Starting phenix.real_space_refine on Wed Mar 4 13:59:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nco_49261/03_2026/9nco_49261.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nco_49261/03_2026/9nco_49261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nco_49261/03_2026/9nco_49261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nco_49261/03_2026/9nco_49261.map" model { file = "/net/cci-nas-00/data/ceres_data/9nco_49261/03_2026/9nco_49261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nco_49261/03_2026/9nco_49261.cif" } resolution = 3.4 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= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 8596 2.51 5 N 2344 2.21 5 O 2563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13604 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6674 Classifications: {'peptide': 831} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 783} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 6530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6530 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 765} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 158 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Modifications used: {'PEPT-D': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "D" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Time building chain proxies: 3.28, per 1000 atoms: 0.24 Number of scatterers: 13604 At special positions: 0 Unit cell: (95.312, 112.924, 174.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 101 16.00 O 2563 8.00 N 2344 7.00 C 8596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.02 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.02 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.02 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=2.02 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 294 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 323 " distance=2.02 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 458 " distance=2.04 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS B 514 " distance=2.04 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 849 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.02 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.04 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " 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 TRANS " DHI C 24 " - " GLY C 23 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 717.8 milliseconds 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DHI C 24 " Number of C-beta restraints generated: 3180 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 30 sheets defined 17.0% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.810A pdb=" N LEU A 16 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 17 " --> pdb=" O GLN A 14 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG A 18 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 20 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.570A pdb=" N LEU A 129 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.870A pdb=" N CYS A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 248 through 255 removed outlier: 4.272A pdb=" N CYS A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'A' and resid 340 through 348 removed outlier: 4.348A pdb=" N ASN A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 4.402A pdb=" N PHE A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 removed outlier: 4.055A pdb=" N MET A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 623 through 630 removed outlier: 3.830A pdb=" N LEU A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 703 removed outlier: 3.637A pdb=" N PHE A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 852 through 859 removed outlier: 4.695A pdb=" N LYS A 857 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 19 Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.820A pdb=" N LEU B 129 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.627A pdb=" N ASN B 137 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.894A pdb=" N GLU B 147 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 186 through 190 Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.709A pdb=" N ALA B 253 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 319 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 368 through 372 removed outlier: 4.255A pdb=" N PHE B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 425 through 437 Processing helix chain 'B' and resid 438 through 441 Processing helix chain 'B' and resid 624 through 629 Processing helix chain 'B' and resid 677 through 691 removed outlier: 3.642A pdb=" N ALA B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 696 removed outlier: 3.661A pdb=" N ASN B 696 " --> pdb=" O LYS B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 701 Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 852 through 859 Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'D' and resid 57 through 64 removed outlier: 3.667A pdb=" N THR D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 72 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 8.827A pdb=" N ILE A 25 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 51 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TRP A 79 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU A 53 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 9 removed outlier: 6.342A pdb=" N ILE A 7 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU A 32 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N PHE A 58 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 31 " --> pdb=" O PHE A 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 89 removed outlier: 7.580A pdb=" N ARG A 112 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLU A 114 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 167 removed outlier: 3.683A pdb=" N ASN A 172 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 177 removed outlier: 6.685A pdb=" N ARG A 180 " --> pdb=" O TRP A 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 