Starting phenix.real_space_refine on Fri Sep 19 13:51:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v3p_31671/09_2025/7v3p_31671_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v3p_31671/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7v3p_31671/09_2025/7v3p_31671_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v3p_31671/09_2025/7v3p_31671_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v3p_31671/09_2025/7v3p_31671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v3p_31671/09_2025/7v3p_31671.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.047 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.78, per 1000 atoms: 0.18 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: 2.40 Conformation dependent library (CDL) restraints added in 781.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.74 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: 6.84 Time building geometry restraints manager: 3.26 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 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 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.170 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.270 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- 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 : 12.87 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (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 ARG 0.009 0.001 ARG B 59 TYR 0.038 0.002 TYR A 628 PHE 0.022 0.002 PHE A 45 TRP 0.029 0.003 TRP B 176 HIS 0.010 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00817 (13833) covalent geometry : angle 1.13603 (18750) SS BOND : bond 0.00842 ( 36) SS BOND : angle 1.85902 ( 72) hydrogen bonds : bond 0.26675 ( 322) hydrogen bonds : angle 11.03552 ( 858) link_NAG-ASN : bond 0.00467 ( 4) link_NAG-ASN : angle 1.88317 ( 12) *********************** 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 : 0.691 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: A 1 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.6017 (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: 0.7669 (mt) REVERT: B 403 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.4973 (t0) outliers start: 34 outliers final: 10 residues processed: 173 average time/residue: 0.2521 time to fit residues: 64.0299 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 : 0.788 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.166255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.133258 restraints weight = 76498.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.134206 restraints weight = 51334.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.135502 restraints weight = 47963.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.136973 restraints weight = 30657.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.137632 restraints weight = 26914.484| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13873 Z= 0.143 Angle : 0.671 10.914 18834 Z= 0.366 Chirality : 0.057 1.375 2028 Planarity : 0.005 0.070 2430 Dihedral : 8.200 70.161 1968 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.93 % Favored : 92.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.20), residues: 1644 helix: -2.46 (0.35), residues: 160 sheet: -1.00 (0.26), residues: 372 loop : -1.29 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 865 TYR 0.026 0.002 TYR A 628 PHE 0.023 0.001 PHE A 701 TRP 0.012 0.001 TRP B 176 HIS 0.006 0.001 HIS A 774 Details of bonding type rmsd covalent geometry : bond 0.00319 (13833) covalent geometry : angle 0.66743 (18750) SS BOND : bond 0.00471 ( 36) SS BOND : angle 1.17032 ( 72) hydrogen bonds : bond 0.05752 ( 322) hydrogen bonds : angle 8.33851 ( 858) link_NAG-ASN : bond 0.00207 ( 4) link_NAG-ASN : angle 1.29802 ( 12) *********************** 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 : 0.720 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: A 1 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6232 (mt-10) outliers start: 24 outliers final: 14 residues processed: 112 average time/residue: 0.2190 time to fit residues: 38.6369 Evaluate side-chains 106 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 117 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 48 optimal weight: 0.0870 chunk 121 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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** B 680 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.163358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.123754 restraints weight = 75310.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.128843 restraints weight = 45130.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.130068 restraints weight = 31119.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.131480 restraints weight = 24920.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.132273 restraints weight = 21287.494| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13873 Z= 0.168 Angle : 0.636 10.874 18834 Z= 0.343 Chirality : 0.057 1.389 2028 Planarity : 0.005 0.057 2430 Dihedral : 7.654 61.248 1963 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.88 % Favored : 90.94 % Rotamer: Outliers : 1.40 % Allowed : 7.61 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.20), residues: 1644 helix: -2.37 (0.36), residues: 161 sheet: -1.33 (0.25), residues: 386 loop : -1.35 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 245 TYR 0.025 0.002 TYR A 628 PHE 0.017 0.002 PHE A 695 TRP 0.015 0.001 TRP B 618 HIS 0.007 0.001 HIS A 774 Details of bonding type rmsd covalent geometry : bond 0.00380 (13833) covalent geometry : angle 0.63222 (18750) SS BOND : bond 0.00523 ( 36) SS BOND : angle 1.16895 ( 72) hydrogen bonds : bond 0.04689 ( 322) hydrogen bonds : angle 7.35753 ( 858) link_NAG-ASN : bond 0.00260 ( 4) link_NAG-ASN : angle 1.21584 ( 12) *********************** 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 122 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.814 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: 0.6595 (OUTLIER) cc_final: 0.6227 (mt-10) REVERT: A 289 MET cc_start: 0.7217 (mpp) cc_final: 0.6733 (mtp) outliers start: 21 outliers final: 13 residues processed: 119 average time/residue: 0.2312 time to fit residues: 42.2743 Evaluate side-chains 103 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 4 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 102 optimal weight: 0.1980 chunk 132 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 B 680 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.163725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.130507 restraints weight = 74629.