8760 (mmm) REVERT: D 565 MET cc_start: 0.8416 (mtt) cc_final: 0.7846 (mmt) REVERT: D 620 MET cc_start: 0.8779 (mpp) cc_final: 0.8523 (mpp) REVERT: D 691 MET cc_start: 0.8446 (pmm) cc_final: 0.8014 (pmm) REVERT: D 705 MET cc_start: 0.9235 (mmp) cc_final: 0.8900 (mmp) REVERT: D 794 MET cc_start: 0.9472 (ptm) cc_final: 0.9227 (ptm) REVERT: E 137 MET cc_start: 0.8274 (mmt) cc_final: 0.7991 (mmm) outliers start: 2 outliers final: 1 residues processed: 153 average time/residue: 0.1530 time to fit residues: 40.0200 Evaluate side-chains 130 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 39 optimal weight: 20.0000 chunk 335 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 308 optimal weight: 3.9990 chunk 201 optimal weight: 8.9990 chunk 282 optimal weight: 9.9990 chunk 293 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 167 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 HIS D 610 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.049383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.035827 restraints weight = 269232.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.036798 restraints weight = 166227.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.036902 restraints weight = 106973.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.037055 restraints weight = 98573.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.037088 restraints weight = 90455.023| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 28493 Z= 0.252 Angle : 0.734 15.307 38636 Z= 0.370 Chirality : 0.046 0.564 4375 Planarity : 0.005 0.049 4859 Dihedral : 8.198 89.371 4323 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.07 (0.14), residues: 3456 helix: 0.80 (0.14), residues: 1441 sheet: -1.78 (0.25), residues: 470 loop : -1.84 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 300 TYR 0.021 0.002 TYR D 252 PHE 0.033 0.002 PHE C 836 TRP 0.037 0.002 TRP A 640 HIS 0.009 0.002 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00549 (28460) covalent geometry : angle 0.71557 (38542) SS BOND : bond 0.00098 ( 5) SS BOND : angle 0.55433 ( 10) hydrogen bonds : bond 0.04284 ( 1144) hydrogen bonds : angle 5.04028 ( 3291) link_BETA1-4 : bond 0.00810 ( 8) link_BETA1-4 : angle 3.71535 ( 24) link_NAG-ASN : bond 0.00636 ( 20) link_NAG-ASN : angle 3.47588 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8423 (tpp) cc_final: 0.8080 (tpp) REVERT: A 276 MET cc_start: 0.8792 (mtm) cc_final: 0.8440 (mtm) REVERT: A 413 MET cc_start: 0.7697 (tpt) cc_final: 0.7475 (tpp) REVERT: B 248 MET cc_start: 0.8905 (tpp) cc_final: 0.8670 (tpp) REVERT: B 794 MET cc_start: 0.8444 (ppp) cc_final: 0.7936 (ppp) REVERT: C 33 THR cc_start: 0.6865 (p) cc_final: 0.6638 (t) REVERT: C 247 MET cc_start: 0.8121 (tpp) cc_final: 0.7525 (tpp) REVERT: C 276 MET cc_start: 0.8493 (mpp) cc_final: 0.8069 (mmm) REVERT: C 360 MET cc_start: 0.8856 (tpp) cc_final: 0.8346 (mmt) REVERT: C 605 ASN cc_start: 0.9385 (t0) cc_final: 0.9039 (t0) REVERT: C 620 MET cc_start: 0.9224 (tpp) cc_final: 0.8904 (mmt) REVERT: C 664 MET cc_start: 0.9195 (ppp) cc_final: 0.8880 (ppp) REVERT: C 793 MET cc_start: 0.9083 (mpp) cc_final: 0.8815 (mpp) REVERT: C 794 MET cc_start: 0.9341 (ptm) cc_final: 0.9122 (ptm) REVERT: D 64 ILE cc_start: 0.8271 (mm) cc_final: 0.7939 (pt) REVERT: D 247 MET cc_start: 0.8848 (tpp) cc_final: 0.8216 (tpp) REVERT: D 565 MET cc_start: 0.8446 (mtt) cc_final: 0.7948 (mmt) REVERT: D 620 MET cc_start: 0.8796 (mpp) cc_final: 0.8560 (mpp) REVERT: D 691 MET cc_start: 0.8579 (pmm) cc_final: 0.8173 (pmm) REVERT: D 705 MET cc_start: 0.9100 (mmp) cc_final: 0.8790 (mmp) REVERT: D 794 MET cc_start: 0.9401 (ptm) cc_final: 0.9099 (ptm) REVERT: E 124 MET cc_start: 0.0473 (mmp) cc_final: 0.0157 (mmp) REVERT: E 137 MET cc_start: 0.8277 (mmt) cc_final: 0.7976 (mmm) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1594 time to fit residues: 38.6659 Evaluate side-chains 130 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 139 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 263 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 114 optimal weight: 30.0000 chunk 331 optimal weight: 40.