229 through 231 removed outlier: 3.841A pdb=" N TYR A 224 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR A 225 " --> pdb=" O CYS A 246 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 247 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR A 239 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ARG A 240 " --> pdb=" O CYS A 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 281 through 283 Processing sheet with id=AA8, first strand: chain 'A' and resid 308 through 311 removed outlier: 6.316A pdb=" N LEU A 330 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ARG A 361 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 332 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ALA A 419 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL A 392 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AB1, first strand: chain 'A' and resid 465 through 471 Processing sheet with id=AB2, first strand: chain 'A' and resid 520 through 524 removed outlier: 3.641A pdb=" N SER A 492 " --> pdb=" O VAL A 554 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 590 through 593 removed outlier: 4.196A pdb=" N ASN A 592 " --> pdb=" O GLN A 596 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLN A 596 " --> pdb=" O ASN A 592 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 750 through 752 removed outlier: 3.681A pdb=" N TYR A 613 " --> pdb=" O CYS A 776 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 772 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 809 through 813 Processing sheet with id=AB6, first strand: chain 'A' and resid 846 through 851 removed outlier: 6.611A pdb=" N ILE A 875 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TRP A 886 " --> pdb=" O ILE A 875 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA A 877 " --> pdb=" O GLY A 884 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 846 through 851 Processing sheet with id=AB8, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AB9, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.208A pdb=" N LEU B 29 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE B 58 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE B 31 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL B 60 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU B 33 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE B 90 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU B 57 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ARG B 112 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU B 114 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE B 90 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 164 through 167 Processing sheet with id=AC2, first strand: chain 'B' and resid 206 through 209 removed outlier: 7.354A pdb=" N SER B 208 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N CYS B 218 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 245 through 247 removed outlier: 3.671A pdb=" N ARG B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG B 240 " --> pdb=" O CYS B 273 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AC5, first strand: chain 'B' and resid 308 through 311 removed outlier: 6.732A pdb=" N LYS B 309 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU B 330 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ARG B 361 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 332 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR B 417 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR B 391 " --> pdb=" O TYR B 417 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AC7, first strand: chain 'B' and resid 465 through 471 Processing sheet with id=AC8, first strand: chain 'B' and resid 520 through 525 Processing sheet with id=AC9, first strand: chain 'B' and resid 585 through 590 removed outlier: 5.565A pdb=" N ASP B 586 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASN B 602 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 747 through 752 removed outlier: 3.841A pdb=" N TRP B 618 " --> pdb=" O PHE B 748 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 809 through 813 Processing sheet with id=AD3, first strand: chain 'B' and resid 846 through 851 removed outlier: 3.867A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR B 872 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 869 " --> pdb=" O VAL B 894 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 807 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: 3.00 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4477 1.35 - 1.47: 3307 1.47 - 1.59: 6015 1.59 - 1.71: 0 1.71 - 1.84: 126 Bond restraints: 13925 Sorted by residual: bond pdb=" CB CYS A 175 " pdb=" SG CYS A 175 " ideal model delta sigma weight residual 1.808 1.749 0.059 3.30e-02 9.18e+02 3.16e+00 bond pdb=" C TYR C 26 " pdb=" N THR C 27 " ideal model delta sigma weight residual 1.335 1.382 -0.047 3.59e-02 7.76e+02 1.72e+00 bond pdb=" CB CYS B 776 " pdb=" SG CYS B 776 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.61e+00 bond pdb=" CB VAL A 134 " pdb=" CG2 VAL A 134 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" CA LYS B 17 " pdb=" C LYS B 17 " ideal model delta sigma weight residual 1.518 1.564 -0.046 4.01e-02 6.22e+02 1.34e+00 ... (remaining 13920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 17044 1.59 - 3.17: 1530 3.17 - 4.76: 257 4.76 - 6.35: 43 6.35 - 7.94: 7 Bond angle restraints: 18881 Sorted by residual: angle pdb=" CA TYR A 391 " pdb=" CB TYR A 391 " pdb=" CG TYR A 391 " ideal model delta sigma weight residual 113.90 120.91 -7.01 1.80e+00 3.09e-01 1.52e+01 angle pdb=" N HIS B 778 " pdb=" CA HIS B 778 " pdb=" C HIS B 778 " ideal model delta sigma weight residual 111.37 117.18 -5.81 1.65e+00 3.67e-01 1.24e+01 angle pdb=" C HIS A 480 " pdb=" N ARG A 481 " pdb=" CA ARG A 481 " ideal model delta sigma weight residual 122.46 127.31 -4.85 1.41e+00 5.03e-01 1.18e+01 angle pdb=" CA TRP B 402 " pdb=" CB TRP B 402 " pdb=" CG TRP B 402 " ideal model delta sigma weight residual 113.60 119.82 -6.22 1.90e+00 2.77e-01 1.07e+01 angle pdb=" N PRO B 422 " pdb=" CA