Starting phenix.real_space_refine on Mon Oct 26 06:24:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wql_66175/10_2026/9wql_66175.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wql_66175/10_2026/9wql_66175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wql_66175/10_2026/9wql_66175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wql_66175/10_2026/9wql_66175.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wql_66175/10_2026/9wql_66175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wql_66175/10_2026/9wql_66175.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 159 5.16 5 Cl 2 4.86 5 C 12407 2.51 5 N 3239 2.21 5 O 3580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19387 Number of models: 1 Model: "" Number of chains: 8 Chain: "X" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6247 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 31, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 6081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6081 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 737} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1876 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "F" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1786 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "X" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 207 Unusual residues: {' CL': 1, 'CLR': 4, 'NAG': 4, 'YKU': 1} Inner-chain residues flagged as termini: ['pdbres="GGL X 902 "'] Classifications: {'peptide': 1, 'undetermined': 10} Modifications used: {'COO': 1} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {' CL': 1, 'CLR': 3, 'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" C1 NAG X 903 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG X 903 " occ=0.70 residue: pdb=" C1 NAG X 904 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG X 904 " occ=0.70 residue: pdb=" C1 NAG X 905 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG X 905 " occ=0.70 residue: pdb=" C1 NAG X 906 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG X 906 " occ=0.70 residue: pdb=" C1 NAG Y2002 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG Y2002 " occ=0.70 residue: pdb=" C1 NAG Y2003 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG Y2003 " occ=0.70 residue: pdb=" C1 NAG Y2004 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG Y2004 " occ=0.70 residue: pdb=" C1 NAG Y2005 " occ=0.70 ... (12 atoms not shown) pdb=" O7 NAG Y2005 " occ=0.70 Time building chain proxies: 4.39, per 1000 atoms: 0.23 Number of scatterers: 19387 At special positions: 0 Unit cell: (106.02, 132.99, 242.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 159 16.00 O 3580 8.00 N 3239 7.00 C 12407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS X 57 " - pdb=" SG CYS X 99 " distance=2.03 Simple disulfide: pdb=" SG CYS X 241 " - pdb=" SG CYS X 530 " distance=2.03 Simple disulfide: pdb=" SG CYS X 365 " - pdb=" SG CYS X 381 " distance=2.03 Simple disulfide: pdb=" SG CYS X 419 " - pdb=" SG CYS X 426 " distance=2.03 Simple disulfide: pdb=" SG CYS X 511 " - pdb=" SG CYS X 531 " distance=2.03 Simple disulfide: pdb=" SG CYS X 515 " - pdb=" SG CYS X 534 " distance=2.03 Simple disulfide: pdb=" SG CYS X 537 " - pdb=" SG CYS X 549 " distance=2.03 Simple disulfide: pdb=" SG CYS X 644 " - pdb=" SG CYS X 733 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 57 " - pdb=" SG CYS Y 99 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 241 " - pdb=" SG CYS Y 530 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 365 " - pdb=" SG CYS Y 381 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 419 " - pdb=" SG CYS Y 426 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 511 " - pdb=" SG CYS Y 531 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 515 " - pdb=" SG CYS Y 534 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 537 " - pdb=" SG CYS Y 549 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 552 " - pdb=" SG CYS Y 565 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 644 " - pdb=" SG CYS Y 733 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG X 903 " - " ASN X 88 " " NAG X 904 " - " ASN X 210 " " NAG X 905 " - " ASN X 382 " " NAG X 906 " - " ASN X 445 " " NAG Y2002 " - " ASN Y 88 " " NAG Y2003 " - " ASN Y 210 " " NAG Y2004 " - " ASN Y 382 " " NAG Y2005 " - " ASN Y 445 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 879.8 milliseconds 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4526 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 27 sheets defined 42.9% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'X' and resid 62 through 81 Processing helix chain 'X' and resid 101 through 118 removed outlier: 4.730A pdb=" N ASP X 115 " --> pdb=" O GLU X 111 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N SER X 116 " --> pdb=" O PHE X 112 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE X 118 " --> pdb=" O ARG X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 163 Processing helix chain 'X' and resid 164 through 166 No H-bonds generated for 'chain 'X' and resid 164 through 166' Processing helix chain 'X' and resid 176 through 181 removed outlier: 3.673A pdb=" N ASP X 181 " --> pdb=" O ASP X 178 " (cutoff:3.500A) Processing helix chain 'X' and resid 194 through 209 removed outlier: 4.107A pdb=" N GLN X 198 " --> pdb=" O SER X 194 " (cutoff:3.500A) Processing helix chain 'X' and resid 221 through 238 Processing helix chain 'X' and resid 253 through 266 Processing helix chain 'X' and resid 279 through 294 Processing helix chain 'X' and resid 310 through 315 removed outlier: 4.127A pdb=" N THR X 314 " --> pdb=" O ARG X 310 " (cutoff:3.500A) Processing helix chain 'X' and resid 317 through 322 removed outlier: 3.835A pdb=" N VAL X 322 " --> pdb=" O ARG X 319 " (cutoff:3.500A) Processing helix chain 'X' and resid 334 through 342 Processing helix chain 'X' and resid 354 through 364 Processing helix chain 'X' and resid 396 through 419 Processing helix chain 'X' and resid 426 through 430 removed outlier: 3.551A pdb=" N LYS X 430 " --> pdb=" O ASP X 427 " (cutoff:3.500A) Processing helix chain 'X' and resid 433 through 444 Processing helix chain 'X' and resid 495 through 500 Processing helix chain 'X' and resid 502 through 506 Processing helix chain 'X' and resid 577 through 604 Processing helix chain 'X' and resid 607 through 612 Processing helix chain 'X' and resid 614 through 637 removed outlier: 3.955A pdb=" N THR X 632 " --> pdb=" O GLY X 628 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE X 633 " --> pdb=" O TYR X 629 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA X 637 " --> pdb=" O PHE X 633 " (cutoff:3.500A) Processing helix chain 'X' and resid 640 through 673 Proline residue: X 655 - end of helix Processing helix chain 'X' and resid 689 through 715 removed outlier: 3.559A pdb=" N LEU X 700 " --> pdb=" O ILE X 696 " (cutoff:3.500A) Processing helix chain 'X' and resid 736 through 761 Proline residue: X 743 - end of helix Processing helix chain 'X' and resid 770 through 794 Proline residue: X 790 - end of helix Processing helix chain 'X' and resid 797 through 818 Processing helix chain 'X' and resid 818 through 828 removed outlier: 3.547A pdb=" N LYS X 828 " --> pdb=" O ILE X 824 " (cutoff:3.500A) Processing helix chain 'X' and resid 829 through 832 Processing helix chain 'Y' and resid 48 through 52 Processing helix chain 'Y' and resid 64 through 81 removed outlier: 3.593A pdb=" N ARG Y 68 " --> pdb=" O TYR Y 64 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 114 Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 151 through 163 Processing helix chain 'Y' and resid 164 through 166 No H-bonds generated for 'chain 'Y' and resid 164 through 166' Processing helix chain 'Y' and resid 176 through 181 removed outlier: 3.616A pdb=" N ASP Y 181 " --> pdb=" O ASP Y 178 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 