Starting phenix.real_space_refine on Sun Jun 22 20:23:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v3p_31671/06_2025/7v3p_31671_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v3p_31671/06_2025/7v3p_31671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v3p_31671/06_2025/7v3p_31671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v3p_31671/06_2025/7v3p_31671.map" model { file = "/net/cci-nas-00/data/ceres_data/7v3p_31671/06_2025/7v3p_31671_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v3p_31671/06_2025/7v3p_31671_neut_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.047 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: 5 Type Number sf(0) Gaussians S 101 5.16 5 C 8545 2.51 5 N 2330 2.21 5 O 2541 1.98 5 H 12814 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26331 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 12605 Classifications: {'peptide': 807} Link IDs: {'PTRANS': 44, 'TRANS': 762} Chain breaks: 6 Chain: "B" Number of atoms: 12900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 12900 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 46, 'TRANS': 769} Chain breaks: 5 Chain: "E" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 299 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "F" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 471 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.04, per 1000 atoms: 0.50 Number of scatterers: 26331 At special positions: 0 Unit cell: (93.96, 116.64, 187.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 O 2541 8.00 N 2330 7.00 C 8545 6.00 H 12814 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.05 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 670 " - pdb=" SG CYS B 670 " distance=2.03 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=1.99 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.04 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 323 " distance=2.02 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 458 " distance=2.04 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 849 " distance=2.03 Simple disulfide: pdb=" SG CYS B 776 " - pdb=" SG CYS B 785 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 11 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS F 19 " 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 NAG-ASN " NAG A1001 " - " ASN A 21 " " NAG A1002 " - " ASN A 387 " " NAG A1003 " - " ASN A 105 " " NAG B1001 " - " ASN B 504 " Time building additional restraints: 7.06 Conformation dependent library (CDL) restraints added in 2.2 seconds 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 38 sheets defined 15.8% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'A' and resid 14 through 20 Processing helix chain 'A' and resid 39 through 43 removed outlier: 4.012A pdb=" N TYR A 43 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.761A pdb=" N CYS A 189 " --> pdb=" O PRO A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 339 through 349 removed outlier: 4.066A pdb=" N GLU A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 4.405A pdb=" N PHE A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 437 removed outlier: 3.839A pdb=" N ILE A 429 " --> pdb=" O CYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.711A pdb=" N ILE A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 675 through 697 removed outlier: 4.049A pdb=" N ALA A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE A 692 " --> pdb=" O TYR A 688 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU A 693 " --> pdb=" O ARG A 689 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.642A pdb=" N GLN B 15 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 17 " --> pdb=" O GLN B 14 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 126 through 130 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 248 through 254 removed outlier: 3.935A pdb=" N CYS B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.889A pdb=" N GLU B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 625 through 630 removed outlier: 4.010A pdb=" N ARG B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS B 630 " --> pdb=" O TYR B 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 625 through 630' Processing helix chain 'B' and resid 631 through 635 removed outlier: 3.986A pdb=" N LYS B 635 " --> pdb=" O TYR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.816A pdb=" N GLN B 680 " --> pdb=" O GLU B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 852 through 859 Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 12 through 20 removed outlier: 4.288A pdb=" N GLU E 17 " --> pdb=" O TYR E 14 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASN E 18 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR E 19 " --> pdb=" O LEU E 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 20 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 9 removed