PRO B 422 " pdb=" C PRO B 422 " ideal model delta sigma weight residual 112.47 119.20 -6.73 2.06e+00 2.36e-01 1.07e+01 ... (remaining 18876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 7663 17.84 - 35.68: 685 35.68 - 53.51: 98 53.51 - 71.35: 35 71.35 - 89.19: 19 Dihedral angle restraints: 8500 sinusoidal: 3544 harmonic: 4956 Sorted by residual: dihedral pdb=" CB CYS A 152 " pdb=" SG CYS A 152 " pdb=" SG CYS A 175 " pdb=" CB CYS A 175 " ideal model delta sinusoidal sigma weight residual 93.00 153.97 -60.97 1 1.00e+01 1.00e-02 4.94e+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 93.00 150.46 -57.46 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS B 425 " pdb=" SG CYS B 425 " pdb=" SG CYS B 458 " pdb=" CB CYS B 458 " ideal model delta sinusoidal sigma weight residual 93.00 146.22 -53.22 1 1.00e+01 1.00e-02 3.85e+01 ... (remaining 8497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1276 0.049 - 0.099: 535 0.099 - 0.148: 181 0.148 - 0.198: 28 0.198 - 0.247: 6 Chirality restraints: 2026 Sorted by residual: chirality pdb=" CA TRP B 402 " pdb=" N TRP B 402 " pdb=" C TRP B 402 " pdb=" CB TRP B 402 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA ARG A 59 " pdb=" N ARG A 59 " pdb=" C ARG A 59 " pdb=" CB ARG A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE A 638 " pdb=" CA ILE A 638 " pdb=" CG1 ILE A 638 " pdb=" CG2 ILE A 638 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 2023 not shown) Planarity restraints: 2460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 641 " -0.243 9.50e-02 1.11e+02 1.10e-01 9.68e+00 pdb=" NE ARG A 641 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 641 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG A 641 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 641 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 101 " -0.018 2.00e-02 2.50e+03 2.20e-02 9.64e+00 pdb=" CG TYR B 101 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 101 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 101 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 101 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR B 101 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 101 " 0.025 2.00e-02 2.50e+03 pdb=" OH TYR B 101 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 112 " 0.243 9.50e-02 1.11e+02 1.09e-01 8.69e+00 pdb=" NE ARG B 112 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 112 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 112 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 112 " 0.002 2.00e-02 2.50e+03 ... (remaining 2457 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 5262 2.89 - 3.39: 13081 3.39 - 3.90: 22215 3.90 - 4.40: 25624 4.40 - 4.90: 42402 Nonbonded interactions: 108584 Sorted by model distance: nonbonded pdb=" OG SER B 591 " pdb=" O SER B 593 " model vdw 2.391 3.040 nonbonded pdb=" O PRO A 581 " pdb=" OG SER A 786 " model vdw 2.392 3.040 nonbonded pdb=" O ILE A 491 " pdb=" OG SER A 492 " model vdw 2.446 3.040 nonbonded pdb=" OD1 ASP A 126 " pdb=" OG SER A 128 " model vdw 2.446 3.040 nonbonded pdb=" OE1 GLU B 26 " pdb=" OH TYR C 32 " model vdw 2.449 3.040 ... (remaining 108579 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 256 or resid 264 through 294 or resid 297 throug \ h 555 or resid 564 through 642 or resid 677 through 896)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.290 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:1.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 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 : 0.004 0.059 13964 Z= 0.223 Angle : 0.984 7.937 18960 Z= 0.570 Chirality : 0.060 0.247 2026 Planarity : 0.009 0.110 2459 Dihedral : 14.531 89.191 5203 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.06 % Favored : 90.82 % Rotamer: Outliers : 2.19 % Allowed : 6.36 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.19), residues: 1667 helix: -3.09 (0.29), residues: 158 sheet: -1.43 (0.28), residues: 306 loop : -1.51 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG A 641 TYR 0.040 0.006 TYR A 391 PHE 0.039 0.003 PHE B 694 TRP 0.039 0.003 TRP A 544 HIS 0.017 0.002 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00435 (13925) covalent geometry : angle 0.98072 (18881) SS BOND : bond 0.00561 ( 38) SS BOND : angle 1.59002 ( 76) hydrogen bonds : bond 0.19588 ( 322) hydrogen bonds : angle 10.31274 ( 807) link_TRANS : bond 0.00122 ( 1) link_TRANS : angle 0.52537 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 PHE cc_start: 0.7537 (m-10) cc_final: 0.7211 (m-80) REVERT: A 84 ASN cc_start: 0.8846 (m-40) cc_final: 0.8629 (t0) REVERT: A 92 MET cc_start: 0.7847 (ttm) cc_final: 0.7546 (ttm) REVERT: A 136 ASN cc_start: 0.8597 (m-40) cc_final: 0.8305 (t0) REVERT: A 147 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6322 (mp0) REVERT: A 177 THR cc_start: 0.7975 (t) cc_final: 0.7767 (t) REVERT: A 373 LYS cc_start: 0.9040 (tttt) cc_final: 0.8819 (ttmm) REVERT: A 486 ASP cc_start: 0.8598 (t0) cc_final: 0.8329 (t0) REVERT: A 555 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8867 (m) REVERT: A 628 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.6277 (m-80) REVERT: A 796 MET cc_start: 0.8132 (ttp) cc_final: 0.7661 (ttp) REVERT: A 834 MET cc_start: 0.7103 (ttp) cc_final: 0.6680 (ttp) REVERT: A 871 TYR cc_start: 0.3305 (OUTLIER) cc_final: 0.1702 (m-80) REVERT: B 63 LEU cc_start: 0.8150 (tp) cc_final: 0.7950 (tp) REVERT: B 77 ARG cc_start: 0.7807 (mmm-85) cc_final: 0.7078 (mtt180) REVERT: B 102 ASN cc_start: 0.8786 (m-40) cc_final: 0.8531 (m110) REVERT: B 156 MET cc_start: 0.8013 (mmm) cc_final: 0.7361 (ptt) REVERT: B 206 LEU cc_start: 0.8851 (tp) cc_final: 0.8560 (tp) REVERT: B 244 TRP cc_start: 0.7462 (m-90) cc_final: 0.7023 (m-90) REVERT: B 289 MET cc_start: 0.6828 (pmm) cc_final: 0.6371 (pmm) REVERT: B 340 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.7243 (pp) REVERT: B 416 MET cc_start: 0.7615 (mtm) cc_final: 0.7386 (mtp) REVERT: B 462 VAL cc_start: 0.7108 (t) cc_final: 0.6886 (t) REVERT: B 602 ASN cc_start: 0.8811 (m-40) cc_final: 0.8306 (m-40) REVERT: B 791 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8277 (m) REVERT: B 796 MET cc_start: 0.7685 (ptm) cc_final: 0.7018 (ptm) REVERT: B 837 ILE cc_start: 0.8681 (mt) cc_final: 0.8274 (mp) outliers start: 33 outliers final: 7 residues processed: 319 average time/residue: 0.1467 time to fit residues: 64.3634 Evaluate side-chains 157 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 628 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 878 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.0030 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.5310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 ASN A 895 GLN B 94 ASN B 895 GLN ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.127863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.103621 restraints weight = 38975.825| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 4.71 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13964 Z= 0.153 Angle : 0.781 9.323 18960 Z= 0.419 Chirality : 0.050 0.171 2026 Planarity : 0.005 0.057 2459 Dihedral : 8.731 76.301 1900 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.45 % Allowed : 11.46 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.19), residues: 1667 helix: -2.45 (0.32), residues: 172 sheet: -1.10 (0.27), residues: 323 loop : -1.10 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 770 TYR 0.023 0.002 TYR B 497 PHE 0.015 0.002 PHE B 45 TRP 0.026 0.002 TRP A 404 HIS 0.015 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00325 (13925) covalent geometry : angle 0.77571 (18881) SS BOND : bond 0.00832 ( 38) SS BOND : angle 1.65191 ( 76) hydrogen bonds : bond 0.04273 ( 322) hydrogen bonds : angle 7.93120 ( 807) link_TRANS : bond 0.00088 ( 1) link_TRANS : angle 0.74197 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 PHE cc_start: 0.7252 (m-10) cc_final: 0.6874 (m-80) REVERT: A 84 ASN cc_start: 0.8606 (m-40) cc_final: 0.8398 (t0) REVERT: A 92 MET cc_start: 0.7266 (ttm) cc_final: 0.7056 (ttm) REVERT: A 136 ASN cc_start: 0.8304 (m-40) cc_final: 0.8049 (t0) REVERT: A 177 THR cc_start: 0.7868 (t) cc_final: 0.7662 (t) REVERT: A 274 MET cc_start: 0.6493 (mmt) cc_final: 0.6249 (mmm) REVERT: A 373 LYS cc_start: 0.8704 (tttt) cc_final: 0.8440 (ttmm) REVERT: A 385 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7858 (tm-30) REVERT: A 558 MET cc_start: 0.7403 (pmm) cc_final: 0.7150 (pmm) REVERT: B 102 ASN cc_start: 0.8812 (m-40) cc_final: 0.8520 (m110) REVERT: B 156 MET cc_start: 0.7886 (mmm) cc_final: 0.7360 (ptt) REVERT: B 289 MET cc_start: 0.6669 (pmm) cc_final: 0.6278 (pmm) REVERT: B 373 LYS cc_start: 0.8830 (tttt) cc_final: 0.8617 (tppp) REVERT: B 682 GLN cc_start: 0.8346 (tp40) cc_final: 0.8057 (tp40) REVERT: B 796 MET cc_start: 0.7627 (ptm) cc_final: 0.7098 (ptm) REVERT: B 820 LEU cc_start: 0.8816 (mm) cc_final: 0.8526 (tp) outliers start: 37 outliers final: 14 residues processed: 193 average time/residue: 0.1257 time to fit residues: 34.9548 Evaluate side-chains 148 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 878 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 165 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 63 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 ASN A 623 GLN B 94 ASN B 172 ASN C 5 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.130553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.105838 restraints weight = 40148.269| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 4.89 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13964 Z= 0.134 Angle : 0.682 8.592 18960 Z= 0.368 Chirality : 0.048 0.181 2026 Planarity : 0.005 0.062 2459 Dihedral : 7.452 69.735 1886 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.12 % Allowed : 12.65 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.20), residues: 1667 helix: -2.16 (0.34), residues: 172 sheet: -0.99 (0.27), residues: 323 loop : -1.02 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 856 TYR 0.029 0.002 TYR A 871 PHE 0.014 0.001 PHE A 82 TRP 0.019 0.002 TRP A 404 HIS 0.014 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00285 (13925) covalent geometry : angle 0.67970 (18881) SS BOND : bond 0.00271 ( 38) SS BOND : angle 1.14487 ( 76) hydrogen bonds : bond 0.04065 ( 322) hydrogen bonds : angle 7.39027 ( 807) link_TRANS : bond 0.00049 ( 1) link_TRANS : angle 0.35922 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 PHE cc_start: 0.7287 (m-10) cc_final: 0.6845 (m-80) REVERT: A 84 ASN cc_start: 0.8529 (m-40) cc_final: 0.8295 (t0) REVERT: A 136 ASN cc_start: 0.8273 (m-40) cc_final: 0.7987 (t0) REVERT: A 170 GLU cc_start: 0.8500 (pt0) cc_final: 0.8173 (pm20) REVERT: A 177 THR cc_start: 0.7864 (t) cc_final: 0.7656 (t) REVERT: A 267 VAL cc_start: 0.4143 (OUTLIER) cc_final: 0.1248 (m) REVERT: A 336 ARG cc_start: 0.7577 (mtp-110) cc_final: 0.7349 (mtp-110) REVERT: A 339 ASN cc_start: 0.8536 (t0) cc_final: 0.8325 (t0) REVERT: A 364 HIS cc_start: 0.8227 (m-70) cc_final: 0.7269 (m90) REVERT: A 373 LYS cc_start: 0.8697 (tttt) cc_final: 0.8420 (ttmm) REVERT: A 385 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7910 (tm-30) REVERT: A 396 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7461 (mp10) REVERT: A 455 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7712 (ttm110) REVERT: A 558 MET cc_start: 0.7549 (pmm) cc_final: 0.7335 (pmm) REVERT: A 753 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7570 (p0) REVERT: A 834 MET cc_start: 0.7004 (mtm) cc_final: 0.6723 (mtp) REVERT: A 839 TYR cc_start: 0.6618 (p90) cc_final: 0.6178 (p90) REVERT: B 102 ASN cc_start: 0.8906 (m-40) cc_final: 0.8475 (m110) REVERT: B 156 MET cc_start: 0.7942 (mmm) cc_final: 0.7457 (ptt) REVERT: B 206 LEU cc_start: 0.8568 (tp) cc_final: 0.8207 (mt) REVERT: B 289 MET cc_start: 0.6713 (pmm) cc_final: 0.6331 (pmm) REVERT: B 373 LYS cc_start: 0.8863 (tttt) cc_final: 0.8624 (tppp) REVERT: B 626 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7383 (p90) REVERT: B 682 GLN cc_start: 0.8360 (tp-100) cc_final: 0.8011 (tp40) REVERT: B 796 MET cc_start: 0.7720 (ptm) cc_final: 0.7052 (ptm) REVERT: B 820 LEU cc_start: 