209 removed outlier: 4.119A pdb=" N GLN Y 198 " --> pdb=" O SER Y 194 " (cutoff:3.500A) Processing helix chain 'Y' and resid 221 through 238 removed outlier: 3.558A pdb=" N LYS Y 237 " --> pdb=" O ASP Y 233 " (cutoff:3.500A) Processing helix chain 'Y' and resid 253 through 267 removed outlier: 3.837A pdb=" N HIS Y 267 " --> pdb=" O LYS Y 263 " (cutoff:3.500A) Processing helix chain 'Y' and resid 279 through 294 Processing helix chain 'Y' and resid 310 through 315 removed outlier: 4.088A pdb=" N THR Y 314 " --> pdb=" O ARG Y 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 317 through 322 Processing helix chain 'Y' and resid 334 through 342 removed outlier: 3.528A pdb=" N TYR Y 340 " --> pdb=" O TRP Y 336 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 364 Processing helix chain 'Y' and resid 396 through 419 Processing helix chain 'Y' and resid 426 through 430 removed outlier: 3.566A pdb=" N LYS Y 430 " --> pdb=" O ASP Y 427 " (cutoff:3.500A) Processing helix chain 'Y' and resid 433 through 444 Processing helix chain 'Y' and resid 495 through 500 Processing helix chain 'Y' and resid 502 through 506 removed outlier: 3.542A pdb=" N ILE Y 506 " --> pdb=" O LYS Y 503 " (cutoff:3.500A) Processing helix chain 'Y' and resid 577 through 604 Processing helix chain 'Y' and resid 607 through 612 Processing helix chain 'Y' and resid 614 through 637 removed outlier: 3.960A pdb=" N THR Y 632 " --> pdb=" O GLY Y 628 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE Y 633 " --> pdb=" O TYR Y 629 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA Y 637 " --> pdb=" O PHE Y 633 " (cutoff:3.500A) Processing helix chain 'Y' and resid 640 through 673 Proline residue: Y 655 - end of helix Processing helix chain 'Y' and resid 689 through 715 Processing helix chain 'Y' and resid 736 through 761 removed outlier: 3.616A pdb=" N VAL Y 740 " --> pdb=" O THR Y 736 " (cutoff:3.500A) Proline residue: Y 743 - end of helix Processing helix chain 'Y' and resid 769 through 793 Proline residue: Y 790 - end of helix Processing helix chain 'Y' and resid 797 through 827 removed outlier: 3.900A pdb=" N VAL Y 819 " --> pdb=" O GLY Y 815 " (cutoff:3.500A) Proline residue: Y 820 - end of helix Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.031A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.986A pdb=" N LEU A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.563A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.158A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 183 through 205 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 53 through 56 removed outlier: 3.847A pdb=" N GLY F 56 " --> pdb=" O SER F 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 53 through 56' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.707A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'X' and resid 29 through 31 removed outlier: 6.329A pdb=" N ILE X 35 " --> pdb=" O GLY X 92 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLU X 94 " --> pdb=" O ILE X 35 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE X 37 " --> pdb=" O GLU X 94 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ARG X 96 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA X 39 " --> pdb=" O ARG X 96 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILE X 36 " --> pdb=" O ILE X 143 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY X 145 " --> pdb=" O ILE X 36 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ILE X 170 " --> pdb=" O VAL X 144 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL X 146 " --> pdb=" O ILE X 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 241 through 248 removed outlier: 7.892A pdb=" N VAL X 214 " --> pdb=" O ALA X 243 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER X 245 " --> pdb=" O VAL X 214 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA X 216 " --> pdb=" O SER X 245 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS X 247 " --> pdb=" O ALA X 216 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N HIS X 218 " --> pdb=" O LYS X 247 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL X 273 " --> pdb=" O TYR X 213 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU X 301 " --> pdb=" O ILE X 325 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE X 327 " --> pdb=" O LEU X 301 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLY X 303 " --> pdb=" O ILE X 327 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N LEU X 329 " --> pdb=" O GLY X 303 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR X 466 " --> pdb=" O SER X 486 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER X 486 " --> pdb=" O TYR X 466 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE X 468 " --> pdb=" O VAL X 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 445 through 447 Processing sheet with id=AA4, first strand: chain 'X' and resid 519 through 523 Processing sheet with id=AA5, first strand: chain 'X' and resid 541 through 545 removed outlier: 6.692A pdb=" N THR X 548 " --> pdb=" O PHE X 544 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 556 through 558 Processing sheet with id=AA7, first strand: chain 'X' and resid 719 through 722 Processing sheet with id=AA8, first strand: chain 'Y' and resid 29 through 31 removed outlier: 6.369A pdb=" N ILE Y 35 " --> pdb=" O GLY Y 92 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLU Y 94 " --> pdb=" O ILE Y 35 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE Y 37 " --> pdb=" O GLU Y 94 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ARG Y 96 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA Y 39 " --> pdb=" O ARG Y 96 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE Y 36 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY Y 145 " --> pdb=" O ILE Y 36 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ILE Y 170 " --> pdb=" O VAL Y 144 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL Y 146 " --> pdb=" O ILE Y 170 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLN Y 169 " --> pdb=" O MET Y 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 241 through 248 removed outlier: 7.731A pdb=" N VAL Y 214 " --> pdb=" O ALA Y 243 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER Y 245 " --> pdb=" O VAL Y 214 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA Y 216 " --> pdb=" O SER Y 245 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LYS Y 247 " --> pdb=" O ALA Y 216 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS Y 218 " --> pdb=" O LYS Y 247 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL Y 273 " --> pdb=" O TYR Y 213 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR Y 466 " --> pdb=" O SER Y 486 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER Y 486 " --> pdb=" O TYR Y 466 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE Y 468 " --> pdb=" O VAL Y 484 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR Y 478 " --> pdb=" O MET Y 474 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 445 through 447 Processing sheet with id=AB2, first strand: chain 'Y' and resid 519 through 522 Processing sheet with id=AB3, first strand: chain 'Y' and resid 541 through 545 removed outlier: 6.679A pdb=" N THR Y 548 " --> pdb=" O PHE Y 544 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 556 through 558 Processing sheet with id=AB5, first strand: chain 'Y' and resid 719 through 722 Processing sheet with id=AB6, first strand: chain 'A' and resid 70 through 76 removed outlier: 3.734A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.272A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.543A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.912A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.069A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.553A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.501A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.772A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.312A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.312A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE F 110 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 140 through 141 Processing sheet with id=AC9, first strand: chain 'F' and resid 146 through 149 removed outlier: 6.581A pdb=" N LEU F 174 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR F 190 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TRP F 176 " --> pdb=" O LEU F 188 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2778 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: 3.94 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 3117 1.27 - 1.41: 4923 1.41 - 1.54: 11430 1.54 - 1.68: 103 1.68 - 1.82: 249 Bond restraints: 19822 Sorted by residual: bond pdb=" C5 CLR X 908 " pdb=" C6 CLR X 908 " ideal model delta sigma weight residual 1.332 1.658 -0.326 2.00e-02 2.50e+03 2.66e+02 bond pdb=" C5 CLR Y2007 " pdb=" C6 CLR Y2007 " ideal model delta sigma weight residual 1.332 1.657 -0.325 2.00e-02 2.50e+03 2.65e+02 bond pdb=" C5 CLR X 911 " pdb=" C6 CLR X 911 " ideal model delta sigma weight residual 1.332 1.657 -0.325 2.00e-02 2.50e+03 2.64e+02 bond pdb=" C5 CLR X 910 " pdb=" C6 CLR X 910 " ideal model delta sigma weight residual 1.332 1.657 -0.325 2.00e-02 2.50e+03 2.64e+02 bond pdb=" C5 CLR X 909 " pdb=" C6 CLR X 909 " ideal model delta sigma weight residual 1.332 1.656 -0.324 2.00e-02 2.50e+03 2.63e+02 ... (remaining 19817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 26612 2.85 - 5.70: 209 5.70 - 8.54: 41 8.54 - 11.39: 9 11.39 - 14.24: 13 Bond angle restraints: 26884 Sorted by residual: angle pdb=" C5 CLR Y2009 " pdb=" C6 CLR Y2009 " pdb=" C7 CLR Y2009 " ideal model delta sigma weight residual 125.11 110.87 14.24 3.00e+00 1.11e-01 2.25e+01 angle pdb=" C5 CLR Y2007 " pdb=" C6 CLR Y2007 " pdb=" C7 CLR Y2007 " ideal model delta sigma weight residual 125.11 111.23 13.88 3.00e+00 1.11e-01 2.14e+01 angle pdb=" C5 CLR X 911 " pdb=" C6 CLR X 911 " pdb=" C7 CLR X 911 " ideal model delta sigma weight residual 125.11 111.47 13.64 3.00e+00 1.11e-01 2.07e+01 angle pdb=" C5 CLR X 910 " pdb=" C6 CLR X 910 " pdb=" C7 CLR X 910 " ideal model delta sigma weight residual 125.11 111.62 13.49 3.00e+00 1.11e-01 2.02e+01 angle pdb=" C5 CLR Y2008 " pdb=" C6 CLR Y2008 " pdb=" C7 CLR Y2008 " ideal model delta sigma weight residual 125.11 111.74 13.37 3.00e+00 1.11e-01 1.99e+01 ... (remaining 26879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11117 17.94 - 35.88: 983 35.88 - 53.82: 169 53.82 - 71.77: 44 71.77 - 89.71: 9 Dihedral angle restraints: 12322 sinusoidal: 5278 harmonic: 7044 Sorted by residual: dihedral pdb=" CB CYS X 241 " pdb=" SG CYS X 241 " pdb=" SG CYS X 530 " pdb=" CB CYS X 530 " ideal model delta sinusoidal sigma weight residual -86.00 -175.71 89.71 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual 93.00 59.42 33.58 1 1.00e+01 1.00e-02 1.60e+01 dihedral pdb=" CA CYS X 276 " pdb=" C CYS X 276 " pdb=" N PHE X 277 " pdb=" CA PHE X 277 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 12319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2976 0.119 - 0.238: 39 0.238 - 0.357: 7 0.357 - 0.476: 8 0.476 - 0.595: 10 Chirality restraints: 3040 Sorted by residual: chirality pdb=" C13 CLR X 909 " pdb=" C12 CLR X 909 " pdb=" C14 CLR X 909 " pdb=" C17 CLR X 909 " both_signs ideal model delta sigma weight residual False -2.93 -2.34 -0.60 2.00e-01 2.50e+01 8.86e+00 chirality pdb=" C13 CLR Y2009 " pdb=" C12 CLR Y2009 " pdb=" C14 CLR Y2009 " pdb=" C17 CLR Y2009 " both_signs ideal model delta sigma weight residual False -2.93 -2.34 -0.59 2.00e-01 2.50e+01 8.76e+00 chirality pdb=" C13 CLR Y2008 " pdb=" C12 CLR Y2008 " pdb=" C14 CLR Y2008 " pdb=" C17 CLR Y2008 " both_signs ideal model delta sigma weight residual False -2.93 -2.34 -0.59 2.00e-01 2.50e+01 8.66e+00 ... (remaining 3037 not shown) Planarity restraints: 3375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN X 88 " -0.212 2.00e-02 2.50e+03 2.56e-01 8.21e+02 pdb=" CG ASN X 88 " 0.089 2.00e-02 2.50e+03 pdb=" OD1 ASN X 88 " 0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN X 88 " 0.408 2.00e-02 2.50e+03 pdb=" C1 NAG X 903 " -0.328 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN Y 382 " -0.131 2.00e-02 2.50e+03 1.72e-01 3.69e+02 pdb=" CG ASN Y 382 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN Y 382 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN Y 382 " 0.297 2.00e-02 2.50e+03 pdb=" C1 NAG Y2004 " -0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN X 382 " 0.117 2.00e-02 2.50e+03 1.30e-01 2.12e+02 pdb=" CG ASN X 382 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN X 382 " -0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN X 382 " -0.207 2.00e-02 2.50e+03 pdb=" C1 NAG X 905 " 0.160 2.00e-02 2.50e+03 ... (remaining 3372 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1128 2.73 - 3.27: 19158 3.27 - 3.82: 33062 3.82 - 4.36: 39737 4.36 - 4.90: 68849 Nonbonded interactions: 161934 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR F 175 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.204 3.040 nonbonded pdb=" O TYR Y 213 " pdb=" OG SER Y 509 " model vdw 2.217 3.040 nonbonded pdb=" O TYR X 213 " pdb=" OG SER X 509 " model vdw 2.233 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.240 3.040 ... (remaining 161929 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 'X' and ((resid 25 and (name N or name CA or name C or name O or name CB \ )) or resid 26 through 117 or resid 141 through 673 or resid 687 through 831 or \ resid 904 through 906 or resid 909 through 911)) selection = (chain 'Y' and (resid 25 through 831 or resid 2002 through 2004 or resid 2007 th \ rough 2009)) } 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=0.70 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: 5.810 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.510 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 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 : 0.011 0.326 19849 Z= 0.527 Angle : 0.724 19.577 26946 Z= 0.300 Chirality : 0.060 0.595 3040 Planarity : 0.003 0.039 3367 Dihedral : 13.899 87.995 7739 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: 1.49 (0.18), residues: 2404 helix: 2.52 (0.17), residues: 927 sheet: -0.26 (0.23), residues: 470 loop : 0.26 (0.21), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 96 TYR 0.015 0.001 TYR X 779 PHE 0.019 0.001 PHE Y 277 TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.01054 / 0.52 (19822) covalent geometry : angle 0.68000 / 0.29 (26884) SS BOND : bond 0.00212 / 0.14 ( 19) SS BOND : angle 0.67909 / 0.51 ( 38) hydrogen bonds : bond 0.11724 / 7.97 ( 974) hydrogen bonds : angle 5.03886 / 3.59 ( 2778) link_NAG-ASN : bond 0.05940 / 2.81 ( 8) link_NAG-ASN : angle 8.36571 / 6.66 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 247 LYS cc_start: 0.9239 (pttt) cc_final: 0.9004 (pttm) REVERT: X 439 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7428 (mt-10) REVERT: X 525 LYS cc_start: 0.8954 (tttt) cc_final: 0.8743 (tttp) REVERT: X 528 VAL cc_start: 0.8561 (m) cc_final: 0.8188 (m) REVERT: X 548 THR cc_start: 0.8635 (m) cc_final: 0.8310 (p) REVERT: X 586 PHE cc_start: 0.8886 (t80) cc_final: 0.8565 (t80) REVERT: X 605 ARG cc_start: 0.8465 (ptt180) cc_final: 0.8192 (ptp90) REVERT: X 627 LEU cc_start: 0.8911 (tp) cc_final: 0.8548 (tp) REVERT: X 762 ARG cc_start: 0.8075 (ptt-90) cc_final: 0.7523 (tpt170) REVERT: Y 233 ASP cc_start: 0.8403 (t70) cc_final: 0.8149 (t0) REVERT: Y 546 GLU cc_start: 0.7691 (pt0) cc_final: 0.7438 (pt0) REVERT: Y 607 THR cc_start: 0.8656 (t) cc_final: 0.8443 (t) REVERT: Y 627 LEU cc_start: 0.8072 (tp) cc_final: 0.7701 (tp) REVERT: Y 641 GLN cc_start: 0.8202 (tt0) cc_final: 0.7696 (tt0) REVERT: Y 642 ILE cc_start: 0.8282 (tt) cc_final: 0.8060 (mt) REVERT: Y 738 LEU cc_start: 0.8629 (tp) cc_final: 0.8250 (tp) REVERT: Y 803 CYS cc_start: 0.8016 (m) cc_final: 0.7753 (m) REVERT: A 17 LYS cc_start: 0.8847 (mttt) cc_final: 0.8632 (mtmm) REVERT: A 98 GLN cc_start: 0.8541 (mt0) cc_final: 0.8290 (pt0) REVERT: A 165 PRO cc_start: 0.9299 (Cg_exo) cc_final: 0.8111 (Cg_endo) REVERT: A 232 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8661 (mttt) REVERT: A 233 ASP cc_start: 0.8555 (t0) cc_final: 0.8314 (t0) REVERT: B 301 LYS cc_start: 0.9087 (mttt) cc_final: 0.8828 (mttp) REVERT: G 36 ASP cc_start: 0.7954 (m-30) cc_final: 0.7752 (m-30) REVERT: F 11 LEU cc_start: 0.8982 (tt) cc_final: 0.8774 (tt) REVERT: F 186 GLN cc_start: 0.8023 (tt0) cc_final: 0.7821 (tt0) REVERT: F 219 LEU cc_start: 0.8844 (tt) cc_final: 0.8438 (tt) REVERT: F 244 LYS cc_start: 0.8892 (tttt) cc_final: 0.8551 (ttpp) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.1772 time to fit residues: 110.2803 Evaluate side-chains 319 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.0770 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 832 ASN Y 489 ASN F 3 GLN F 82 GLN F 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.077653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.059686 restraints weight = 42328.821| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.12 r_work: 0.2678 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19849 Z= 0.178 Angle : 0.537 6.077 26946 Z= 0.279 Chirality : 0.044 0.311 3040 Planarity : 0.004 0.063 3367 Dihedral : 7.653 67.740 3289 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.01 % Allowed : 7.16 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: 1.37 (0.17), residues: 2404 helix: 2.42 (0.16), residues: 933 sheet: -0.35 (0.23), residues: 470 loop : 0.19 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 135 TYR 0.018 0.001 TYR F 190 PHE 0.018 0.001 PHE Y 544 TRP 0.013 0.001 TRP B 82 HIS 0.009 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (19822) covalent geometry : angle 0.53441 / 0.28 (26884) SS BOND : bond 0.00234 / 0.17 ( 19) SS BOND : angle 0.69226 / 0.46 ( 38) hydrogen bonds : bond 0.04401 / 3.02 ( 974) hydrogen bonds : angle 4.45521 / 3.16 ( 2778) link_NAG-ASN : bond 0.00302 / 0.18 ( 8) link_NAG-ASN : angle 1.91772 / 1.35 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 327 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 498 GLU cc_start: 0.9017 (tp30) cc_final: 0.8803 (tp30) REVERT: X 525 LYS cc_start: 0.9101 (tttt) cc_final: 0.8881 (tttp) REVERT: X 528 VAL cc_start: 0.8693 (m) cc_final: 0.8478 (m) REVERT: X 548 THR cc_start: 0.8799 (m) cc_final: 0.8551 (p) REVERT: X 586 PHE cc_start: 0.9061 (t80) cc_final: 0.8828 (t80) REVERT: X 762 ARG cc_start: 0.8386 (ptt-90) cc_final: 0.7573 (tpt170) REVERT: X 823 TYR cc_start: 0.8528 (t80) cc_final: 0.8111 (t80) REVERT: Y 233 ASP cc_start: 0.9057 (t70) cc_final: 0.8830 (t0) REVERT: Y 546 GLU cc_start: 0.8196 (pt0) cc_final: 0.7986 (pt0) REVERT: Y 627 LEU cc_start: 0.8665 (tp) cc_final: 0.8291 (tp) REVERT: Y 641 GLN cc_start: 0.8618 (tt0) cc_final: 0.8220 (tt0) REVERT: Y 642 ILE cc_start: 0.8629 (tt) cc_final: 0.8406 (mt) REVERT: Y 688 MET cc_start: 0.8554 (mpp) cc_final: 0.8276 (mmm) REVERT: Y 738 LEU cc_start: 0.9006 (tp) cc_final: 0.8728 (tp) REVERT: Y 803 CYS cc_start: 0.8655 (m) cc_final: 0.8442 (m) REVERT: A 98 GLN cc_start: 0.8841 (mt0) cc_final: 0.8505 (pt0) REVERT: A 232 LYS cc_start: 0.9178 (ttmt) cc_final: 0.8927 (mttt) REVERT: A 233 ASP cc_start: 0.8793 (t0) cc_final: 0.8498 (t0) REVERT: A 237 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8774 (mm-40) REVERT: B 19 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.8279 (ttp-110) REVERT: B 217 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7879 (ppp) REVERT: B 266 HIS cc_start: 0.8637 (t-90) cc_final: 0.8165 (t-90) REVERT: G 17 GLU cc_start: 0.9086 (tp30) cc_final: 0.8780 (tp30) REVERT: G 36 ASP cc_start: 0.8443 (m-30) cc_final: 0.8240 (m-30) REVERT: F 11 LEU cc_start: 0.9082 (tt) cc_final: 0.8869 (tt) REVERT: F 87 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.7745 (mtm-85) REVERT: F 202 ARG cc_start: 0.8525 (ptt-90) cc_final: 0.8047 (ptt180) REVERT: F 244 LYS cc_start: 0.8915 (tttt) cc_final: 0.8644 (ttpp) outliers start: 21 outliers final: 12 residues processed: 333 average time/residue: 0.1631 time to fit residues: 79.8782 Evaluate side-chains 321 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 308 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 554 LEU Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain Y residue 554 LEU Chi-restraints excluded: chain Y residue 599 VAL Chi-restraints excluded: chain Y residue 658 SER Chi-restraints excluded: chain Y residue 719 ILE Chi-restraints excluded: chain Y residue 796 ASN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [18, 113, 194, 65, 191, 27, 71, 40, 34, 95, 176] chunk 18 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 71 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 0.0070 chunk 95 optimal weight: 1.9990 chunk 176 optimal weight: 0.0030 overall best weight: 0.3608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 3 GLN F 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.078676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.060870 restraints weight = 42551.093| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.12 r_work: 0.2707 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19849 Z= 0.109 Angle : 0.496 6.473 26946 Z= 0.257 Chirality : 0.042 0.228 3040 Planarity : 0.003 0.048 3367 Dihedral : 7.161 65.250 3289 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.01 % Allowed : 9.03 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: 1.45 (0.17), residues: 2404 helix: 2.54 (0.16), residues: 932 sheet: -0.34 (0.23), residues: 469 loop : 0.18 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 180 TYR 0.019 0.001 TYR F 190 PHE 0.011 0.001 PHE A 74 TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (19822) covalent geometry : angle 0.49315 / 0.26 (26884) SS BOND : bond 0.00177 / 0.12 ( 19) SS BOND : angle 0.54244 / 0.36 ( 38) hydrogen bonds : bond 0.03891 / 2.68 ( 974) hydrogen bonds : angle 4.28994 / 3.03 ( 2778) link_NAG-ASN : bond 0.00306 / 0.16 ( 8) link_NAG-ASN : angle 1.68372 / 1.12 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 310 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 498 GLU cc_start: 0.9003 (tp30) cc_final: 0.8788 (tp30) REVERT: X 525 LYS cc_start: 0.9053 (tttt) cc_final: 0.8844 (tttp) REVERT: X 528 VAL cc_start: 0.8657 (m) cc_final: 0.8443 (m) REVERT: X 548 THR cc_start: 0.8791 (m) cc_final: 0.8544 (p) REVERT: X 586 PHE cc_start: 0.9046 (t80) cc_final: 0.8845 (t80) REVERT: X 627 LEU cc_start: 0.9094 (tp) cc_final: 0.8754 (tp) REVERT: X 762 ARG cc_start: 0.8353 (ptt-90) cc_final: 0.7572 (tpt170) REVERT: Y 233 ASP cc_start: 0.9028 (t70) cc_final: 0.8788 (t0) REVERT: Y 627 LEU cc_start: 0.8559 (tp) cc_final: 0.8190 (tp) REVERT: Y 642 ILE cc_start: 0.8630 (tt) cc_final: 0.8365 (mt) REVERT: Y 687 PHE cc_start: 0.7233 (m-80) cc_final: 0.6956 (m-80) REVERT: Y 688 MET cc_start: 0.8469 (mpp) cc_final: 0.8202 (mmm) REVERT: Y 718 ASP cc_start: 0.8633 (t0) cc_final: 0.8372 (m-30) REVERT: Y 738 LEU cc_start: 0.8951 (tp) cc_final: 0.8668 (tp) REVERT: Y 803 CYS cc_start: 0.8656 (m) cc_final: 0.8414 (m) REVERT: A 98 GLN cc_start: 0.8806 (mt0) cc_final: 0.8492 (pt0) REVERT: A 169 ARG cc_start: 0.8374 (ptp90) cc_final: 0.8147 (ptp90) REVERT: A 232 LYS cc_start: 0.9178 (ttmt) cc_final: 0.8916 (mttt) REVERT: A 233 ASP cc_start: 0.8785 (t0) cc_final: 0.8571 (t0) REVERT: B 19 ARG cc_start: 0.8498 (ttp-110) cc_final: 0.8218 (ttp-110) REVERT: B 266 HIS cc_start: 0.8630 (t-90) cc_final: 0.8163 (t-90) REVERT: G 36 ASP cc_start: 0.8401 (m-30) cc_final: 0.8170 (m-30) REVERT: F 11 LEU cc_start: 0.9069 (tt) cc_final: 0.8845 (tt) REVERT: F 87 ARG cc_start: 0.8546 (mtm-85) cc_final: 0.7723 (mtm-85) REVERT: F 202 ARG cc_start: 0.8431 (ptt-90) cc_final: 0.7917 (ptt180) REVERT: F 220 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8514 (mp0) REVERT: F 244 LYS cc_start: 0.8925 (tttt) cc_final: 0.8720 (ttpp) outliers start: 21 outliers final: 11 residues processed: 319 average time/residue: 0.1658 time to fit residues: 78.4081 Evaluate side-chains 304 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 293 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 62 GLU Chi-restraints excluded: chain X residue 672 ILE Chi-restraints excluded: chain Y residue 177 MET Chi-restraints excluded: chain Y residue 658 SER Chi-restraints excluded: chain Y residue 719 ILE Chi-restraints excluded: chain Y residue 796 ASN Chi-restraints excluded: chain Y residue 817 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 83 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [154, 160, 155, 232, 111, 1, 28, 30, 77, 94, 207] chunk 154 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 232 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.0270 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 3 GLN F 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.077891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.060060 restraints weight = 42536.672| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.12 r_work: 0.2688 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19849 Z= 0.147 Angle : 0.507 7.742 26946 Z= 0.261 Chirality : 0.042 0.211 3040 Planarity : 0.003 0.062 3367 Dihedral : 6.955 65.673 3289 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.35 % Allowed : 10.00 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: 1.40 (0.17), residues: 2404 helix: 2.50 (0.16), residues: 932 sheet: -0.36 (0.24), residues: 469 loop : 0.16 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.016 0.001 TYR F 190 PHE 0.012 0.001 PHE X 337 TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (19822) covalent geometry : angle 0.50539 / 0.26 (26884) SS BOND : bond 0.00215 / 0.15 ( 19) SS BOND : angle 0.62623 / 0.41 ( 38) hydrogen bonds : bond 0.03992 / 2.75 ( 974) hydrogen bonds : angle 4.28286 / 3.04 ( 2778) link_NAG-ASN : bond 0.00268 / 0.15 ( 8) link_NAG-ASN : angle 1.52942 / 1.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 304 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 72 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8529 (ttm) REVERT: X 525 LYS cc_start: 0.9079 (tttt) cc_final: 0.8874 (tttp) REVERT: X 528 VAL cc_start: 0.8654 (m) cc_final: 0.8433 (m) REVERT: X 548 THR cc_start: 0.8805 (m) cc_final: 0.8562 (p) REVERT: X 762 ARG cc_start: 0.8385 (ptt-90) cc_final: 0.7573 (tpt170) REVERT: Y 72 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8434 (ttt) REVERT: Y 233 ASP cc_start: 0.9050 (t70) cc_final: 0.8824 (t0) REVERT: Y 498 GLU cc_start: 0.8791 (tp30) cc_final: 0.8490 (tp30) REVERT: Y 627 LEU cc_start: 0.8612 (tp) cc_final: 0.8244 (tp) REVERT: Y 642 ILE cc_start: 0.8649 (tt) cc_final: 0.8389 (mt) REVERT: Y 688 MET cc_start: 0.8422 (mpp) cc_final: 0.8197 (mmm) REVERT: Y 718 ASP cc_start: 0.8654 (t0) cc_final: 0.8390 (m-30) REVERT: Y 738 LEU cc_start: 0.8964 (tp) cc_final: 0.8679 (tp) REVERT: Y 752 LEU cc_start: 0.9035 (mt) cc_final: 0.8700 (mp) REVERT: Y 803 CYS cc_start: 0.8644 (m) cc_final: 0.8417 (m) REVERT: A 98 GLN cc_start: 0.8782 (mt0) cc_final: 0.8449 (pt0) REVERT: A 232 LYS cc_start: 0.9177 (ttmt) cc_final: 0.8926 (mttt) REVERT: A 233 ASP cc_start: 0.8804 (t0) cc_final: 0.8589 (t0) REVERT: B 19 ARG cc_start: 0.8540 (ttp-110) cc_final: 0.8257 (ttp-110) REVERT: B 262 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8377 (mmm) REVERT: B 266 HIS cc_start: 0.8603 (t-90) cc_final: 0.8156 (t-90) REVERT: G 17 GLU cc_start: 0.8962 (tp30) cc_final: 0.8664 (tp30) REVERT: G 20 LYS cc_start: 0.9000 (ptpt) cc_final: 0.8671 (ptpp) REVERT: G 32 LYS cc_start: 0.8731 (mtpp) cc_final: 0.8399 (mtpp) REVERT: G 36 ASP cc_start: 0.8421 (m-30) cc_final: 0.8200 (m-30) REVERT: F 6 GLU cc_start: 0.7233 (mp0) cc_final: 0.6991 (mp0) REVERT: F 11 LEU cc_start: 0.9086 (tt) cc_final: 0.8861 (tt) REVERT: F 87 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.7746 (mtm-85) REVERT: F 113 GLN cc_start: 0.8739 (pt0) cc_final: 0.8533 (pm20) REVERT: F 202 ARG cc_start: 0.8480 (ptt-90) cc_final: 0.7908 (ptt180) REVERT: F 220 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8621 (mm-30) REVERT: F 244 LYS cc_start: 0.8934 (tttt) cc_final: 0.8733 (ttpp) outliers start: 28 outliers final: 14 residues processed: 313 average time/residue: 0.1580 time to fit residues: 74.0863 Evaluate side-chains 308 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 291 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 62 GLU Chi-restraints excluded: chain X residue 72 MET Chi-restraints excluded: chain X residue 465 ARG Chi-restraints excluded: chain X residue 509 SER Chi-restraints excluded: chain X residue 711 LEU Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 177 MET Chi-restraints excluded: chain Y residue 560 ASP Chi-restraints excluded: chain Y residue 567 LEU Chi-restraints excluded: chain Y residue 658 SER Chi-restraints excluded: chain Y residue 796 ASN Chi-restraints excluded: chain Y residue 817 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [100, 166, 11, 184, 89, 10, 122, 56, 50, 80, 75] chunk 100 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 18 GLN F 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.077317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.059470 restraints weight = 42488.282| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.12 r_work: 0.2670 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19849 Z= 0.171 Angle : 0.516 9.364 26946 Z= 0.266 Chirality : 0.043 0.212 3040 Planarity : 0.004 0.063 3367 Dihedral : 6.850 66.282 3289 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.49 % Allowed : 10.91 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: 1.29 (0.17), residues: 2404 helix: 2.39 (0.16), residues: 938 sheet: -0.44 (0.24), residues: 455 loop : 0.10 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 180 TYR 0.014 0.001 TYR F 190 PHE 0.014 0.001 PHE X 586 TRP 0.011 0.001 TRP X 336 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (19822) covalent geometry : angle 0.51429 / 0.27 (26884) SS BOND : bond 0.00240 / 0.17 ( 19) SS BOND : angle 0.66754 / 0.45 ( 38) hydrogen bonds : bond 0.04080 / 2.81 ( 974) hydrogen bonds : angle 4.30917 / 3.05 ( 2778) link_NAG-ASN : bond 0.00264 / 0.14 ( 8) link_NAG-ASN : angle 1.49807 / 0.97 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 291 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 72 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8551 (ttm) REVERT: X 528 VAL cc_start: 0.8634 (m) cc_final: 0.8416 (m) REVERT: X 548 THR cc_start: 0.8791 (m) cc_final: 0.8548 (p) REVERT: X 762 ARG cc_start: 0.8387 (ptt-90) cc_final: 0.7572 (tpt170) REVERT: Y 72 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8515 (ttt) REVERT: Y 233 ASP cc_start: 0.9044 (t70) cc_final: 0.8819 (t0) REVERT: Y 498 GLU cc_start: 0.8825 (tp30) cc_final: 0.8517 (tp30) REVERT: Y 627 LEU cc_start: 0.8631 (tp) cc_final: 0.8235 (tp) REVERT: Y 642 ILE cc_start: 0.8648 (tt) cc_final: 0.8381 (mt) REVERT: Y 688 MET cc_start: 0.8457 (mpp) cc_final: 0.8169 (mmm) REVERT: Y 718 ASP cc_start: 0.8622 (t0) cc_final: 0.8363 (m-30) REVERT: Y 738 LEU cc_start: 0.8966 (tp) cc_final: 0.8681 (tp) REVERT: Y 803 CYS cc_start: 0.8693 (m) cc_final: 0.8451 (m) REVERT: A 232 LYS cc_start: 0.9191 (ttmt) cc_final: 0.8937 (mttt) REVERT: A 233 ASP cc_start: 0.8804 (t0) cc_final: 0.8595 (t0) REVERT: B 19 ARG cc_start: 0.8553 (ttp-110) cc_final: 0.8249 (ttp-110) REVERT: B 266 HIS cc_start: 0.8623 (t-90) cc_final: 0.8151 (t-90) REVERT: G 17 GLU cc_start: 0.8941 (tp30) cc_final: 0.8641 (tp30) REVERT: G 20 LYS cc_start: 0.8958 (ptpt) cc_final: 0.8696 (ptpt) REVERT: G 32 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8401 (mtpp) REVERT: G 36 ASP cc_start: 0.8429 (m-30) cc_final: 0.8209 (m-30) REVERT: F 11 LEU cc_start: 0.9115 (tt) cc_final: 0.8867 (tt) REVERT: F 87 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.7755 (mtm-85) REVERT: F 202 ARG cc_start: 0.8552 (ptt-90) cc_final: 0.8078 (ptt180) REVERT: F 246 GLU cc_start: 0.7681 (pm20) cc_final: 0.7354 (pm20) outliers start: 31 outliers final: 20 residues processed: 305 average time/residue: 0.1552 time to fit residues: 70.9283 Evaluate side-chains 306 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 284 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 62 GLU Chi-restraints excluded: chain X residue 72 MET Chi-restraints excluded: chain X residue 295 LEU Chi-restraints excluded: chain X residue 465 ARG Chi-restraints excluded: chain X residue 509 SER Chi-restraints excluded: chain X residue 711 LEU Chi-restraints excluded: chain Y residue 56 LYS Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 177 MET Chi-restraints excluded: chain Y residue 560 ASP Chi-restraints excluded: chain Y residue 567 LEU Chi-restraints excluded: chain Y residue 599 VAL Chi-restraints excluded: chain Y residue 658 SER Chi-restraints excluded: chain Y residue 796 ASN Chi-restraints excluded: chain Y residue 802 MET Chi-restraints excluded: chain Y residue 812 VAL Chi-restraints excluded: chain Y residue 817 MET Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [238, 26, 163, 151, 213, 36, 172, 120, 148, 202, 23] chunk 238 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 163 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 213 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 172 optimal weight: 0.0670 chunk 120 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN F 3 GLN F 113 GLN F 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.078063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.060322 restraints weight = 42233.776| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.11 r_work: 0.2696 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19849 Z= 0.126 Angle : 0.515 11.737 26946 Z= 0.264 Chirality : 0.042 0.257 3040 Planarity : 0.003 0.066 3367 Dihedral : 6.736 64.644 3289 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.35 % Allowed : 11.92 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: 1.35 (0.17), residues: 2404 helix: 2.44 (0.16), residues: 938 sheet: -0.34 (0.24), residues: 463 loop : 0.11 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 135 TYR 0.015 0.001 TYR F 190 PHE 0.012 0.001 PHE A 74 TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (19822) covalent geometry : angle 0.51351 / 0.26 (26884) SS BOND : bond 0.00187 / 0.13 ( 19) SS BOND : angle 0.58875 / 0.41 ( 38) hydrogen bonds : bond 0.03843 / 2.64 ( 974) hydrogen bonds : angle 4.23162 / 3.00 ( 2778) link_NAG-ASN : bond 0.00247 / 0.14 ( 8) link_NAG-ASN : angle 1.43286 / 0.92 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 0.761 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: X 72 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8532 (ttm) REVERT: X 528 VAL cc_start: 0.8611 (m) cc_final: 0.8384 (m) REVERT: X 548 THR cc_start: 0.8789 (m) cc_final: 0.8561 (p) REVERT: X 762 ARG cc_start: 0.8389 (ptt-90) cc_final: 0.7569 (tpt170) REVERT: Y 72 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8441 (ttt) REVERT: Y 233 ASP cc_start: 0.9045 (t70) cc_final: 0.8832 (t0) REVERT: Y 498 GLU cc_start: 0.8822 (tp30) cc_final: 0.8506 (tp30) REVERT: Y 627 LEU cc_start: 0.8601 (tp) cc_final: 0.8209 (tp) REVERT: Y 641 GLN cc_start: 0.8542 (tt0) cc_final: 0.8250 (tt0) REVERT: Y 642 ILE cc_start: 0.8633 (tt) cc_final: 0.8353 (mt) REVERT: Y 688 MET cc_start: 0.8435 (mpp) cc_final: 0.8181 (mmm) REVERT: Y 738 LEU cc_start: 0.8942 (tp) cc_final: 0.8667 (tp) REVERT: Y 752 LEU cc_start: 0.9023 (mt) cc_final: 0.8668 (mp) REVERT: Y 803 CYS cc_start: 0.8651 (m) cc_final: 0.8420 (m) REVERT: A 232 LYS cc_start: 0.9179 (ttmt) cc_final: 0.8928 (mttt) REVERT: A 233 ASP cc_start: 0.8798 (t0) cc_final: 0.8583 (t0) REVERT: B 19 ARG cc_start: 0.8571 (ttp-110) cc_final: 0.8261 (ttp-110) REVERT: B 266 HIS cc_start: 0.8593 (t-90) cc_final: 0.8142 (t-90) REVERT: G 17 GLU cc_start: 0.8916 (tp30) cc_final: 0.8713 (tp30) REVERT: G 20 LYS cc_start: 0.8966 (ptpt) cc_final: 0.8739 (ptpt) REVERT: G 32 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8386 (mtpp) REVERT: G 36 ASP cc_start: 0.8418 (m-30) cc_final: 0.8202 (m-30) REVERT: F 11 LEU cc_start: 0.9121 (tt) cc_final: 0.8870 (tt) REVERT: F 87 ARG cc_start: 0.8556 (mtm-85) cc_final: 0.7735 (mtm-85) REVERT: F 202 ARG cc_start: 0.8626 (ptt-90) cc_final: 0.7747 (ptt180) REVERT: F 220 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8463 (mp0) outliers start: 28 outliers final: 20 residues processed: 305 average time/residue: 0.1551 time to fit residues: 71.3411 Evaluate side-chains 306 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 284 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 62 GLU Chi-restraints excluded: chain X residue 72 MET Chi-restraints excluded: chain X residue 295 LEU Chi-restraints excluded: chain X residue 465 ARG Chi-restraints excluded: chain X residue 509 SER Chi-restraints excluded: chain X residue 711 LEU Chi-restraints excluded: chain Y residue 56 LYS Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 177 MET Chi-restraints excluded: chain Y residue 560 ASP Chi-restraints excluded: chain Y residue 567 LEU Chi-restraints excluded: chain Y residue 658 SER Chi-restraints excluded: chain Y residue 796 ASN Chi-restraints excluded: chain Y residue 802 MET Chi-restraints excluded: chain Y residue 812 VAL Chi-restraints excluded: chain Y residue 817 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [79, 161, 151, 82, 78, 233, 54, 114, 180, 236, 221] chunk 79 optimal weight: 0.8980 chunk 161 optimal weight: 7.9990 chunk 151 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 233 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 180 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 489 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.077992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.060200 restraints weight = 42364.376| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.12 r_work: 0.2694 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2552 r_free = 0.2552 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19849 Z= 0.135 Angle : 0.513 8.457 26946 Z= 0.263 Chirality : 0.042 0.217 3040 Planarity : 0.003 0.068 3367 Dihedral : 6.688 64.430 3289 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.39 % Allowed : 12.01 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: 1.38 (0.17), residues: 2404 helix: 2.47 (0.16), residues: 932 sheet: -0.32 (0.24), residues: 446 loop : 0.11 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 135 TYR 0.016 0.001 TYR Y 746 PHE 0.012 0.001 PHE Y 544 TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (19822) covalent geometry : angle 0.51087 / 0.26 (26884) SS BOND : bond 0.00199 / 0.14 ( 19) SS BOND : angle 0.62282 / 0.43 ( 38) hydrogen bonds : bond 0.03873 / 2.66 ( 974) hydrogen bonds : angle 4.23608 / 3.01 ( 2778) link_NAG-ASN : bond 0.00247 / 0.14 ( 8) link_NAG-ASN : angle 1.40519 / 0.90 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 291 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 72 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8523 (ttm) REVERT: X 528 VAL cc_start: 0.8607 (m) cc_final: 0.8382 (m) REVERT: X 548 THR cc_start: 0.8775 (m) cc_final: 0.8540 (p) REVERT: X 762 ARG cc_start: 0.8387 (ptt-90) cc_final: 0.7572 (tpt170) REVERT: Y 72 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8423 (ttt) REVERT: Y 233 ASP cc_start: 0.9060 (t70) cc_final: 0.8854 (t0) REVERT: Y 627 LEU cc_start: 0.8610 (tp) cc_final: 0.8222 (tp) REVERT: Y 642 ILE cc_start: 0.8638 (tt) cc_final: 0.8362 (mt) REVERT: Y 688 MET cc_start: 0.8446 (mpp) cc_final: 