outlier: 6.252A pdb=" N LEU A 29 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N PHE A 58 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 31 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N PHE A 90 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 57 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ARG A 112 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLU A 114 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 111 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL A 140 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE A 113 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 25 removed outlier: 3.729A pdb=" N ILE A 76 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 165 removed outlier: 3.927A pdb=" N THR A 165 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 172 " --> pdb=" O THR A 165 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 195 removed outlier: 3.602A pdb=" N GLU A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 205 through 209 removed outlier: 3.850A pdb=" N ALA A 220 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N SER A 208 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N CYS A 218 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA8, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AA9, first strand: chain 'A' and resid 267 through 269 removed outlier: 3.589A pdb=" N MET A 274 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AB2, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AB3, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.900A pdb=" N LEU A 331 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 330 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A 358 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N LEU A 393 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 360 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ALA A 419 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 392 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 465 through 470 Processing sheet with id=AB5, first strand: chain 'A' and resid 520 through 524 removed outlier: 3.973A pdb=" N SER A 492 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA A 567 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 520 through 524 removed outlier: 3.973A pdb=" N SER A 492 " --> pdb=" O VAL A 554 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 585 through 590 removed outlier: 5.804A pdb=" N ASP A 586 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASN A 602 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 748 through 751 removed outlier: 3.950A pdb=" N TYR A 613 " --> pdb=" O CYS A 776 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 773 " --> pdb=" O ASN A 789 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 775 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ALA A 787 " --> pdb=" O SER A 775 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 809 through 813 removed outlier: 3.834A pdb=" N ALA A 861 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 846 through 851 removed outlier: 3.850A pdb=" N ILE A 837 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 846 through 851 removed outlier: 3.850A pdb=" N ILE A 837 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AC4, first strand: chain 'B' and resid 7 through 8 removed outlier: 6.281A pdb=" N ILE B 7 " --> pdb=" O HIS B 30 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU B 32 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU B 29 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE B 58 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE B 31 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 57 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ARG B 112 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLU B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE B 90 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 140 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 164 through 167 removed outlier: 3.564A pdb=" N THR B 165 " --> pdb=" O ASN B 172 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 172 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 205 through 209 removed outlier: 3.531A pdb=" N ALA B 220 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N SER B 208 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N CYS B 218 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AC8, first strand: chain 'B' and resid 239 through 241 Processing sheet with id=AC9, first strand: chain 'B' and resid 267 through 269 Processing sheet with id=AD1, first strand: chain 'B' and resid 281 through 282 removed outlier: 3.735A pdb=" N ILE B 282 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 308 through 311 removed outlier: 3.636A pdb=" N LEU B 331 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 330 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ARG