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 ASN D 610 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.049225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.035713 restraints weight = 269196.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.036242 restraints weight = 169662.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.036623 restraints weight = 122541.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.036834 restraints weight = 100048.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.036894 restraints weight = 89700.999| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28493 Z= 0.203 Angle : 0.670 14.988 38636 Z= 0.340 Chirality : 0.044 0.493 4375 Planarity : 0.004 0.052 4859 Dihedral : 7.654 82.062 4323 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: -0.89 (0.15), residues: 3456 helix: 1.01 (0.14), residues: 1452 sheet: -1.71 (0.24), residues: 473 loop : -1.81 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 358 TYR 0.021 0.002 TYR D 252 PHE 0.037 0.002 PHE D 735 TRP 0.015 0.002 TRP B 798 HIS 0.009 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00439 (28460) covalent geometry : angle 0.65361 (38542) SS BOND : bond 0.00116 ( 5) SS BOND : angle 0.44445 ( 10) hydrogen bonds : bond 0.03949 ( 1144) hydrogen bonds : angle 4.82851 ( 3291) link_BETA1-4 : bond 0.00930 ( 8) link_BETA1-4 : angle 3.57532 ( 24) link_NAG-ASN : bond 0.00536 ( 20) link_NAG-ASN : angle 3.14382 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7961 (ptm) cc_final: 0.7577 (ptm) REVERT: A 276 MET cc_start: 0.8801 (mtm) cc_final: 0.8351 (mtp) REVERT: B 248 MET cc_start: 0.9039 (tpp) cc_final: 0.8735 (tpp) REVERT: B 534 MET cc_start: 0.7794 (tmm) cc_final: 0.7410 (tmm) REVERT: B 794 MET cc_start: 0.8336 (ppp) cc_final: 0.7837 (ppp) REVERT: C 276 MET cc_start: 0.8607 (mpp) cc_final: 0.8144 (mmm) REVERT: C 340 MET cc_start: 0.8043 (tpp) cc_final: 0.7823 (tpp) REVERT: C 501 MET cc_start: 0.8281 (mmt) cc_final: 0.8067 (mmt) REVERT: C 605 ASN cc_start: 0.9390 (t0) cc_final: 0.9041 (t0) REVERT: C 737 MET cc_start: 0.8859 (ptp) cc_final: 0.8584 (ptp) REVERT: C 793 MET cc_start: 0.9053 (mpp) cc_final: 0.8797 (mpp) REVERT: C 794 MET cc_start: 0.9263 (ptm) cc_final: 0.9028 (ptm) REVERT: D 64 ILE cc_start: 0.8104 (mm) cc_final: 0.7860 (mm) REVERT: D 565 MET cc_start: 0.8424 (mtt) cc_final: 0.7936 (mmt) REVERT: D 620 MET cc_start: 0.8833 (mpp) cc_final: 0.8546 (mpp) REVERT: D 691 MET cc_start: 0.8597 (pmm) cc_final: 0.8083 (pmm) REVERT: D 705 MET cc_start: 0.9238 (mmp) cc_final: 0.8197 (mmp) REVERT: D 794 MET cc_start: 0.9479 (ptm) cc_final: 0.9223 (ptm) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1511 time to fit residues: 37.7314 Evaluate side-chains 131 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 57 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 141 optimal weight: 0.0870 chunk 176 optimal weight: 0.0270 chunk 47 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 GLN C 116 ASN C 119 GLN C 137 GLN D 137 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.049895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.036376 restraints weight = 265892.