0.8155 (mmm) REVERT: Y 718 ASP cc_start: 0.8619 (t0) cc_final: 0.8351 (m-30) REVERT: Y 738 LEU cc_start: 0.8928 (tp) cc_final: 0.8654 (tp) REVERT: Y 803 CYS cc_start: 0.8640 (m) cc_final: 0.8405 (m) REVERT: A 52 GLN cc_start: 0.7497 (pp30) cc_final: 0.7147 (pp30) REVERT: A 232 LYS cc_start: 0.9184 (ttmt) cc_final: 0.8932 (mttt) REVERT: A 233 ASP cc_start: 0.8788 (t0) cc_final: 0.8569 (t0) REVERT: B 19 ARG cc_start: 0.8582 (ttp-110) cc_final: 0.8259 (ttp-110) REVERT: B 266 HIS cc_start: 0.8624 (t-90) cc_final: 0.8145 (t-90) REVERT: G 17 GLU cc_start: 0.8905 (tp30) cc_final: 0.8592 (tp30) REVERT: G 20 LYS cc_start: 0.8976 (ptpt) cc_final: 0.8669 (ptpt) REVERT: G 32 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8373 (mtpp) REVERT: G 36 ASP cc_start: 0.8433 (m-30) cc_final: 0.8193 (m-30) REVERT: F 11 LEU cc_start: 0.9137 (tt) cc_final: 0.8877 (tt) REVERT: F 87 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.7724 (mtm-85) REVERT: F 113 GLN cc_start: 0.8492 (pm20) cc_final: 0.8204 (pm20) REVERT: F 202 ARG cc_start: 0.8622 (ptt-90) cc_final: 0.8064 (ptt180) REVERT: F 246 GLU cc_start: 0.7666 (pm20) cc_final: 0.7439 (pm20) outliers start: 29 outliers final: 20 residues processed: 307 average time/residue: 0.1530 time to fit residues: 70.4752 Evaluate side-chains 305 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 72 MET Chi-restraints excluded: chain X residue 465 ARG Chi-restraints excluded: chain X residue 509 SER Chi-restraints excluded: chain X residue 711 LEU Chi-restraints excluded: chain Y residue 56 LYS Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 177 MET Chi-restraints excluded: chain Y residue 560 ASP Chi-restraints excluded: chain Y residue 567 LEU Chi-restraints excluded: chain Y residue 658 SER Chi-restraints excluded: chain Y residue 749 LEU Chi-restraints excluded: chain Y residue 796 ASN Chi-restraints excluded: chain Y residue 802 MET Chi-restraints excluded: chain Y residue 812 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [96, 220, 227, 200, 234, 197, 221, 79, 218, 139, 88] chunk 96 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 139 optimal weight: 0.0470 chunk 88 optimal weight: 2.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 489 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.078068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.060335 restraints weight = 42272.673| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.11 r_work: 0.2696 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19849 Z= 0.132 Angle : 0.515 7.715 26946 Z= 0.264 Chirality : 0.042 0.203 3040 Planarity : 0.004 0.070 3367 Dihedral : 6.620 63.769 3289 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.35 % Allowed : 12.11 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: 1.38 (0.17), residues: 2404 helix: 2.48 (0.16), residues: 932 sheet: -0.30 (0.24), residues: 446 loop : 0.10 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 135 TYR 0.015 0.001 TYR F 190 PHE 0.013 0.001 PHE Y 544 TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (19822) covalent geometry : angle 0.51341 / 0.26 (26884) SS BOND : bond 0.00198 / 0.14 ( 19) SS BOND : angle 0.63480 / 0.43 ( 38) hydrogen bonds : bond 0.03854 / 2.65 ( 974) hydrogen bonds : angle 4.21204 / 2.99 ( 2778) link_NAG-ASN : bond 0.00246 / 0.14 ( 8) link_NAG-ASN : angle 1.37327 / 0.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 0.763 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: X 72 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8484 (ttm) REVERT: X 528 VAL cc_start: 0.8598 (m) cc_final: 0.8374 (m) REVERT: X 548 THR cc_start: 0.8768 (m) cc_final: 0.8540 (p) REVERT: X 762 ARG cc_start: 0.8393 (ptt-90) cc_final: 0.7589 (tpt170) REVERT: Y 72 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8427 (ttt) REVERT: Y 233 ASP cc_start: 0.9053 (t70) cc_final: 0.8848 (t0) REVERT: Y 498 GLU cc_start: 0.8811 (tp30) cc_final: 0.8602 (tp30) REVERT: Y 627 LEU cc_start: 0.8617 (tp) cc_final: 0.8219 (tp) REVERT: Y 642 ILE cc_start: 0.8642 (tt) cc_final: 0.8360 (mt) REVERT: Y 688 MET cc_start: 0.8424 (mpp) cc_final: 0.8119 (mmm) REVERT: Y 718 ASP cc_start: 0.8607 (t0) cc_final: 0.8343 (m-30) REVERT: Y 738 LEU cc_start: 0.8923 (tp) cc_final: 0.8656 (tp) REVERT: Y 803 CYS cc_start: 0.8647 (m) cc_final: 0.8417 (m) REVERT: A 232 LYS cc_start: 0.9174 (ttmt) cc_final: 0.8924 (mttt) REVERT: A 233 ASP cc_start: 0.8787 (t0) cc_final: 0.8565 (t0) REVERT: B 19 ARG cc_start: 0.8586 (ttp-110) cc_final: 0.8254 (ttp-110) REVERT: B 266 HIS cc_start: 0.8594 (t-90) cc_final: 0.8136 (t-90) REVERT: G 32 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8389 (mtpp) REVERT: G 36 ASP cc_start: 0.8413 (m-30) cc_final: 0.8174 (m-30) REVERT: F 11 LEU cc_start: 0.9133 (tt) cc_final: 0.8878 (tt) REVERT: F 87 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.7724 (mtm-85) REVERT: F 202 ARG cc_start: 0.8601 (ptt-90) cc_final: 0.7741 (ptt180) REVERT: F 220 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8328 (mp0) REVERT: F 246 GLU cc_start: 0.7738 (pm20) cc_final: 0.7498 (pm20) outliers start: 28 outliers final: 22 residues processed: 310 average time/residue: 0.1524 time to fit residues: 71.0089 Evaluate side-chains 311 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 72 MET Chi-restraints excluded: chain X residue 444 THR Chi-restraints excluded: chain X residue 465 ARG Chi-restraints excluded: chain X residue 509 SER Chi-restraints excluded: chain X residue 711 LEU Chi-restraints excluded: chain Y residue 56 LYS Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 177 MET Chi-restraints excluded: chain Y residue 560 ASP Chi-restraints excluded: chain Y residue 567 LEU Chi-restraints excluded: chain Y residue 658 SER Chi-restraints excluded: chain Y residue 796 ASN Chi-restraints excluded: chain Y residue 802 MET Chi-restraints excluded: chain Y residue 812 VAL Chi-restraints excluded: chain Y residue 817 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 219 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [98, 202, 213, 185, 56, 89, 127, 43, 68, 7, 99] chunk 98 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 127 optimal weight: 0.0040 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 99 optimal weight: 0.0670 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 489 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.078741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.060869 restraints weight = 42218.561| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.12 r_work: 0.2717 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19849 Z= 0.118 Angle : 0.536 13.392 26946 Z= 0.273 Chirality : 0.042 0.286 3040 Planarity : 0.004 0.072 3367 Dihedral : 6.535 62.336 3289 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.15 % Allowed : 13.12 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: 1.43 (0.17), residues: 2404 helix: 2.52 (0.16), residues: 931 sheet: -0.26 (0.24), residues: 444 loop : 0.11 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 135 TYR 0.012 0.001 TYR F 190 PHE 0.014 0.001 PHE Y 544 TRP 0.014 0.001 TRP X 336 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (19822) covalent geometry : angle 0.53495 / 0.27 (26884) SS BOND : bond 0.00174 / 0.12 ( 19) SS BOND : angle 0.63424 / 0.44 ( 38) hydrogen bonds : bond 0.03760 / 2.59 ( 974) hydrogen bonds : angle 4.20148 / 2.98 ( 2778) link_NAG-ASN : bond 0.00252 / 0.14 ( 8) link_NAG-ASN : angle 1.33131 / 0.85 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 289 time to evaluate : 1.058 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: X 72 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8473 (ttm) REVERT: X 293 LEU cc_start: 0.8988 (mp) cc_final: 0.8783 (mp) REVERT: X 528 VAL cc_start: 0.8583 (m) cc_final: 0.8361 (m) REVERT: X 548 THR cc_start: 0.8765 (m) cc_final: 0.8539 (p) REVERT: X 762 ARG cc_start: 0.8400 (ptt-90) cc_final: 0.7593 (tpt170) REVERT: Y 72 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8440 (ttt) REVERT: Y 225 GLU cc_start: 0.8760 (tp30) cc_final: 0.8550 (tp30) REVERT: Y 233 ASP cc_start: 0.9051 (t70) cc_final: 0.8846 (t0) REVERT: Y 498 GLU cc_start: 0.8815 (tp30) cc_final: 0.8597 (tp30) REVERT: Y 627 LEU cc_start: 0.8603 (tp) cc_final: 0.8205 (tp) REVERT: Y 641 GLN cc_start: 0.8498 (tt0) cc_final: 0.8218 (tt0) REVERT: Y 642 ILE cc_start: 0.8638 (tt) cc_final: 0.8344 (mt) REVERT: Y 688 MET cc_start: 0.8407 (mpp) cc_final: 0.8032 (mmm) REVERT: Y 738 LEU cc_start: 0.8919 (tp) cc_final: 0.8646 (tp) REVERT: Y 803 CYS cc_start: 0.8623 (m) cc_final: 0.8400 (m) REVERT: A 232 LYS cc_start: 0.9181 (ttmt) cc_final: 0.8930 (mttt) REVERT: A 233 ASP cc_start: 0.8795 (t0) cc_final: 0.8562 (t0) REVERT: B 19 ARG cc_start: 0.8593 (ttp-110) cc_final: 0.8265 (ttp-110) REVERT: B 266 HIS cc_start: 0.8601 (t-90) cc_final: 0.8147 (t-90) REVERT: G 32 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8399 (mtpp) REVERT: G 36 ASP cc_start: 0.8409 (m-30) cc_final: 0.8172 (m-30) REVERT: F 11 LEU cc_start: 0.9129 (tt) cc_final: 0.8880 (tt) REVERT: F 87 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.7727 (mtm-85) REVERT: F 202 ARG cc_start: 0.8651 (ptt-90) cc_final: 0.7767 (ptt180) REVERT: F 220 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8413 (mp0) outliers start: 24 outliers final: 21 residues processed: 301 average time/residue: 0.1537 time to fit residues: 69.9722 Evaluate side-chains 309 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 286 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 72 MET Chi-restraints excluded: chain X residue 444 THR Chi-restraints excluded: chain X residue 465 ARG Chi-restraints excluded: chain X residue 509 SER Chi-restraints excluded: chain X residue 711 LEU Chi-restraints excluded: chain Y residue 56 LYS Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 177 MET Chi-restraints excluded: chain Y residue 560 ASP Chi-restraints excluded: chain Y residue 567 LEU Chi-restraints excluded: chain Y residue 658 SER Chi-restraints excluded: chain Y residue 749 LEU Chi-restraints excluded: chain Y residue 796 ASN Chi-restraints excluded: chain Y residue 802 MET Chi-restraints excluded: chain Y residue 812 VAL Chi-restraints excluded: chain Y residue 817 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [222, 104, 34, 226, 57, 4, 144, 198, 196, 165, 161] chunk 222 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 489 ASN F 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.077445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.059677 restraints weight = 42567.760| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.12 r_work: 0.2678 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19849 Z= 0.176 Angle : 0.566 12.136 26946 Z= 0.288 Chirality : 0.044 0.341 3040 Planarity : 0.004 0.067 3367 Dihedral : 6.558 64.649 3289 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.20 % Allowed : 13.12 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: 1.34 (0.17), residues: 2404 helix: 2.42 (0.16), residues: 933 sheet: -0.30 (0.24), residues: 444 loop : 0.08 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 135 TYR 0.013 0.001 TYR Y 659 PHE 0.014 0.001 PHE X 337 TRP 0.011 0.001 TRP F 47 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (19822) covalent geometry : angle 0.56498 / 0.29 (26884) SS BOND : bond 0.00228 / 0.16 ( 19) SS BOND : angle 0.74172 / 0.51 ( 38) hydrogen bonds : bond 0.04056 / 2.79 ( 974) hydrogen bonds : angle 4.32755 / 3.06 ( 2778) link_NAG-ASN : bond 0.00277 / 0.15 ( 8) link_NAG-ASN : angle 1.37076 / 0.88 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 290 time to evaluate : 0.793 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: X 72 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8534 (ttm) REVERT: X 528 VAL cc_start: 0.8600 (m) cc_final: 0.8374 (m) REVERT: X 548 THR cc_start: 0.8773 (m) cc_final: 0.8535 (p) REVERT: X 762 ARG cc_start: 0.8418 (ptt-90) cc_final: 0.7585 (tpt170) REVERT: Y 72 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8510 (ttt) REVERT: Y 233 ASP cc_start: 0.9054 (t70) cc_final: 0.8841 (t0) REVERT: Y 498 GLU cc_start: 0.8825 (tp30) cc_final: 0.8581 (tp30) REVERT: Y 627 LEU cc_start: 0.8673 (tp) cc_final: 0.8264 (tp) REVERT: Y 641 GLN cc_start: 0.8541 (tt0) cc_final: 0.8263 (tt0) REVERT: Y 642 ILE cc_start: 0.8649 (tt) cc_final: 0.8357 (mt) REVERT: Y 688 MET cc_start: 0.8426 (mpp) cc_final: 0.8030 (mmm) REVERT: Y 727 ARG cc_start: 0.8810 (ttm-80) cc_final: 0.8585 (mmp80) REVERT: Y 738 LEU cc_start: 0.8941 (tp) cc_final: 0.8669 (tp) REVERT: Y 803 CYS cc_start: 0.8674 (m) cc_final: 0.8438 (m) REVERT: A 232 LYS cc_start: 0.9175 (ttmt) cc_final: 0.8922 (mttt) REVERT: A 233 ASP cc_start: 0.8798 (t0) cc_final: 0.8582 (t0) REVERT: B 19 ARG cc_start: 0.8584 (ttp-110) cc_final: 0.8255 (ttp-110) REVERT: B 266 HIS cc_start: 0.8641 (t-90) cc_final: 0.8158 (t-90) REVERT: G 32 LYS cc_start: 0.8739 (mtpp) cc_final: 0.8403 (mtpp) REVERT: G 36 ASP cc_start: 0.8436 (m-30) cc_final: 0.8200 (m-30) REVERT: F 11 LEU cc_start: 0.9155 (tt) cc_final: 0.8912 (tt) REVERT: F 87 ARG cc_start: 0.8571 (mtm-85) cc_final: 0.7750 (mtm-85) REVERT: F 202 ARG cc_start: 0.8668 (ptt-90) cc_final: 0.7775 (ptt180) REVERT: F 220 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8438 (mp0) outliers start: 25 outliers final: 21 residues processed: 301 average time/residue: 0.1527 time to fit residues: 69.2227 Evaluate side-chains 310 residues out of total 2093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 287 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 72 MET Chi-restraints excluded: chain X residue 444 THR Chi-restraints excluded: chain X residue 465 ARG Chi-restraints excluded: chain X residue 509 SER Chi-restraints excluded: chain X residue 711 LEU Chi-restraints excluded: chain Y residue 56 LYS Chi-restraints excluded: chain Y residue 72 MET Chi-restraints excluded: chain Y residue 560 ASP Chi-restraints excluded: chain Y residue 567 LEU Chi-restraints excluded: chain Y residue 658 SER Chi-restraints excluded: chain Y residue 749 LEU Chi-restraints excluded: chain Y residue 796 ASN Chi-restraints excluded: chain Y residue 802 MET Chi-restraints excluded: chain Y residue 812 VAL Chi-restraints excluded: chain Y residue 817 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [154, 203, 175, 191, 181, 63, 124, 214, 131, 29, 11] chunk 154 optimal weight: 0.8980 chunk 203 optimal weight: 0.3980 chunk 175 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 124 optimal weight: 0.4980 chunk 214 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 29 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 3 GLN F 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.060651 restraints weight = 42159.872| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.12 r_work: 0.2705 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19849 Z= 0.127 Angle : 0.556 12.256 26946 Z= 0.281 Chirality : 0.043 0.323 3040 Planarity : 0.004 0.067 3367 Dihedral : 6.443 62.890 3289 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.11 % Allowed : 13.36 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: 1.39 (0.17), residues: 2404 helix: 2.49 (0.16), residues: 931 sheet: -0.29 (0.24), residues: 446 loop : 0.10 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 135 TYR 0.047 0.001 TYR Y 659 PHE 0.015 0.001 PHE A 74 TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (19822) covalent geometry : angle 0.55508 / 0.28 (26884) SS BOND : bond 0.00187 / 0.13 ( 19) SS BOND : angle 0.62677 / 0.44 ( 38) hydrogen bonds : bond 0.03847 / 2.64 ( 974) hydrogen bonds : angle 4.26562 / 3.02 ( 2778) link_NAG-ASN : bond 0.00246 / 0.14 ( 8) link_NAG-ASN : angle 1.32036 / 0.84 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5413.59 seconds wall clock time: 93 minutes 17.70 seconds (5597.70 seconds total)