B 361 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE B 332 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N TYR B 417 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR B 391 " --> pdb=" O TYR B 417 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ALA B 419 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU B 393 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AD4, first strand: chain 'B' and resid 460 through 461 Processing sheet with id=AD5, first strand: chain 'B' and resid 465 through 470 Processing sheet with id=AD6, first strand: chain 'B' and resid 520 through 522 removed outlier: 3.549A pdb=" N SER B 492 " --> pdb=" O VAL B 554 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 585 through 590 removed outlier: 5.489A pdb=" N ASP B 586 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN B 602 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 750 through 752 removed outlier: 3.928A pdb=" N TYR B 614 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 613 " --> pdb=" O CYS B 776 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 789 " --> pdb=" O ILE B 773 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 809 through 813 Processing sheet with id=AE1, first strand: chain 'B' and resid 846 through 851 removed outlier: 3.823A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 846 through 851 removed outlier: 3.823A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 858 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: 11.35 Time building geometry restraints manager: 8.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 12803 1.02 - 1.22: 109 1.22 - 1.42: 5797 1.42 - 1.62: 7812 1.62 - 1.82: 126 Bond restraints: 26647 Sorted by residual: bond pdb=" CA TRP B 402 " pdb=" C TRP B 402 " ideal model delta sigma weight residual 1.526 1.415 0.112 1.21e-02 6.83e+03 8.55e+01 bond pdb=" CA VAL B 580 " pdb=" C VAL B 580 " ideal model delta sigma weight residual 1.524 1.438 0.087 1.05e-02 9.07e+03 6.80e+01 bond pdb=" CA SER B 579 " pdb=" C SER B 579 " ideal model delta sigma weight residual 1.527 1.418 0.109 1.42e-02 4.96e+03 5.87e+01 bond pdb=" CA SER B 288 " pdb=" C SER B 288 " ideal model delta sigma weight residual 1.529 1.424 0.105 1.40e-02 5.10e+03 5.63e+01 bond pdb=" CA LEU A 696 " pdb=" C LEU A 696 " ideal model delta sigma weight residual 1.523 1.424 0.099 1.35e-02 5.49e+03 5.37e+01 ... (remaining 26642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.25: 47710 5.25 - 10.50: 166 10.50 - 15.75: 12 15.75 - 21.00: 3 21.00 - 26.25: 3 Bond angle restraints: 47894 Sorted by residual: angle pdb=" C ILE A 583 " pdb=" N PRO A 584 " pdb=" CA PRO A 584 " ideal model delta sigma weight residual 119.99 103.72 16.27 1.08e+00 8.57e-01 2.27e+02 angle pdb=" N ASN A 698 " pdb=" CA ASN A 698 " pdb=" C ASN A 698 " ideal model delta sigma weight residual 111.54 97.27 14.27 1.36e+00 5.41e-01 1.10e+02 angle pdb=" N ASN B 284 " pdb=" CA ASN B 284 " pdb=" C ASN B 284 " ideal model delta sigma weight residual 110.46 96.18 14.28 1.48e+00 4.57e-01 9.30e+01 angle pdb=" N LYS B 300 " pdb=" CA LYS B 300 " pdb=" C LYS B 300 " ideal model delta sigma weight residual 109.86 96.23 13.63 1.55e+00 4.16e-01 7.73e+01 angle pdb=" N ILE A 583 " pdb=" CA ILE A 583 " pdb=" C ILE A 583 " ideal model delta sigma weight residual 108.88 127.87 -18.99 2.16e+00 2.14e-01 7.73e+01 ... (remaining 47889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11469 17.92 - 35.85: 936 35.85 - 53.77: 294 53.77 - 71.70: 89 71.70 - 89.62: 34 Dihedral angle restraints: 12822 sinusoidal: 7002 harmonic: 5820 Sorted by residual: dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS A 22 " pdb=" CB CYS A 22 " ideal model delta sinusoidal sigma weight residual -86.00 -175.62 89.62 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS E 7 " pdb=" SG CYS E 7 " pdb=" SG CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sinusoidal sigma weight residual -86.00 -174.67 88.67 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS B 294 " pdb=" SG CYS B 294 " pdb=" SG CYS B 298 " pdb=" CB CYS B 298 " ideal model delta sinusoidal sigma weight residual 93.00 176.62 -83.62 1 1.00e+01 1.00e-02 8.53e+01 ... (remaining 12819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.292: 2023 0.292 - 0.584: 4 0.584 - 0.876: 0 0.876 - 1.168: 0 1.168 - 1.460: 1 Chirality restraints: 2028 Sorted by residual: chirality pdb=" CB THR B 675 " pdb=" CA THR B 675 " pdb=" OG1 THR B 675 " pdb=" CG2 THR B 675 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.33e+01 chirality pdb=" CA ASN B 11 " pdb=" N ASN B 11 " pdb=" C ASN B 11 " pdb=" CB ASN B 11 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA PRO B 581 " pdb=" N PRO B 581 " pdb=" C PRO B 581 " pdb=" CB PRO B 581 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 2025 not shown) Planarity restraints: 3972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 