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.130637 restraints weight = 51332.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.131940 restraints weight = 50413.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.133737 restraints weight = 31727.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.134619 restraints weight = 27397.736| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13873 Z= 0.120 Angle : 0.579 11.001 18834 Z= 0.310 Chirality : 0.056 1.407 2028 Planarity : 0.004 0.052 2430 Dihedral : 7.291 62.728 1961 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.48 % Favored : 92.34 % Rotamer: Outliers : 1.40 % Allowed : 9.01 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.20), residues: 1644 helix: -2.14 (0.38), residues: 161 sheet: -1.25 (0.25), residues: 391 loop : -1.27 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 874 TYR 0.025 0.001 TYR A 628 PHE 0.012 0.001 PHE A 701 TRP 0.008 0.001 TRP A 544 HIS 0.005 0.001 HIS B 774 Details of bonding type rmsd covalent geometry : bond 0.00275 (13833) covalent geometry : angle 0.57628 (18750) SS BOND : bond 0.00354 ( 36) SS BOND : angle 1.00611 ( 72) hydrogen bonds : bond 0.03830 ( 322) hydrogen bonds : angle 6.95977 ( 858) link_NAG-ASN : bond 0.00188 ( 4) link_NAG-ASN : angle 1.17723 ( 12) *********************** 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 125 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.610 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 289 MET cc_start: 0.7293 (mpp) cc_final: 0.6808 (mtp) REVERT: A 377 LEU cc_start: 0.7283 (mt) cc_final: 0.7077 (mp) outliers start: 21 outliers final: 14 residues processed: 120 average time/residue: 0.2480 time to fit residues: 44.4296 Evaluate side-chains 111 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU 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 400 GLN Chi-restraints excluded: chain B residue 402 TRP Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 511 GLN 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 26 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 123 optimal weight: 0.0770 chunk 27 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.163261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.130167 restraints weight = 75224.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.131366 restraints weight = 51814.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.132508 restraints weight = 48463.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.133333 restraints weight = 29596.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.134105 restraints weight = 27022.182| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13873 Z= 0.119 Angle : 0.570 11.002 18834 Z= 0.305 Chirality : 0.055 1.381 2028 Planarity : 0.004 0.051 2430 Dihedral : 6.969 61.727 1956 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.33 % Favored : 91.55 % Rotamer: Outliers : 0.93 % Allowed : 9.75 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.20), residues: 1644 helix: -2.00 (0.38), residues: 162 sheet: -1.27 (0.24), residues: 392 loop : -1.25 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 112 TYR 0.025 0.001 TYR B 430 PHE 0.011 0.001 PHE F 24 TRP 0.008 0.001 TRP B 618 HIS 0.005 0.001 HIS B 774 Details of bonding type rmsd covalent geometry : bond 0.00274 (13833) covalent geometry : angle 0.56725 (18750) SS BOND : bond 0.00281 ( 36) SS BOND : angle 0.93728 ( 72) hydrogen bonds : bond 0.03729 ( 322) hydrogen bonds : angle 6.79974 ( 858) link_NAG-ASN : bond 0.00205 ( 4) link_NAG-ASN : angle 1.11254 ( 12) *********************** 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 110 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.731 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: A 289 MET cc_start: 0.7292 (mpp) cc_final: 0.7083 (ptp) REVERT: A 385 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7939 (tm-30) REVERT: B 822 TRP cc_start: 0.5346 (p90) cc_final: 0.4751 (p90) outliers start: 14 outliers final: 11 residues processed: 108 average time/residue: 0.2432 time to fit residues: 39.4202 Evaluate side-chains 107 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 696 LEU 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 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 41 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 147 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.163232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.126297 restraints weight = 74763.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.129107 restraints weight = 42600.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.128893 restraints weight = 30760.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.130316 restraints weight = 30947.