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.037242 restraints weight = 160472.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.037366 restraints weight = 105564.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.037490 restraints weight = 107391.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.037510 restraints weight = 92252.960| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28493 Z= 0.122 Angle : 0.623 14.373 38636 Z= 0.310 Chirality : 0.043 0.475 4375 Planarity : 0.004 0.050 4859 Dihedral : 7.238 74.393 4323 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: -0.59 (0.15), residues: 3456 helix: 1.28 (0.14), residues: 1448 sheet: -1.42 (0.25), residues: 453 loop : -1.72 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 358 TYR 0.030 0.001 TYR C 44 PHE 0.036 0.001 PHE C 836 TRP 0.011 0.001 TRP D 296 HIS 0.007 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00262 (28460) covalent geometry : angle 0.60724 (38542) SS BOND : bond 0.00271 ( 5) SS BOND : angle 0.42037 ( 10) hydrogen bonds : bond 0.03595 ( 1144) hydrogen bonds : angle 4.56929 ( 3291) link_BETA1-4 : bond 0.00866 ( 8) link_BETA1-4 : angle 3.41865 ( 24) link_NAG-ASN : bond 0.00535 ( 20) link_NAG-ASN : angle 2.95223 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8718 (mtm) cc_final: 0.8278 (mtp) REVERT: B 248 MET cc_start: 0.9101 (tpp) cc_final: 0.8747 (tpp) REVERT: B 691 MET cc_start: 0.8777 (tmm) cc_final: 0.8391 (tmm) REVERT: B 794 MET cc_start: 0.8429 (ppp) cc_final: 0.7936 (ppp) REVERT: C 247 MET cc_start: 0.8331 (tpp) cc_final: 0.8101 (tpp) REVERT: C 276 MET cc_start: 0.8582 (mpp) cc_final: 0.8000 (mmm) REVERT: C 340 MET cc_start: 0.8263 (tpp) cc_final: 0.8038 (tpp) REVERT: C 605 ASN cc_start: 0.9403 (t0) cc_final: 0.9094 (t0) REVERT: C 620 MET cc_start: 0.9346 (mmt) cc_final: 0.8677 (mmt) REVERT: C 627 MET cc_start: 0.8066 (ppp) cc_final: 0.7835 (ppp) REVERT: C 793 MET cc_start: 0.9169 (mpp) cc_final: 0.8922 (mpp) REVERT: C 794 MET cc_start: 0.9331 (ptm) cc_final: 0.9104 (ptm) REVERT: D 64 ILE cc_start: 0.8094 (mm) cc_final: 0.7848 (mm) REVERT: D 360 MET cc_start: 0.8576 (tpp) cc_final: 0.8274 (tpp) REVERT: D 565 MET cc_start: 0.8393 (mtt) cc_final: 0.7914 (mmt) REVERT: D 620 MET cc_start: 0.8763 (mpp) cc_final: 0.8490 (mpp) REVERT: D 691 MET cc_start: 0.8716 (pmm) cc_final: 0.8313 (pmm) REVERT: D 705 MET cc_start: 0.9213 (mmp) cc_final: 0.9002 (mmp) REVERT: D 709 MET cc_start: 0.9003 (ptt) cc_final: 0.8720 (ppp) REVERT: D 794 MET cc_start: 0.9483 (ptm) cc_final: 0.9244 (ptm) REVERT: E 124 MET cc_start: 0.0422 (mmp) cc_final: 0.0035 (mmp) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1551 time to fit residues: 38.0199 Evaluate side-chains 132 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 14 optimal weight: 8.9990 chunk 218 optimal weight: 9.9990 chunk 288 optimal weight: 0.0770 chunk 234 optimal weight: 0.0980 chunk 186 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 291 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 254 optimal weight: 0.8980 chunk 204 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 overall best weight: 3.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 119 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** 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 = 0.3531 r_free = 0.3531 target = 0.049381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.035781 restraints weight = 265681.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.036561 restraints weight = 163321.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.036727 restraints weight = 109630.