452 " 0.059 2.00e-02 2.50e+03 4.89e-01 3.59e+03 pdb=" CG ASN A 452 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 452 " -0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A 452 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 452 " 0.844 2.00e-02 2.50e+03 pdb="HD22 ASN A 452 " -0.847 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 400 " 0.037 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CD GLN B 400 " -0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN B 400 " -0.034 2.00e-02 2.50e+03 pdb=" NE2 GLN B 400 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 400 " 0.768 2.00e-02 2.50e+03 pdb="HE22 GLN B 400 " -0.761 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 608 " -0.059 2.00e-02 2.50e+03 4.40e-01 2.90e+03 pdb=" CG ASN A 608 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN A 608 " 0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN A 608 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 608 " 0.758 2.00e-02 2.50e+03 pdb="HD22 ASN A 608 " -0.761 2.00e-02 2.50e+03 ... (remaining 3969 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1009 2.15 - 2.76: 49273 2.76 - 3.38: 70029 3.38 - 3.99: 89635 3.99 - 4.60: 139051 Nonbonded interactions: 348997 Sorted by model distance: nonbonded pdb=" O PRO B 71 " pdb="HD21 ASN B 102 " model vdw 1.539 2.450 nonbonded pdb=" O TYR B 628 " pdb="HE21 GLN B 853 " model vdw 1.551 2.450 nonbonded pdb=" O PRO B 584 " pdb="HD21 ASN B 789 " model vdw 1.569 2.450 nonbonded pdb="HE21 GLN B 680 " pdb=" OE2 GLU B 684 " model vdw 1.578 2.450 nonbonded pdb=" O ASN A 631 " pdb=" HG SER A 634 " model vdw 1.595 2.450 ... (remaining 348992 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 1 through 37 or resid 41 through 154 or resid 162 through \ 424 or (resid 425 and (name N or name CA or name C or name O or name CB or name \ SG or name H or name HA or name HB2 or name HB3)) or resid 426 through 897 or re \ sid 1001)) selection = (chain 'B' and (resid 1 through 20 or (resid 21 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3 or name HD21)) or resid 22 through 104 or (resid 105 and ( \ name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 106 thr \ ough 257 or resid 266 through 293 or resid 299 through 386 or (resid 387 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name ND \ 2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 388 throu \ gh 672 or (resid 673 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD )) or (resid 674 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name CE or name NZ )) or (resid 675 and (name N \ or name CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 6 \ 76 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name OE1 or name OE2)) or (resid 677 and (name N or name CA or name C or name \ O or name CB )) or (resid 678 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name OE2)) or (resid 679 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ )) or (resid 680 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name OE1 or name NE2)) or (resid 681 and (name N or name CA \ or name C or name O or name CB )) or (resid 682 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (resid \ 683 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name CE or name NZ )) or (resid 684 through 685 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (res \ id 686 and (name N or name CA or name C or name O or name CB )) or (resid 687 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e OE1 or name OE2)) or (resid 688 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or \ name OH )) or (resid 689 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid \ 690 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name CE or name NZ )) or (resid 691 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or (resid 692 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or nam \ e CE2 or name CZ )) or (resid 693 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name OE2)) or (resid 694 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2)) \ or (resid 695 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 696 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2)) or (resid 697 and (name N or name CA or name C or name O or name CB or na \ me CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 698 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2)) \ or resid 699 through 704 or resid 744 through 897 or resid 1001)) } 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.420 Extract box with map and model: 0.990 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 59.310 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 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 : 0.008 0.112 13873 Z= 0.552 Angle : 1.140 18.985 18834 Z= 0.712 Chirality : 0.067 1.460 2028 Planarity : 0.008 0.106 2430 Dihedral : 14.313 89.506 5228 