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.130384 restraints weight = 26839.926| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13873 Z= 0.106 Angle : 0.547 11.149 18834 Z= 0.292 Chirality : 0.055 1.405 2028 Planarity : 0.004 0.050 2430 Dihedral : 6.627 59.799 1954 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.48 % Favored : 92.40 % Rotamer: Outliers : 0.87 % Allowed : 10.68 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.21), residues: 1644 helix: -1.85 (0.39), residues: 171 sheet: -1.22 (0.25), residues: 395 loop : -1.15 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 376 TYR 0.022 0.001 TYR B 430 PHE 0.017 0.001 PHE B 790 TRP 0.008 0.001 TRP A 544 HIS 0.004 0.001 HIS B 774 Details of bonding type rmsd covalent geometry : bond 0.00244 (13833) covalent geometry : angle 0.54485 (18750) SS BOND : bond 0.00244 ( 36) SS BOND : angle 0.95838 ( 72) hydrogen bonds : bond 0.03377 ( 322) hydrogen bonds : angle 6.53071 ( 858) link_NAG-ASN : bond 0.00188 ( 4) link_NAG-ASN : angle 1.04000 ( 12) *********************** 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 112 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.776 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: A 385 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 822 TRP cc_start: 0.5692 (p90) cc_final: 0.4945 (p90) outliers start: 13 outliers final: 9 residues processed: 110 average time/residue: 0.2798 time to fit residues: 45.2418 Evaluate side-chains 103 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU 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 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 105 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** 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 = 0.4291 r_free = 0.4291 target = 0.161027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.121274 restraints weight = 73684.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.125295 restraints weight = 41067.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.128030 restraints weight = 28585.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.129804 restraints weight = 22619.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.130892 restraints weight = 19462.108| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13873 Z= 0.141 Angle : 0.565 11.094 18834 Z= 0.303 Chirality : 0.055 1.394 2028 Planarity : 0.004 0.049 2430 Dihedral : 6.559 58.348 1952 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.06 % Favored : 90.82 % Rotamer: Outliers : 1.13 % Allowed : 10.81 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.20), residues: 1644 helix: -1.90 (0.38), residues: 172 sheet: -1.23 (0.25), residues: 392 loop : -1.24 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 794 TYR 0.019 0.001 TYR A 628 PHE 0.015 0.001 PHE F 24 TRP 0.014 0.001 TRP B 404 HIS 0.007 0.001 HIS B 774 Details of bonding type rmsd covalent geometry : bond 0.00326 (13833) covalent geometry : angle 0.56241 (18750) SS BOND : bond 0.00327 ( 36) SS BOND : angle 0.94114 ( 72) hydrogen bonds : bond 0.03596 ( 322) hydrogen bonds : angle 6.51729 ( 858) link_NAG-ASN : bond 0.00213 ( 4) link_NAG-ASN : angle 1.05083 ( 12) *********************** 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 113 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.722 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: A 1 GLU cc_start: 0.6235 (OUTLIER) cc_final: 0.5833 (mt-10) REVERT: A 385 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7960 (tm-30) REVERT: B 577 ASN cc_start: 0.5647 (OUTLIER) cc_final: 0.5358 (m-40) REVERT: B 822 TRP cc_start: 0.5619 (p90) cc_final: 0.4920 (p90) outliers start: 17 outliers final: 11 residues processed: 112 average time/residue: 0.2693 time to fit residues: 44.8481 Evaluate side-chains 106 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 429 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 107 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 136 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN ** A 774 HIS ** 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 = 0.4292 r_free = 0.4292 target = 0.160984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.120717 restraints weight = 74604.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.126345 restraints weight = 43447.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.128021 restraints weight = 28206.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.129492 restraints weight = 21647.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.129795 restraints weight = 19539.651| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13873 Z= 0.141 Angle : 0.584 11.190 18834 Z= 0.313 Chirality : 0.055 1.386 2028 Planarity : 0.004 0.050 2430 Dihedral : 6.668 58.668 1952 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.00 % Favored : 90.88 % Rotamer: Outliers : 1.00 % Allowed : 11.28 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.20), residues: 1644 helix: -1.82 (0.38), residues: 172 sheet: -1.26 (0.25), residues: 395 loop : -1.29 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 764 TYR 0.019 0.001 TYR A 628 PHE 0.018 0.001 PHE F 24 TRP 0.028 0.001 TRP B 404 HIS 0.008 0.001 HIS B 774 Details of bonding type rmsd covalent geometry : bond 0.00323 (13833) covalent geometry : angle 0.57758 (18750) SS BOND : bond 0.00357 ( 36) SS BOND : angle 1.51305 ( 72) hydrogen bonds : bond 0.03600 ( 322) hydrogen bonds : angle 6.52504 ( 858) link_NAG-ASN : bond 0.00202 ( 4) link_NAG-ASN : angle 1.01600 ( 12) *********************** 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 112 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.742 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 385 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7959 (tm-30) outliers start: 15 outliers final: 11 residues processed: 109 average time/residue: 0.2733 time to fit residues: 43.9329 Evaluate side-chains 100 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 635 LYS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain F residue 16 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 20 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 chunk 108 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 162 optimal weight: 0.1980 chunk 133 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 680 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.159473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.119701 restraints weight = 73675.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.125417 restraints weight = 42598.