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.036927 restraints weight = 101321.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.036940 restraints weight = 93922.119| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28493 Z= 0.160 Angle : 0.640 14.086 38636 Z= 0.317 Chirality : 0.043 0.491 4375 Planarity : 0.004 0.050 4859 Dihedral : 7.053 67.287 4323 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.51 (0.15), residues: 3456 helix: 1.34 (0.14), residues: 1459 sheet: -1.38 (0.25), residues: 463 loop : -1.68 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 775 TYR 0.019 0.001 TYR C 44 PHE 0.035 0.001 PHE C 836 TRP 0.015 0.001 TRP D 296 HIS 0.006 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00355 (28460) covalent geometry : angle 0.62344 (38542) SS BOND : bond 0.00121 ( 5) SS BOND : angle 0.68177 ( 10) hydrogen bonds : bond 0.03602 ( 1144) hydrogen bonds : angle 4.56875 ( 3291) link_BETA1-4 : bond 0.00875 ( 8) link_BETA1-4 : angle 3.25174 ( 24) link_NAG-ASN : bond 0.00517 ( 20) link_NAG-ASN : angle 3.10118 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.8533 (tpp) cc_final: 0.8173 (tpp) REVERT: A 276 MET cc_start: 0.8762 (mtm) cc_final: 0.8243 (mtp) REVERT: A 316 MET cc_start: 0.8799 (mmt) cc_final: 0.8046 (mmm) REVERT: B 248 MET cc_start: 0.8996 (tpp) cc_final: 0.8676 (tpp) REVERT: B 534 MET cc_start: 0.7721 (tmm) cc_final: 0.7323 (tmm) REVERT: B 691 MET cc_start: 0.8902 (tmm) cc_final: 0.8570 (tmm) REVERT: B 794 MET cc_start: 0.8367 (ppp) cc_final: 0.7886 (ppp) REVERT: C 276 MET cc_start: 0.8524 (mpp) cc_final: 0.8052 (mmm) REVERT: C 340 MET cc_start: 0.8308 (tpp) cc_final: 0.8086 (tpp) REVERT: C 605 ASN cc_start: 0.9397 (t0) cc_final: 0.9090 (t0) REVERT: C 620 MET cc_start: 0.9399 (mmt) cc_final: 0.8840 (mmt) REVERT: C 737 MET cc_start: 0.8913 (ptp) cc_final: 0.8694 (ptp) REVERT: C 793 MET cc_start: 0.9086 (mpp) cc_final: 0.8834 (mpp) REVERT: D 247 MET cc_start: 0.8767 (tpp) cc_final: 0.8536 (tpp) REVERT: D 413 MET cc_start: 0.7875 (ptp) cc_final: 0.7644 (ptp) REVERT: D 565 MET cc_start: 0.8354 (mtt) cc_final: 0.7889 (mmt) REVERT: D 620 MET cc_start: 0.8744 (mpp) cc_final: 0.8475 (mpp) REVERT: D 691 MET cc_start: 0.8696 (pmm) cc_final: 0.8241 (pmm) REVERT: D 705 MET cc_start: 0.9297 (mmp) cc_final: 0.9009 (mmt) REVERT: D 709 MET cc_start: 0.8981 (ptt) cc_final: 0.8754 (ppp) REVERT: D 794 MET cc_start: 0.9411 (ptm) cc_final: 0.9106 (ptm) REVERT: E 114 PHE cc_start: 0.7644 (t80) cc_final: 0.7373 (t80) REVERT: E 124 MET cc_start: 0.0500 (mmp) cc_final: -0.0003 (mmp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1614 time to fit residues: 38.7797 Evaluate side-chains 126 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 328 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 284 optimal weight: 3.9990 chunk 211 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 182 optimal weight: 0.3980 chunk 111 optimal weight: 7.9990 chunk 162 optimal weight: 30.0000 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 119 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 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 = 0.3528 r_free = 0.3528 target = 0.049282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.035675 restraints weight = 266256.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.036262 restraints weight = 159807.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.036632 restraints weight = 112123.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.036775 restraints weight = 96854.