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.97 % Allowed : 7.73 % Favored : 91.30 % Rotamer: Outliers : 2.27 % Allowed : 1.67 % Favored : 96.06 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.20), residues: 1644 helix: -2.90 (0.36), residues: 151 sheet: -0.97 (0.26), residues: 383 loop : -1.50 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 176 HIS 0.010 0.001 HIS A 364 PHE 0.022 0.002 PHE A 45 TYR 0.038 0.002 TYR A 628 ARG 0.009 0.001 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 4) link_NAG-ASN : angle 1.88317 ( 12) hydrogen bonds : bond 0.26675 ( 322) hydrogen bonds : angle 11.03552 ( 858) SS BOND : bond 0.00842 ( 36) SS BOND : angle 1.85902 ( 72) covalent geometry : bond 0.00817 (13833) covalent geometry : angle 1.13603 (18750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 2.022 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: 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: symmetry clash REVERT: A 1 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.6016 (mt-10) REVERT: A 11 ASN cc_start: 0.6521 (OUTLIER) cc_final: 0.6033 (m-40) REVERT: A 700 ILE cc_start: 0.7402 (mt) cc_final: 0.7036 (tt) REVERT: B 139 ILE cc_start: 0.7923 (mp) cc_final: 0.7668 (mt) REVERT: B 403 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.4970 (t0) outliers start: 34 outliers final: 10 residues processed: 173 average time/residue: 0.5481 time to fit residues: 139.1484 Evaluate side-chains 112 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 GLN B 102 ASN B 287 GLN B 400 GLN ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.166441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.134417 restraints weight = 77166.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.134513 restraints weight = 52460.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.135909 restraints weight = 51558.031| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13873 Z= 0.144 Angle : 0.671 10.917 18834 Z= 0.366 Chirality : 0.057 1.372 2028 Planarity : 0.005 0.069 2430 Dihedral : 8.223 70.384 1968 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.30 % Favored : 92.46 % Rotamer: Outliers : 1.60 % Allowed : 5.94 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.20), residues: 1644 helix: -2.46 (0.35), residues: 159 sheet: -1.02 (0.26), residues: 372 loop : -1.31 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 176 HIS 0.006 0.001 HIS A 774 PHE 0.023 0.001 PHE A 701 TYR 0.026 0.002 TYR A 628 ARG 0.004 0.001 ARG A 865 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 4) link_NAG-ASN : angle 1.30146 ( 12) hydrogen bonds : bond 0.05673 ( 322) hydrogen bonds : angle 8.34431 ( 858) SS BOND : bond 0.00489 ( 36) SS BOND : angle 1.17024 ( 72) covalent geometry : bond 0.00319 (13833) covalent geometry : angle 0.66789 (18750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 2.181 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6279 (mt-10) outliers start: 24 outliers final: 14 residues processed: 112 average time/residue: 0.4655 time to fit residues: 81.5669 Evaluate side-chains 103 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.162948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.130363 restraints weight = 75155.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.130043 restraints weight = 52689.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.131474 restraints weight = 50716.735| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13873 Z= 0.171 Angle : 0.640 10.905 18834 Z= 0.345 Chirality : 0.056 1.388 2028 Planarity : 0.005 0.058 2430 Dihedral : 7.722 62.026 1963 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.12 % Favored : 90.69 % Rotamer: Outliers : 1.34 % Allowed : 7.61 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.20), residues: 1644 helix: -2.35 (0.36), residues: 161 sheet: -1.30 (0.25), residues: 385 loop : -1.39 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 618 HIS 0.007 0.001 HIS B 774 PHE 0.016 0.002 PHE A 695 TYR 0.025 0.002 TYR A 628 ARG 0.005 0.001 ARG B 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 4) link_NAG-ASN : angle 1.25209 ( 12) hydrogen bonds : bond 0.04714 ( 322) hydrogen bonds : angle 7.46939 ( 858) SS BOND : bond 0.00519 ( 36) SS BOND : angle 1.16237 ( 72) covalent geometry : bond 0.00387 (13833) covalent geometry : angle 0.63706 (18750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.979 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: 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 1 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6287 (mt-10) REVERT: A 289 MET cc_start: 0.7245 (mpp) cc_final: 0.6716 (mtp) outliers start: 20 outliers final: 13 residues processed: 116 average time/residue: 0.4835 time to fit residues: 85.7598 Evaluate side-chains 101 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 298 CYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.160584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.120361 restraints weight = 75589.