0.8759 (mm) cc_final: 0.8434 (tp) outliers start: 32 outliers final: 18 residues processed: 176 average time/residue: 0.1049 time to fit residues: 27.0692 Evaluate side-chains 151 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 TYR Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 32 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 19 optimal weight: 0.0770 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 161 optimal weight: 0.3980 chunk 159 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.129114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.104339 restraints weight = 39707.644| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 4.96 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 13964 Z= 0.126 Angle : 0.650 8.129 18960 Z= 0.348 Chirality : 0.047 0.179 2026 Planarity : 0.005 0.065 2459 Dihedral : 7.013 69.678 1886 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.38 % Allowed : 13.05 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.20), residues: 1667 helix: -1.98 (0.35), residues: 176 sheet: -0.97 (0.28), residues: 325 loop : -1.02 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 283 TYR 0.019 0.002 TYR A 871 PHE 0.014 0.001 PHE A 82 TRP 0.020 0.001 TRP A 404 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00283 (13925) covalent geometry : angle 0.64561 (18881) SS BOND : bond 0.00279 ( 38) SS BOND : angle 1.40485 ( 76) hydrogen bonds : bond 0.03601 ( 322) hydrogen bonds : angle 7.12688 ( 807) link_TRANS : bond 0.00069 ( 1) link_TRANS : angle 0.45426 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 PHE cc_start: 0.7279 (m-10) cc_final: 0.6830 (m-80) REVERT: A 84 ASN cc_start: 0.8497 (m-40) cc_final: 0.8291 (t0) REVERT: A 136 ASN cc_start: 0.8256 (m-40) cc_final: 0.7918 (t0) REVERT: A 170 GLU cc_start: 0.8436 (pt0) cc_final: 0.8190 (pm20) REVERT: A 177 THR cc_start: 0.7835 (t) cc_final: 0.7635 (t) REVERT: A 275 GLN cc_start: 0.8751 (pm20) cc_final: 0.8448 (tp-100) REVERT: A 339 ASN cc_start: 0.8484 (t0) cc_final: 0.8204 (t0) REVERT: A 364 HIS cc_start: 0.8172 (m-70) cc_final: 0.7111 (m90) REVERT: A 373 LYS cc_start: 0.8684 (tttt) cc_final: 0.8419 (ttmm) REVERT: A 396 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7479 (mp10) REVERT: A 466 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7712 (p) REVERT: A 558 MET cc_start: 0.7577 (pmm) cc_final: 0.7336 (pmm) REVERT: A 753 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7616 (p0) REVERT: A 834 MET cc_start: 0.7058 (mtm) cc_final: 0.6613 (mmm) REVERT: A 839 TYR cc_start: 0.6592 (p90) cc_final: 0.6229 (p90) REVERT: B 102 ASN cc_start: 0.8854 (m-40) cc_final: 0.8385 (m-40) REVERT: B 156 MET cc_start: 0.7978 (mmm) cc_final: 0.7518 (ptt) REVERT: B 289 MET cc_start: 0.6672 (pmm) cc_final: 0.6320 (pmm) REVERT: B 340 ILE cc_start: 0.8205 (pp) cc_final: 0.7045 (pp) REVERT: B 343 GLU cc_start: 0.7865 (mp0) cc_final: 0.7327 (mp0) REVERT: B 373 LYS cc_start: 0.8832 (tttt) cc_final: 0.8601 (tppp) REVERT: B 626 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7564 (p90) REVERT: B 682 GLN cc_start: 0.8423 (tp-100) cc_final: 0.8039 (tp40) REVERT: B 686 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8959 (mt-10) REVERT: B 796 MET cc_start: 0.7682 (ptm) cc_final: 0.7012 (ptm) REVERT: B 820 LEU cc_start: 0.8774 (mm) cc_final: 0.8445 (tp) REVERT: C 26 TYR cc_start: 0.6897 (t80) cc_final: 0.6330 (t80) outliers start: 36 outliers final: 17 residues processed: 177 average time/residue: 0.1066 time to fit residues: 28.5945 Evaluate side-chains 162 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 TYR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 110 optimal weight: 0.0770 chunk 131 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 88 optimal weight: 0.2980 chunk 138 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.130267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.105641 restraints weight = 40217.164| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 4.93 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13964 Z= 0.126 Angle : 0.628 7.426 18960 Z= 0.336 Chirality : 0.047 0.198 2026 Planarity : 0.005 0.064 2459 Dihedral : 6.780 70.428 1883 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.78 % Allowed : 13.18 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.20), residues: 1667 helix: -1.83 (0.35), residues: 176 sheet: -0.95 (0.28), residues: 331 loop : -1.04 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 283 TYR 0.023 0.002 TYR A 871 PHE 0.016 0.001 PHE A 82 TRP 0.018 0.001 TRP A 404 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00278 (13925) covalent geometry : angle 0.62515 (18881) SS BOND : bond 0.00295 ( 38) SS BOND : angle 1.13813 ( 76) hydrogen bonds : bond 0.03455 ( 322) hydrogen bonds : angle 6.95394 ( 807) link_TRANS : bond 0.00049 ( 1) link_TRANS : angle 0.31820 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7369 (ptm) REVERT: A 136 ASN cc_start: 0.8269 (m-40) cc_final: 0.7913 (t0) REVERT: A 170 GLU cc_start: 0.8525 (pt0) cc_final: 0.8270 (pm20) REVERT: A 177 THR cc_start: 0.7875 (t) cc_final: 0.7655 (t) REVERT: A 275 GLN cc_start: 0.8769 (pm20) cc_final: 0.8520 (tp40) REVERT: A 306 LYS cc_start: 0.9096 (tppp) cc_final: 0.8890 (tppp) REVERT: A 339 ASN cc_start: 0.8502 (t0) cc_final: 0.8219 (t0) REVERT: A 348 MET cc_start: 0.8029 (mtp) cc_final: 0.7805 (mtp) REVERT: A 364 HIS cc_start: 0.8212 (m-70) cc_final: 0.6949 (m170) REVERT: A 373 LYS cc_start: 0.8714 (tttt) cc_final: 0.8479 (ttmm) REVERT: A 396 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7521 (mp10) REVERT: A 466 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7757 (p) REVERT: A 558 MET cc_start: 0.7493 (pmm) cc_final: 0.7281 (pmm) REVERT: A 571 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8836 (mt) REVERT: A 753 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7663 (p0) REVERT: A 834 MET cc_start: 0.7044 (mtm) cc_final: 0.6643 (mmm) REVERT: A 839 TYR cc_start: 0.6605 (p90) cc_final: 0.6165 (p90) REVERT: B 102 ASN cc_start: 0.8874 (m-40) cc_final: 0.8398 (m-40) REVERT: B 156 MET