Starting phenix.real_space_refine on Sat Sep 12 06:30:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6itc_9731/09_2026/6itc_9731.cif Found real_map, /net/cci-nas-00/data/ceres_data/6itc_9731/09_2026/6itc_9731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6itc_9731/09_2026/6itc_9731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6itc_9731/09_2026/6itc_9731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6itc_9731/09_2026/6itc_9731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6itc_9731/09_2026/6itc_9731.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6itc_9731/09_2026/6itc_9731.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6itc_9731/09_2026/6itc_9731.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 8 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 64 5.16 5 Be 1 3.05 5 C 8811 2.51 5 N 2365 2.21 5 O 2595 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13844 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6107 Classifications: {'peptide': 765} Link IDs: {'PTRANS': 15, 'TRANS': 749} Chain: "Y" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3275 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Chain: "E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 480 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "V" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 312 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain breaks: 1 Chain: "G" Number of atoms: 469 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 62, 466 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Conformer: "B" Number of residues, atoms: 62, 466 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} bond proxies already assigned to first conformer: 473 Chain: "G" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1333 Unusual residues: {'GYS': 1} Classifications: {'peptide': 162, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 155, None: 1} Not linked: pdbres="GYS G 66 " pdbres="VAL G 68 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GYS:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 868 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'PGV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-1': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 8 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N SER V 25 " occ=0.09 ... (4 atoms not shown) pdb=" OG SER V 25 " occ=0.09 residue: pdb=" N LYS V 86 " occ=0.84 ... (3 atoms not shown) pdb=" CB LYS V 86 " occ=0.84 residue: pdb=" N CYS V 95 " occ=0.93 ... (4 atoms not shown) pdb=" SG CYS V 95 " occ=0.93 Time building chain proxies: 3.06, per 1000 atoms: 0.22 Number of scatterers: 13844 At special positions: 0 Unit cell: (128.1, 99.75, 155.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 64 16.00 P 4 15.00 Mg 1 11.99 F 3 9.00 O 2595 8.00 N 2365 7.00 C 8811 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS Y 60 " - pdb=" SG CYS B 29 " distance=2.06 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 95 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " 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 additional links: simple=1, symmetry=0 Simple link: pdb=" C PHE G 64 " - pdb=" N GYS G 66 " Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 582.1 milliseconds 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3206 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 16 sheets defined 48.6% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 14 through 30 removed outlier: 3.606A pdb=" N ARG A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 30 " --> pdb=" O ILE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 40 through 53 Processing helix chain 'A' and resid 61 through 78 removed outlier: 3.650A pdb=" N ALA A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 106 through 118 removed outlier: 3.658A pdb=" N THR A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 130 through 147 removed outlier: 4.921A pdb=" N LYS A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 177 through 188 Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.560A pdb=" N GLN A 195 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET A 196 " --> pdb=" O LYS A 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 196' Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 231 through 242 removed outlier: 3.628A pdb=" N VAL A 235 " --> pdb=" O THR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 removed outlier: 3.570A pdb=" N ASP A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 245 through 249' Processing helix chain 'A' and resid 262 through 273 removed outlier: 3.694A pdb=" N THR A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 removed outlier: 3.669A pdb=" N VAL A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.950A pdb=" N ASP A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 341 removed outlier: 3.518A pdb=" N GLU A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 377 through 384 removed outlier: 3.568A pdb=" N PHE A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 427 removed outlier: 3.750A pdb=" N LYS A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 449 Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 466 through 