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.124351 restraints weight = 43300.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.126954 restraints weight = 30547.750| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13873 Z= 0.177 Angle : 0.622 10.889 18834 Z= 0.335 Chirality : 0.057 1.403 2028 Planarity : 0.004 0.054 2430 Dihedral : 7.533 62.750 1961 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.37 % Favored : 90.45 % Rotamer: Outliers : 1.60 % Allowed : 9.28 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.20), residues: 1644 helix: -2.34 (0.36), residues: 163 sheet: -1.29 (0.25), residues: 387 loop : -1.49 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 618 HIS 0.009 0.001 HIS B 774 PHE 0.020 0.002 PHE F 24 TYR 0.026 0.002 TYR A 628 ARG 0.005 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 4) link_NAG-ASN : angle 1.29186 ( 12) hydrogen bonds : bond 0.04276 ( 322) hydrogen bonds : angle 7.10570 ( 858) SS BOND : bond 0.00385 ( 36) SS BOND : angle 1.08049 ( 72) covalent geometry : bond 0.00407 (13833) covalent geometry : angle 0.61900 (18750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 2.106 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8438 (mm) cc_final: 0.8237 (mm) REVERT: A 289 MET cc_start: 0.7236 (mpp) cc_final: 0.6811 (mtp) REVERT: B 400 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8123 (tt0) outliers start: 24 outliers final: 14 residues processed: 122 average time/residue: 0.5281 time to fit residues: 97.7838 Evaluate side-chains 110 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 387 ASN Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 577 ASN Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 154 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 127 optimal weight: 0.1980 chunk 29 optimal weight: 0.0970 chunk 121 optimal weight: 0.9990 chunk 14 optimal weight: 0.0270 chunk 125 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.162673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.128920 restraints weight = 74939.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.129426 restraints weight = 50378.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.131004 restraints weight = 45158.476| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13873 Z= 0.102 Angle : 0.570 11.095 18834 Z= 0.304 Chirality : 0.055 1.389 2028 Planarity : 0.004 0.052 2430 Dihedral : 7.002 61.814 1956 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.85 % Favored : 92.03 % Rotamer: Outliers : 1.20 % Allowed : 10.08 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.20), residues: 1644 helix: -2.02 (0.38), residues: 162 sheet: -1.30 (0.25), residues: 388 loop : -1.29 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 404 HIS 0.004 0.001 HIS B 774 PHE 0.015 0.001 PHE A 45 TYR 0.023 0.001 TYR A 628 ARG 0.003 0.000 ARG A 455 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 4) link_NAG-ASN : angle 1.12163 ( 12) hydrogen bonds : bond 0.03676 ( 322) hydrogen bonds : angle 6.75045 ( 858) SS BOND : bond 0.00463 ( 36) SS BOND : angle 0.96587 ( 72) covalent geometry : bond 0.00231 (13833) covalent geometry : angle 0.56730 (18750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 1.922 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7970 (tm-30) REVERT: B 558 MET cc_start: 0.5639 (pp-130) cc_final: 0.5330 (pp-130) REVERT: B 822 TRP cc_start: 0.5384 (p90) cc_final: 0.4805 (p90) outliers start: 18 outliers final: 13 residues processed: 114 average time/residue: 0.5850 time to fit residues: 98.9291 Evaluate side-chains 108 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 33 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.160844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.128002 restraints weight = 73865.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.128993 restraints weight = 50589.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.130429 restraints weight = 44400.977| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13873 Z= 0.128 Angle : 0.571 11.046 18834 Z= 0.304 Chirality : 0.055 1.394 2028 Planarity : 0.004 0.051 2430 Dihedral : 6.742 60.574 1952 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.06 % Favored : 90.82 % Rotamer: Outliers : 1.20 % Allowed : 11.01 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.20), residues: 1644 helix: -1.95 (0.37), residues: 171 sheet: -1.32 (0.24), residues: 389 loop : -1.29 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 544 HIS 0.006 0.001 HIS B 774 PHE 0.021 0.001 PHE A 45 TYR 0.022 0.001 TYR A 628 ARG 0.003 0.000 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 4) link_NAG-ASN : angle 1.13410 ( 12) hydrogen bonds : bond 0.03658 ( 322) hydrogen bonds : angle 6.62575 ( 858) SS BOND : bond 0.00308 ( 36) SS BOND : angle 1.02226 ( 72) covalent geometry : bond 0.00297 (13833) covalent geometry : angle 0.56760 (18750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 2.151 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: 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 385 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8035 (tm-30) REVERT: B 822 TRP cc_start: 0.5084 (p90) cc_final: 0.4652 (p90) outliers start: 18 outliers final: 13 residues processed: 110 average time/residue: 0.5573 time to fit residues: 92.0540 Evaluate side-chains 110 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 21 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.159903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.125746 restraints weight = 74845.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.126289 restraints weight = 50808.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.127659 restraints weight = 45848.456| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13873 Z= 0.148 Angle : 0.595 11.154 18834 Z= 0.319 Chirality : 0.056 1.405 2028 Planarity : 0.004 0.051 2430 Dihedral : 6.758 59.533 1952 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.04 % Favored : 89.84 % Rotamer: Outliers : 1.27 % Allowed : 11.48 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.20), residues: 1644 helix: -1.89 (0.38), residues: 172 sheet: -1.34 (0.24), residues: 391 loop : -1.35 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 544 HIS 0.009 0.001 HIS B 774 PHE 0.021 0.002 PHE F 24 TYR 0.022 0.001 TYR A 628 ARG 0.003 0.000 ARG A 794 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 4) link_NAG-ASN : angle 1.07398 ( 12) hydrogen bonds : bond 0.03755 ( 322) hydrogen bonds : angle 6.58086 ( 858) SS BOND : bond 0.00413 ( 36) SS BOND : angle 1.48188 ( 72) covalent geometry : bond 0.00341 (13833) covalent geometry : angle 0.58828 (18750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 2.220 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: 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 385 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8070 (tm-30) REVERT: A 878 THR cc_start: 0.6435 (OUTLIER) cc_final: 0.6212 (p) outliers start: 19 outliers final: 13 residues processed: 115 average time/residue: 0.5689 time to fit residues: 97.5716 Evaluate side-chains 109 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 138 optimal weight: 0.0060 chunk 14 optimal weight: 0.0770 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 75 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.161284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.121424 restraints weight = 73336.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.125576 restraints weight = 40562.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.128309 restraints weight = 28106.940| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 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 : 0.002 0.029 13873 Z= 0.095 Angle : 0.557 11.176 18834 Z= 0.296 Chirality : 0.055 1.387 2028 Planarity : 0.004 0.056 2430 Dihedral : 6.610 59.736 1952 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.60 % Favored : 92.27 % Rotamer: Outliers : 0.87 % Allowed : 11.88 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.21), residues: 1644 helix: -1.61 (0.40), residues: 171 sheet: -1.25 (0.25), residues: 393 loop : -1.23 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 618 HIS 0.003 0.001 HIS A 697 PHE 0.016 0.001 PHE B 747 TYR 0.022 0.001 TYR A 628 ARG 0.005 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 4) link_NAG-ASN : angle 0.96293 ( 12) hydrogen bonds : bond 0.03283 ( 322) hydrogen bonds : angle 6.37724 ( 858) SS BOND : bond 0.00328 ( 36) SS BOND : angle 1.43634 ( 72) covalent geometry : bond 0.00219 (13833) covalent geometry : angle 0.55077 (18750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 1.991 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: 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 319 MET cc_start: 0.7261 (mtt) cc_final: 0.7049 (mtm) REVERT: A 385 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7975 (tm-30) outliers start: 13 outliers final: 12 residues processed: 110 average time/residue: 0.6234 time to fit residues: 106.3472 Evaluate side-chains 107 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 160 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.156951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.116695 restraints weight = 74724.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.120643 restraints weight = 42780.