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.126537 restraints weight = 27629.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.127655 restraints weight = 23007.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.128692 restraints weight = 19814.676| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13873 Z= 0.153 Angle : 0.588 11.174 18834 Z= 0.314 Chirality : 0.056 1.395 2028 Planarity : 0.004 0.050 2430 Dihedral : 6.700 59.822 1952 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.67 % Favored : 90.15 % Rotamer: Outliers : 1.07 % Allowed : 11.35 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.20), residues: 1644 helix: -1.79 (0.39), residues: 172 sheet: -1.26 (0.25), residues: 389 loop : -1.37 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.020 0.001 TYR A 628 PHE 0.026 0.002 PHE A 45 TRP 0.019 0.001 TRP B 404 HIS 0.009 0.001 HIS B 774 Details of bonding type rmsd covalent geometry : bond 0.00353 (13833) covalent geometry : angle 0.58304 (18750) SS BOND : bond 0.00435 ( 36) SS BOND : angle 1.26339 ( 72) hydrogen bonds : bond 0.03738 ( 322) hydrogen bonds : angle 6.48368 ( 858) link_NAG-ASN : bond 0.00221 ( 4) link_NAG-ASN : angle 1.10614 ( 12) *********************** 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 108 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.715 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: 0.6301 (OUTLIER) cc_final: 0.5934 (mt-10) REVERT: A 32 LEU cc_start: 0.7179 (mt) cc_final: 0.6952 (mt) REVERT: A 319 MET cc_start: 0.7264 (mtt) cc_final: 0.7057 (mtm) REVERT: A 385 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7963 (tm-30) outliers start: 16 outliers final: 12 residues processed: 104 average time/residue: 0.2253 time to fit residues: 36.4356 Evaluate side-chains 105 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU 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 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 626 TYR Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 802 ASP 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 1 optimal weight: 0.0570 chunk 18 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 680 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.160822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.127381 restraints weight = 74645.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.128287 restraints weight = 50363.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.129412 restraints weight = 48148.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.130833 restraints weight = 29872.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.131472 restraints weight = 26244.635| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13873 Z= 0.110 Angle : 0.550 11.220 18834 Z= 0.294 Chirality : 0.055 1.393 2028 Planarity : 0.004 0.050 2430 Dihedral : 6.405 59.736 1948 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.24 % Favored : 92.58 % Rotamer: Outliers : 0.60 % Allowed : 11.68 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.21), residues: 1644 helix: -1.60 (0.40), residues: 171 sheet: -1.30 (0.25), residues: 396 loop : -1.24 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 794 TYR 0.021 0.001 TYR A 628 PHE 0.014 0.001 PHE F 24 TRP 0.019 0.001 TRP B 404 HIS 0.005 0.001 HIS B 774 Details of bonding type rmsd covalent geometry : bond 0.00254 (13833) covalent geometry : angle 0.54598 (18750) SS BOND : bond 0.00306 ( 36) SS BOND : angle 1.09722 ( 72) hydrogen bonds : bond 0.03381 ( 322) hydrogen bonds : angle 6.34022 ( 858) link_NAG-ASN : bond 0.00186 ( 4) link_NAG-ASN : angle 0.97689 ( 12) ********************** 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 105 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.776 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 32 LEU cc_start: 0.7289 (mt) cc_final: 0.7041 (mt) REVERT: A 319 MET cc_start: 0.7371 (mtt) cc_final: 0.7166 (mtm) REVERT: A 385 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8090 (tm-30) REVERT: B 560 GLU cc_start: 0.5637 (mm-30) cc_final: 0.5432 (mm-30) outliers start: 9 outliers final: 9 residues processed: 104 average time/residue: 0.2586 time to fit residues: 40.9866 Evaluate side-chains 97 residues out of total 1498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 49 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 81 optimal weight: 0.0370 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 ASN B 680 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.161050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.127646 restraints weight = 74805.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.127585 restraints weight = 50323.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.128922 restraints weight = 48719.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.130506 restraints weight = 31816.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.131017 restraints weight = 27580.388| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13873 Z= 0.105 Angle : 0.546 11.181 18834 Z= 0.291 Chirality : 0.055 1.390 2028 Planarity : 0.004 0.072 2430 Dihedral : 6.304 59.712 1948 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.33 % Favored : 91.55 % Rotamer: Outliers : 0.87 % Allowed : 11.68 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.21), residues: 1644 helix: -1.60 (0.40), residues: 171 sheet: -1.23 (0.25), residues: 396 loop : -1.19 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 192 TYR 0.021 0.001 TYR A 628 PHE 0.014 0.001 PHE F 24 TRP 0.020 0.001 TRP B 404 HIS 0.005 0.001 HIS B 774 Details of bonding type rmsd covalent geometry : bond 0.00245 (13833) covalent geometry : angle 0.54296 (18750) SS BOND : bond 0.00337 ( 36) SS BOND : angle 1.05632 ( 72) hydrogen bonds : bond 0.03275 ( 322) hydrogen bonds : angle 6.21753 ( 858) link_NAG-ASN : bond 0.00175 ( 4) link_NAG-ASN : angle 0.89690 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3970.79 seconds wall clock time: 68 minutes 34.23 seconds (4114.23 seconds total)