cc_start: 0.7880 (mmm) cc_final: 0.7562 (ptt) REVERT: B 289 MET cc_start: 0.6671 (pmm) cc_final: 0.6319 (pmm) REVERT: B 340 ILE cc_start: 0.8151 (pp) cc_final: 0.6977 (pp) REVERT: B 343 GLU cc_start: 0.7899 (mp0) cc_final: 0.7404 (mp0) REVERT: B 373 LYS cc_start: 0.8840 (tttt) cc_final: 0.8615 (tppp) REVERT: B 376 ARG cc_start: 0.7588 (mtp-110) cc_final: 0.7331 (mtp-110) REVERT: B 416 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6696 (mtm) REVERT: B 521 MET cc_start: 0.8256 (ptp) cc_final: 0.7632 (ptp) REVERT: B 626 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7567 (p90) REVERT: B 682 GLN cc_start: 0.8492 (tp-100) cc_final: 0.8254 (tp40) REVERT: B 796 MET cc_start: 0.7695 (ptm) cc_final: 0.7003 (ptm) REVERT: B 820 LEU cc_start: 0.8747 (mm) cc_final: 0.8409 (tp) REVERT: C 26 TYR cc_start: 0.6908 (t80) cc_final: 0.6325 (t80) outliers start: 42 outliers final: 25 residues processed: 175 average time/residue: 0.1136 time to fit residues: 29.9089 Evaluate side-chains 165 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 TYR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 78 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 HIS B 700 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.124535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.099334 restraints weight = 39535.837| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 4.90 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 13964 Z= 0.226 Angle : 0.714 8.510 18960 Z= 0.380 Chirality : 0.049 0.179 2026 Planarity : 0.005 0.087 2459 Dihedral : 6.858 71.117 1881 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.92 % Favored : 92.02 % Rotamer: Outliers : 3.51 % Allowed : 13.31 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.20), residues: 1667 helix: -1.81 (0.36), residues: 175 sheet: -1.26 (0.28), residues: 332 loop : -1.27 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 59 TYR 0.026 0.002 TYR A 391 PHE 0.023 0.002 PHE A 371 TRP 0.018 0.002 TRP A 618 HIS 0.008 0.002 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00506 (13925) covalent geometry : angle 0.71073 (18881) SS BOND : bond 0.00441 ( 38) SS BOND : angle 1.23946 ( 76) hydrogen bonds : bond 0.03808 ( 322) hydrogen bonds : angle 7.03400 ( 807) link_TRANS : bond 0.00054 ( 1) link_TRANS : angle 0.13192 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7097 (ptp) REVERT: A 136 ASN cc_start: 0.8391 (m-40) cc_final: 0.8062 (t0) REVERT: A 177 THR cc_start: 0.8054 (t) cc_final: 0.7795 (t) REVERT: A 275 GLN cc_start: 0.8670 (pm20) cc_final: 0.8372 (tp40) REVERT: A 339 ASN cc_start: 0.8503 (t0) cc_final: 0.8223 (t0) REVERT: A 373 LYS cc_start: 0.8782 (tttt) cc_final: 0.8578 (ttmm) REVERT: A 466 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7763 (p) REVERT: A 753 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7607 (p0) REVERT: A 834 MET cc_start: 0.7080 (mtm) cc_final: 0.6748 (mmm) REVERT: A 839 TYR cc_start: 0.6677 (p90) cc_final: 0.5885 (p90) REVERT: B 59 ARG cc_start: 0.7378 (mmt180) cc_final: 0.7122 (mmt180) REVERT: B 156 MET cc_start: 0.7936 (mmm) cc_final: 0.7577 (ptt) REVERT: B 289 MET cc_start: 0.6788 (pmm) cc_final: 0.6385 (pmm) REVERT: B 339 ASN cc_start: 0.8450 (m-40) cc_final: 0.8124 (m-40) REVERT: B 340 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7109 (pp) REVERT: B 343 GLU cc_start: 0.7957 (mp0) cc_final: 0.7277 (mp0) REVERT: B 373 LYS cc_start: 0.8932 (tttt) cc_final: 0.8699 (tppp) REVERT: B 376 ARG cc_start: 0.7866 (mtp-110) cc_final: 0.7466 (mtp-110) REVERT: B 416 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6890 (mtm) REVERT: B 459 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7840 (tp30) REVERT: B 626 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7750 (p90) REVERT: B 682 GLN cc_start: 0.8688 (tp-100) cc_final: 0.8309 (tp40) REVERT: B 796 MET cc_start: 0.7765 (ptm) cc_final: 0.7137 (ptm) REVERT: B 820 LEU cc_start: 0.8760 (mm) cc_final: 0.8421 (tp) REVERT: C 16 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6623 (t80) REVERT: C 26 TYR cc_start: 0.7046 (t80) cc_final: 0.6413 (t80) outliers start: 53 outliers final: 26 residues processed: 176 average time/residue: 0.1102 time to fit residues: 29.3368 Evaluate side-chains 161 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 TYR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 583 ILE Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 16 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 146 optimal weight: 0.1980 chunk 94 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.128877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.104344 restraints weight = 39422.716| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 4.91 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13964 Z= 0.119 Angle : 0.647 12.364 18960 Z= 0.338 Chirality : 0.047 0.181 2026 Planarity : 0.005 0.075 2459 Dihedral : 6.487 71.705 1881 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.72 % Allowed : 14.64 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.20), residues: 1667 helix: -1.70 (0.36), residues: 176 sheet: -1.10 (0.28), residues: 338 loop : -1.11 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 336 TYR 0.017 0.002 TYR A 839 PHE 0.014 0.001 PHE A 694 TRP 0.011 0.001 TRP A 404 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00266 (13925) covalent geometry : angle 0.64495 (18881) SS BOND : bond 0.00243 ( 38) SS BOND : angle 0.99001 ( 76) hydrogen bonds : bond 0.03342 ( 322) hydrogen bonds : angle 6.89421 ( 807) link_TRANS : bond 0.00080 ( 1) link_TRANS : angle 0.47628 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.7949 (ptp) cc_final: 0.7729 (ptm) REVERT: A 136 ASN cc_start: 0.8285 (m-40) cc_final: 0.7941 (t0) REVERT: A 177 THR cc_start: 0.7877 (t) cc_final: 0.7653 (t) REVERT: A 339 ASN cc_start: 0.8515 (t0) cc_final: 0.8241 (t0) REVERT: A 364 HIS cc_start: 0.8310 (m-70) cc_final: 0.6961 (m170) REVERT: A 373 LYS cc_start: 0.8709 (tttt) cc_final: 0.8488 (ttmm) REVERT: A 396 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7430 (mp10) REVERT: A 466 