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.123271 restraints weight = 30185.651| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13873 Z= 0.221 Angle : 0.654 11.270 18834 Z= 0.351 Chirality : 0.058 1.402 2028 Planarity : 0.005 0.050 2430 Dihedral : 6.929 57.322 1952 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.50 % Favored : 88.38 % Rotamer: Outliers : 1.27 % Allowed : 11.75 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.20), residues: 1644 helix: -1.90 (0.37), residues: 172 sheet: -1.40 (0.25), residues: 381 loop : -1.59 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 544 HIS 0.014 0.002 HIS B 774 PHE 0.030 0.002 PHE F 24 TYR 0.023 0.002 TYR B 391 ARG 0.005 0.001 ARG A 794 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 4) link_NAG-ASN : angle 1.27938 ( 12) hydrogen bonds : bond 0.04422 ( 322) hydrogen bonds : angle 6.70711 ( 858) SS BOND : bond 0.00414 ( 36) SS BOND : angle 1.50990 ( 72) covalent geometry : bond 0.00512 (13833) covalent geometry : angle 0.64816 (18750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 3.447 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: 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 385 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7985 (tm-30) outliers start: 19 outliers final: 15 residues processed: 105 average time/residue: 0.8450 time to fit residues: 135.0218 Evaluate side-chains 103 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 234 CYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain F residue 16 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 24 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 chunk 82 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 133 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 442 GLN ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.159672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.121363 restraints weight = 73320.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.125199 restraints weight = 43247.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.125426 restraints weight = 28140.050| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13873 Z= 0.099 Angle : 0.563 11.199 18834 Z= 0.300 Chirality : 0.055 1.396 2028 Planarity : 0.004 0.051 2430 Dihedral : 6.621 57.874 1952 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.12 % Favored : 92.70 % Rotamer: Outliers : 0.73 % Allowed : 12.22 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.21), residues: 1644 helix: -1.56 (0.40), residues: 171 sheet: -1.36 (0.25), residues: 394 loop : -1.35 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 544 HIS 0.003 0.001 HIS B 774 PHE 0.011 0.001 PHE A 45 TYR 0.023 0.001 TYR A 628 ARG 0.003 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 4) link_NAG-ASN : angle 0.96768 ( 12) hydrogen bonds : bond 0.03417 ( 322) hydrogen bonds : angle 6.40724 ( 858) SS BOND : bond 0.00300 ( 36) SS BOND : angle 1.24231 ( 72) covalent geometry : bond 0.00228 (13833) covalent geometry : angle 0.55852 (18750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 2 is missing expected H atoms. Skipping. Residue ILE 10 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 2.833 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: 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 385 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8100 (tm-30) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 0.6813 time to fit residues: 110.6777 Evaluate side-chains 98 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 874 ARG Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 758 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 6 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 143 optimal weight: 0.0060 chunk 155 optimal weight: 9.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.159857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.119696 restraints weight = 74318.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.123753 restraints weight = 41763.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 74)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.126444 restraints weight = 29160.801| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13873 Z= 0.106 Angle : 0.555 11.153 18834 Z= 0.296 Chirality : 0.055 1.384 2028 Planarity : 0.004 0.049 2430 Dihedral : 6.334 56.285 1948 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.76 % Favored : 91.06 % Rotamer: Outliers : 0.73 % Allowed : 12.48 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.21), residues: 1644 helix: -1.52 (0.40), residues: 171 sheet: -1.31 (0.25), residues: 395 loop : -1.28 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 544 HIS 0.006 0.001 HIS B 774 PHE 0.017 0.001 PHE F 24 TYR 0.024 0.001 TYR A 628 ARG 0.003 0.000 ARG B 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 4) link_NAG-ASN : angle 0.93015 ( 12) hydrogen bonds : bond 0.03346 ( 322) hydrogen bonds : angle 6.26665 ( 858) SS BOND : bond 0.00285 ( 36) SS BOND : angle 1.18017 ( 72) covalent geometry : bond 0.00246 (13833) covalent geometry : angle 0.55123 (18750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8068.32 seconds wall clock time: 142 minutes 30.78 seconds (8550.78 seconds total)