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.036804 restraints weight = 89107.015| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28493 Z= 0.158 Angle : 0.635 13.702 38636 Z= 0.316 Chirality : 0.043 0.486 4375 Planarity : 0.004 0.065 4859 Dihedral : 6.915 61.866 4323 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: -0.45 (0.15), residues: 3456 helix: 1.41 (0.14), residues: 1462 sheet: -1.35 (0.24), residues: 477 loop : -1.68 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 91 TYR 0.022 0.001 TYR C 44 PHE 0.032 0.001 PHE C 836 TRP 0.012 0.001 TRP B 798 HIS 0.006 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00351 (28460) covalent geometry : angle 0.61942 (38542) SS BOND : bond 0.00118 ( 5) SS BOND : angle 0.54858 ( 10) hydrogen bonds : bond 0.03570 ( 1144) hydrogen bonds : angle 4.51257 ( 3291) link_BETA1-4 : bond 0.00982 ( 8) link_BETA1-4 : angle 3.21243 ( 24) link_NAG-ASN : bond 0.00490 ( 20) link_NAG-ASN : angle 3.02113 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8786 (mtm) cc_final: 0.8351 (mtp) REVERT: A 316 MET cc_start: 0.8879 (mmt) cc_final: 0.8245 (mmm) REVERT: B 248 MET cc_start: 0.9000 (tpp) cc_final: 0.8688 (tpp) REVERT: B 534 MET cc_start: 0.7740 (tmm) cc_final: 0.7323 (tmm) REVERT: B 794 MET cc_start: 0.8324 (ppp) cc_final: 0.7834 (ppp) REVERT: C 276 MET cc_start: 0.8436 (mpp) cc_final: 0.7956 (mmm) REVERT: C 340 MET cc_start: 0.8296 (tpp) cc_final: 0.8080 (tpp) REVERT: C 605 ASN cc_start: 0.9393 (t0) cc_final: 0.9094 (t0) REVERT: C 620 MET cc_start: 0.9387 (mmt) cc_final: 0.8807 (mmt) REVERT: C 627 MET cc_start: 0.8080 (ppp) cc_final: 0.7875 (ppp) REVERT: C 737 MET cc_start: 0.8901 (ptp) cc_final: 0.8654 (ptp) REVERT: C 793 MET cc_start: 0.9105 (mpp) cc_final: 0.8852 (mpp) REVERT: D 565 MET cc_start: 0.8362 (mtt) cc_final: 0.7878 (mmt) REVERT: D 620 MET cc_start: 0.8710 (mpp) cc_final: 0.8431 (mpp) REVERT: D 691 MET cc_start: 0.8697 (pmm) cc_final: 0.8223 (pmm) REVERT: D 705 MET cc_start: 0.9328 (mmp) cc_final: 0.9005 (mmt) REVERT: D 709 MET cc_start: 0.8997 (ptt) cc_final: 0.8750 (ppp) REVERT: D 794 MET cc_start: 0.9393 (ptm) cc_final: 0.8959 (ptm) REVERT: E 114 PHE cc_start: 0.7740 (t80) cc_final: 0.7451 (t80) REVERT: E 124 MET cc_start: 0.0270 (mmp) cc_final: -0.0438 (mmt) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1607 time to fit residues: 37.8462 Evaluate side-chains 127 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 196 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 299 optimal weight: 10.0000 chunk 162 optimal weight: 30.0000 chunk 141 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 313 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 chunk 272 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.048458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.034632 restraints weight = 269722.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.035592 restraints weight = 166233.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.035647 restraints weight = 104605.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.035823 restraints weight = 101686.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.035838 restraints weight = 91144.550| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28493 Z= 0.244 Angle : 0.721 13.545 38636 Z= 0.361 Chirality : 0.045 0.488 4375 Planarity : 0.004 0.051 4859 Dihedral : 7.053 59.992 4323 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.67 (0.15), residues: 3456 helix: 1.19 (0.14), residues: 1469 sheet: -1.54 (0.24), residues: 501 loop : -1.73 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 468 TYR 0.028 0.002 TYR C 44 PHE 0.029 0.002 PHE C 836 TRP 0.018 0.002 TRP B 