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7571 (p) REVERT: A 558 MET cc_start: 0.7336 (pmm) cc_final: 0.7133 (pmm) REVERT: A 753 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7631 (p0) REVERT: A 871 TYR cc_start: 0.4347 (OUTLIER) cc_final: 0.3488 (m-80) REVERT: B 156 MET cc_start: 0.7907 (mmm) cc_final: 0.7571 (ptt) REVERT: B 289 MET cc_start: 0.6633 (pmm) cc_final: 0.6285 (pmm) REVERT: B 340 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.6902 (pp) REVERT: B 343 GLU cc_start: 0.7988 (mp0) cc_final: 0.7442 (mp0) REVERT: B 373 LYS cc_start: 0.8901 (tttt) cc_final: 0.8655 (tppp) REVERT: B 376 ARG cc_start: 0.7882 (mtp-110) cc_final: 0.7469 (mtp-110) REVERT: B 416 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6005 (mtm) REVERT: B 459 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7902 (tp30) REVERT: B 626 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.7663 (p90) REVERT: B 682 GLN cc_start: 0.8676 (tp-100) cc_final: 0.8359 (tp40) REVERT: B 796 MET cc_start: 0.7700 (ptm) cc_final: 0.7046 (ptm) REVERT: B 820 LEU cc_start: 0.8798 (mm) cc_final: 0.8488 (tp) REVERT: C 26 TYR cc_start: 0.6884 (t80) cc_final: 0.6326 (t80) outliers start: 41 outliers final: 20 residues processed: 167 average time/residue: 0.1156 time to fit residues: 29.0565 Evaluate side-chains 156 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 810 TRP Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 59 optimal weight: 0.7980 chunk 157 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 63 optimal weight: 0.0020 chunk 108 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.128690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.104204 restraints weight = 39379.335| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 4.86 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13964 Z= 0.119 Angle : 0.645 11.301 18960 Z= 0.337 Chirality : 0.047 0.214 2026 Planarity : 0.005 0.079 2459 Dihedral : 6.262 72.022 1880 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.32 % Allowed : 14.83 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.20), residues: 1667 helix: -1.64 (0.36), residues: 176 sheet: -1.10 (0.28), residues: 345 loop : -1.09 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 474 TYR 0.032 0.002 TYR A 839 PHE 0.025 0.001 PHE A 266 TRP 0.014 0.001 TRP A 404 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00267 (13925) covalent geometry : angle 0.64401 (18881) SS BOND : bond 0.00233 ( 38) SS BOND : angle 0.93831 ( 76) hydrogen bonds : bond 0.03261 ( 322) hydrogen bonds : angle 6.79747 ( 807) link_TRANS : bond 0.00073 ( 1) link_TRANS : angle 0.44598 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.455 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: A 92 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7721 (ptm) REVERT: A 136 ASN cc_start: 0.8265 (m-40) cc_final: 0.7879 (m110) REVERT: A 177 THR cc_start: 0.7901 (t) cc_final: 0.7685 (t) REVERT: A 339 ASN cc_start: 0.8558 (t0) cc_final: 0.8337 (t0) REVERT: A 364 HIS cc_start: 0.8203 (m-70) cc_final: 0.7368 (m90) REVERT: A 396 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7713 (mp10) REVERT: A 466 THR cc_start: 0.7880 (OUTLIER) cc_final: 0.7611 (p) REVERT: A 558 MET cc_start: 0.7380 (pmm) cc_final: 0.7077 (pmm) REVERT: A 753 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7621 (p0) REVERT: A 834 MET cc_start: 0.7534 (tpp) cc_final: 0.6478 (mmp) REVERT: B 15 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7932 (mm-40) REVERT: B 156 MET cc_start: 0.7943 (mmm) cc_final: 0.7520 (ptt) REVERT: B 289 MET cc_start: 0.6612 (pmm) cc_final: 0.6265 (pmm) REVERT: B 339 ASN cc_start: 0.8517 (m-40) cc_final: 0.8218 (m-40) REVERT: B 340 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.6819 (pp) REVERT: B 343 GLU cc_start: 0.8026 (mp0) cc_final: 0.7488 (mp0) REVERT: B 373 LYS cc_start: 0.8894 (tttt) cc_final: 0.8647 (tppp) REVERT: B 459 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7899 (tp30) REVERT: B 626 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7569 (p90) REVERT: B 682 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8371 (tp40) REVERT: B 796 MET cc_start: 0.7704 (ptm) cc_final: 0.7130 (ptm) REVERT: B 820 LEU cc_start: 0.8804 (mm) cc_final: 0.8502 (tp) REVERT: C 26 TYR cc_start: 0.6886 (t80) cc_final: 0.6325 (t80) outliers start: 35 outliers final: 25 residues processed: 167 average time/residue: 0.1181 time to fit residues: 28.9805 Evaluate side-chains 164 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 TYR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 3 optimal weight: 0.0770 chunk 113 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 63 optimal weight: 0.4980 chunk 126 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.129074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.104644 restraints weight = 39805.321| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 4.91 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13964 Z= 0.113 Angle : 0.632 11.661 18960 Z= 0.328 Chirality : 0.046 0.161 2026 Planarity : 0.005 0.069 2459 Dihedral : 6.120 72.108 1880 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.45 % Allowed : 14.83 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.20), residues: 1667 helix: -1.55 (0.36), residues: 176 sheet: -1.07 (0.28), residues: 357 loop : -1.03 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 283 TYR 0.024 0.001 TYR A 839 PHE 0.012 0.001 PHE A 266 TRP 0.015 0.001 TRP B 79 HIS 0.011 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00254 (13925) covalent geometry : angle 0.63007 (18881) SS BOND : bond 0.00238 ( 38) SS BOND : angle 0.98933 ( 76) hydrogen bonds : bond 0.03142 ( 322) hydrogen bonds : angle 6.70483 ( 807) link_TRANS : bond 0.00073 ( 1) link_TRANS : angle 0.45171 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7367 (ptp) REVERT: A 136 ASN cc_start: 0.8266 (m-40) cc_final: 0.7857 (m110) REVERT: A 177 THR cc_start: 0.7896 (t) cc_final: 0.7662 (t) REVERT: A 339 ASN cc_start: 0.8545 (t0) cc_final: 0.8329 (t0) REVERT: A 364 HIS cc_start: 0.8278 (m-70) cc_final: 0.7143 (m90) REVERT: A 396 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7563 (mp10) REVERT: A 466 THR cc_start: 0.7902 (OUTLIER) cc_final: 0.7651 (p) REVERT: A 558 MET cc_start: 0.7521 (pmm) cc_final: 0.7240 (pmm) REVERT: A 571 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8660 (mt) REVERT: A 753 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7622 (p0) REVERT: A 834 MET cc_start: 0.7429 (tpp) cc_final: 0.6405 (mmp) REVERT: B 15 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7986 (mm-40) REVERT: B 156 MET cc_start: 0.7836 (mmm) cc_final: 0.7512 (ptt) REVERT: B 289 MET cc_start: 0.6611 (pmm) cc_final: 0.6263 (pmm) REVERT: B 339 ASN cc_start: 0.8630 (m-40) cc_final: 0.8332 (m-40) REVERT: B 340 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.6966 (pp) REVERT: B 343 GLU cc_start: 0.8046 (mp0) cc_final: 0.7514 (mp0) REVERT: B 373 LYS cc_start: 0.8896 (tttt) cc_final: 0.8642 (tppp) REVERT: B 459 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7864 (tp30) REVERT: B 626 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7493 (p90) REVERT: B 682 GLN cc_start: 0.8715 (tp-100) cc_final: 0.8381 (tp40) REVERT: B 796 MET cc_start: 0.7717 (ptm) cc_final: 0.7105 (ptm) REVERT: B 820 LEU cc_start: 0.8806 (mm) cc_final: 0.8506 (tp) REVERT: B 886 TRP cc_start: 0.7509 (p-90) cc_final: 0.7202 (p-90) REVERT: C 26 TYR cc_start: 0.6870 (t80) cc_final: 0.6307 (t80) outliers start: 37 outliers final: 23 residues processed: 167 average time/residue: 0.1062 time to fit residues: 27.0150 Evaluate side-chains 162 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 TYR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 112 optimal weight: 8.9990 chunk 96 optimal weight: 0.1980 chunk 72 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 64 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.128403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.103683 restraints weight = 39348.250| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 4.91 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13964 Z= 0.128 Angle : 0.653 11.690 18960 Z= 0.340 Chirality : 0.047 0.335 2026 Planarity : 0.005 0.076 2459 Dihedral : 6.090 72.138 1880 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.85 % Allowed : 15.63 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.20), residues: 1667 helix: -1.64 (0.36), residues: 176 sheet: -1.06 (0.28), residues: 355 loop : -1.03 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 283 TYR 0.026 0.002 TYR A 839 PHE 0.011 0.001 PHE A 82 TRP 0.015 0.001 TRP B 79 HIS 0.011 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00289 (13925) covalent geometry : angle 0.65110 (18881) SS BOND : bond 0.00267 ( 38) SS BOND : angle 1.04447 ( 76) hydrogen bonds : bond 0.03236 ( 322) hydrogen bonds : angle 6.76378 ( 807) link_TRANS : bond 0.00066 ( 1) link_TRANS : angle 0.43627 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7129 (ptp) REVERT: A 136 ASN cc_start: 0.8295 (m-40) cc_final: 0.7883 (m110) REVERT: A 177 THR cc_start: 0.7913 (t) cc_final: 0.7684 (t) REVERT: A 339 ASN cc_start: 0.8526 (t0) cc_final: 0.8223 (t0) REVERT: A 364 HIS cc_start: 0.8205 (m-70) cc_final: 0.7331 (m90) REVERT: A 396 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7573 (mp10) REVERT: A 466 THR cc_start: 0.7920 (OUTLIER) cc_final: 0.7671 (p) REVERT: A 558 MET cc_start: 0.7578 (pmm) cc_final: 0.7293 (pmm) REVERT: A 571 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8688 (mt) REVERT: A 753 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7628 (p0) REVERT: A 834 MET cc_start: 0.7394 (tpp) cc_final: 0.6347 (mmp) REVERT: A 871 TYR cc_start: 0.4127 (OUTLIER) cc_final: 0.2757 (m-80) REVERT: B 156 MET cc_start: 0.7810 (mmm) cc_final: 0.7503 (ptt) REVERT: B 289 MET cc_start: 0.6680 (pmm) cc_final: 0.6325 (pmm) REVERT: B 340 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.6723 (pp) REVERT: B 343 GLU cc_start: 0.7930 (mp0) cc_final: 0.7263 (mp0) REVERT: B 373 LYS cc_start: 0.8905 (tttt) cc_final: 0.8652 (tppp) REVERT: B 459 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7950 (tp30) REVERT: B 682 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8382 (tp40) REVERT: B 796 MET cc_start: 0.7697 (ptm) cc_final: 0.7081 (ptm) REVERT: B 820 LEU cc_start: 0.8789 (mm) cc_final: 0.8492 (tp) REVERT: B 886 TRP cc_start: 0.7492 (p-90) cc_final: 0.7190 (p-90) REVERT: C 26 TYR cc_start: 0.6892 (t80) cc_final: 0.6340 (t80) outliers start: 28 outliers final: 21 residues processed: 154 average time/residue: 0.1034 time to fit residues: 24.6662 Evaluate side-chains 155 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 632 TYR Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 404 TRP Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain C residue 7 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 140 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.128243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.103436 restraints weight = 39451.274| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 4.96 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13964 Z= 0.125 Angle : 0.640 11.849 18960 Z= 0.333 Chirality : 0.047 0.205 2026 Planarity : 0.005 0.062 2459 Dihedral : 5.997 72.159 1879 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.12 % Allowed : 15.43 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.20), residues: 1667 helix: -1.63 (0.36), residues: 177 sheet: -1.02 (0.28), residues: 355 loop : -1.02 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 474 TYR 0.016 0.001 TYR A 391 PHE 0.011 0.001 PHE A 82 TRP 0.020 0.002 TRP B 519 HIS 0.010 0.001 HIS C 5 Details of bonding type rmsd covalent geometry : bond 0.00283 (13925) covalent geometry : angle 0.63774 (18881) SS BOND : bond 0.00269 ( 38) SS BOND : angle 0.98800 ( 76) hydrogen bonds : bond 0.03200 ( 322) hydrogen bonds : angle 6.70263 ( 807) link_TRANS : bond 0.00064 ( 1) link_TRANS : angle 0.44232 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2550.44 seconds wall clock time: 44 minutes 44.71 seconds (2684.71 seconds total)