798 HIS 0.008 0.002 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00532 (28460) covalent geometry : angle 0.70667 (38542) SS BOND : bond 0.00145 ( 5) SS BOND : angle 0.64645 ( 10) hydrogen bonds : bond 0.03927 ( 1144) hydrogen bonds : angle 4.75543 ( 3291) link_BETA1-4 : bond 0.00839 ( 8) link_BETA1-4 : angle 3.21368 ( 24) link_NAG-ASN : bond 0.00569 ( 20) link_NAG-ASN : angle 3.08780 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8818 (mtm) cc_final: 0.8480 (mtp) REVERT: A 316 MET cc_start: 0.8872 (mmt) cc_final: 0.8339 (mmm) REVERT: A 501 MET cc_start: 0.9081 (mmp) cc_final: 0.8451 (mmm) REVERT: B 413 MET cc_start: 0.8153 (mtp) cc_final: 0.7830 (mtm) REVERT: B 534 MET cc_start: 0.7676 (tmm) cc_final: 0.7222 (tmm) REVERT: B 691 MET cc_start: 0.9065 (tmm) cc_final: 0.8803 (tmm) REVERT: B 794 MET cc_start: 0.8447 (ppp) cc_final: 0.7932 (ppp) REVERT: C 276 MET cc_start: 0.8376 (mpp) cc_final: 0.7887 (mmm) REVERT: C 340 MET cc_start: 0.8281 (tpp) cc_final: 0.8032 (tpp) REVERT: C 605 ASN cc_start: 0.9413 (t0) cc_final: 0.9096 (t0) REVERT: C 620 MET cc_start: 0.9349 (mmt) cc_final: 0.8788 (mmt) REVERT: C 737 MET cc_start: 0.8884 (ptp) cc_final: 0.8510 (ptt) REVERT: C 793 MET cc_start: 0.9229 (mpp) cc_final: 0.8981 (mpp) REVERT: C 794 MET cc_start: 0.9119 (ppp) cc_final: 0.8795 (ppp) REVERT: D 565 MET cc_start: 0.8408 (mtt) cc_final: 0.7933 (mmt) REVERT: D 620 MET cc_start: 0.8711 (mpp) cc_final: 0.8318 (mpp) REVERT: D 691 MET cc_start: 0.8741 (pmm) cc_final: 0.8264 (pmm) REVERT: D 705 MET cc_start: 0.9330 (mmp) cc_final: 0.9009 (mmt) REVERT: D 709 MET cc_start: 0.8991 (ptt) cc_final: 0.8745 (ppp) REVERT: D 794 MET cc_start: 0.9432 (ptm) cc_final: 0.9187 (ptm) REVERT: E 114 PHE cc_start: 0.7575 (t80) cc_final: 0.7226 (t80) REVERT: E 124 MET cc_start: -0.0044 (mmp) cc_final: -0.0835 (mmt) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1588 time to fit residues: 37.3148 Evaluate side-chains 128 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 192 optimal weight: 0.9990 chunk 330 optimal weight: 20.0000 chunk 297 optimal weight: 30.0000 chunk 77 optimal weight: 9.9990 chunk 298 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 329 optimal weight: 9.9990 chunk 304 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 337 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 119 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.048912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.035371 restraints weight = 266065.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.035776 restraints weight = 164933.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.036041 restraints weight = 126580.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.036202 restraints weight = 106282.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.036265 restraints weight = 97050.060| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28493 Z= 0.161 Angle : 0.659 13.140 38636 Z= 0.327 Chirality : 0.043 0.458 4375 Planarity : 0.004 0.049 4859 Dihedral : 6.770 58.362 4323 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.50 (0.15), residues: 3456 helix: 1.35 (0.14), residues: 1472 sheet: -1.43 (0.24), residues: 494 loop : -1.68 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 300 TYR 0.026 0.001 TYR C 44 PHE 0.031 0.001 PHE C 836 TRP 0.029 0.002 TRP C 613 HIS 0.007 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00356 (28460) covalent geometry : angle 0.64449 (38542) SS BOND : bond 0.00128 ( 5) SS BOND : angle 0.56046 ( 10) hydrogen bonds : bond 0.03605 ( 1144) hydrogen bonds : angle 4.59879 ( 3291) link_BETA1-4 : bond 0.00918 ( 8) link_BETA1-4 : angle 3.11351 ( 24) link_NAG-ASN : bond 0.00482 ( 20) link_NAG-ASN : angle 2.97892 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7790 (ppp) cc_final: 0.7449 (ppp) REVERT: A 276 MET cc_start: 0.8663 (mtm) cc_final: 0.8254 (mtp) REVERT: A 316 MET cc_start: 0.8921 (mmt) cc_final: 0.8240 (mmm) REVERT: A 501 MET cc_start: 0.8953 (mmp) cc_final: 0.8359 (mmm) REVERT: B 50 MET cc_start: 0.8550 (ppp) cc_final: 0.8263 (ppp) REVERT: B 620 MET cc_start: 0.9138 (mmp) cc_final: 0.8622 (mmt) REVERT: B 691 MET cc_start: 0.9000 (tmm) cc_final: 0.8540 (tmm) REVERT: B 794 MET cc_start: 0.8213 (ppp) cc_final: 0.7724 (ppp) REVERT: C 276 MET cc_start: 0.8376 (mpp) cc_final: 0.7902 (mmm) REVERT: C 340 MET cc_start: 0.8342 (tpp) cc_final: 0.8067 (tpp) REVERT: C 605 ASN cc_start: 0.9387 (t0) cc_final: 0.9072 (t0) REVERT: C 620 MET cc_start: 0.9313 (mmt) cc_final: 0.8782 (mmt) REVERT: C 793 MET cc_start: 0.9214 (mpp) cc_final: 0.8968 (mpp) REVERT: C 794 MET cc_start: 0.9052 (ppp) cc_final: 0.8706 (ppp) REVERT: D 247 MET cc_start: 0.8811 (tpp) cc_final: 0.8093 (tpp) REVERT: D 565 MET cc_start: 0.8388 (mtt) cc_final: 0.7922 (mmt) REVERT: D 620 MET cc_start: 0.8760 (mpp) cc_final: 0.8436 (mpp) REVERT: D 691 MET cc_start: 0.8748 (pmm) cc_final: 0.8302 (pmm) REVERT: D 705 MET cc_start: 0.9347 (mmp) cc_final: 0.9003 (mmt) REVERT: D 709 MET cc_start: 0.9046 (ptt) cc_final: 0.8792 (ppp) REVERT: D 794 MET cc_start: 0.9396 (ptm) cc_final: 0.9147 (ptm) REVERT: E 114 PHE cc_start: 0.7573 (t80) cc_final: 0.7198 (t80) REVERT: E 124 MET cc_start: -0.1132 (mmp) cc_final: -0.1680 (mmt) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1621 time to fit residues: 38.3135 Evaluate side-chains 129 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 331 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 310 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 323 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 299 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 119 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 286 ASN ** 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 = 0.3523 r_free = 0.3523 target = 0.049109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.035607 restraints weight = 265581.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.036030 restraints weight = 166499.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.036380 restraints weight = 122028.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.036534 restraints weight = 104014.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.036576 restraints weight = 93232.697| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28493 Z= 0.138 Angle : 0.640 12.699 38636 Z= 0.317 Chirality : 0.043 0.447 4375 Planarity : 0.004 0.077 4859 Dihedral : 6.593 57.072 4323 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.15), residues: 3456 helix: 1.43 (0.14), residues: 1469 sheet: -1.31 (0.25), residues: 476 loop : -1.61 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 634 TYR 0.024 0.001 TYR C 44 PHE 0.031 0.001 PHE C 579 TRP 0.016 0.001 TRP C 613 HIS 0.007 0.001 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00307 (28460) covalent geometry : angle 0.62557 (38542) SS BOND : bond 0.00104 ( 5) SS BOND : angle 0.48960 ( 10) hydrogen bonds : bond 0.03485 ( 1144) hydrogen bonds : angle 4.49890 ( 3291) link_BETA1-4 : bond 0.00956 ( 8) link_BETA1-4 : angle 3.04220 ( 24) link_NAG-ASN : bond 0.00482 ( 20) link_NAG-ASN : angle 2.88045 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3772.15 seconds wall clock time: 66 minutes 35.60 seconds (3995.60 seconds total)