471 removed outlier: 3.770A pdb=" N ILE A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.581A pdb=" N ASP A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 571 through 619 removed outlier: 3.923A pdb=" N SER A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 643 removed outlier: 3.739A pdb=" N VAL A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.766A pdb=" N LEU A 657 " --> pdb=" O LYS A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 704 removed outlier: 4.603A pdb=" N ARG A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 738 removed outlier: 3.742A pdb=" N ARG A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY A 737 " --> pdb=" O GLN A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 743 removed outlier: 3.749A pdb=" N ALA A 742 " --> pdb=" O HIS A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 777 removed outlier: 3.570A pdb=" N GLU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 9 Processing helix chain 'Y' and resid 11 through 31 removed outlier: 3.915A pdb=" N GLY Y 31 " --> pdb=" O VAL Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 47 removed outlier: 3.631A pdb=" N LEU Y 44 " --> pdb=" O ASN Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 74 through 88 Processing helix chain 'Y' and resid 92 through 102 removed outlier: 3.865A pdb=" N ALA Y 96 " --> pdb=" O VAL Y 92 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY Y 102 " --> pdb=" O TRP Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 135 removed outlier: 3.868A pdb=" N LYS Y 108 " --> pdb=" O MET Y 104 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 174 removed outlier: 4.095A pdb=" N ILE Y 152 " --> pdb=" O THR Y 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 177 through 188 removed outlier: 3.694A pdb=" N ILE Y 181 " --> pdb=" O ASN Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 190 through 202 removed outlier: 3.734A pdb=" N THR Y 202 " --> pdb=" O ILE Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 236 Processing helix chain 'Y' and resid 271 through 289 removed outlier: 3.833A pdb=" N ILE Y 275 " --> pdb=" O VAL Y 271 " (cutoff:3.500A) Proline residue: Y 284 - end of helix Processing helix chain 'Y' and resid 294 through 304 removed outlier: 3.905A pdb=" N LEU Y 298 " --> pdb=" O ASN Y 294 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TRP Y 299 " --> pdb=" O ASP Y 295 " (cutoff:3.500A) Processing helix chain 'Y' and resid 310 through 331 Processing helix chain 'Y' and resid 332 through 343 removed outlier: 3.588A pdb=" N GLN Y 343 " --> pdb=" O ASN Y 339 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 381 removed outlier: 4.734A pdb=" N VAL Y 370 " --> pdb=" O ARG Y 366 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY Y 371 " --> pdb=" O LEU Y 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 382 through 390 removed outlier: 4.143A pdb=" N PHE Y 388 " --> pdb=" O PHE Y 384 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN Y 390 " --> pdb=" O VAL Y 386 " (cutoff:3.500A) Processing helix chain 'Y' and resid 399 through 418 removed outlier: 3.867A pdb=" N VAL Y 405 " --> pdb=" O SER Y 401 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY Y 407 " --> pdb=" O LEU Y 403 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN Y 415 " --> pdb=" O GLU Y 411 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 424 Processing helix chain 'E' and resid 3 through 15 removed outlier: 4.276A pdb=" N LYS E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 59 removed outlier: 4.138A pdb=" N LEU E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 90 removed outlier: 3.691A pdb=" N THR V 90 " --> pdb=" O PRO V 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 20 removed outlier: 3.971A pdb=" N LEU B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 24 removed outlier: 3.517A pdb=" N GLN B 24 " --> pdb=" O SER B 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 21 through 24' Processing helix chain 'G' and resid 57 through 62 removed outlier: 4.611A pdb=" N THR G 62 " --> pdb=" O PRO G 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.577A pdb=" N ARG C 31 " --> pdb=" O PRO C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.410A pdb=" N ILE A 97 " --> pdb=" O VAL A 390 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 154 removed outlier: 6.798A pdb=" N GLY A 153 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N THR A 176 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS A 125 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 226 removed outlier: 6.651A pdb=" N LEU A 221 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR A 354 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 223 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 253 removed outlier: 3.697A pdb=" N GLN A 260 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 258 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 309 Processing sheet with id=AA6, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AA7, first strand: chain 'A' and resid 406 through 407 removed outlier: 6.197A pdb=" N LEU A 406 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 480 through 483 removed outlier: 6.142A pdb=" N LEU A 433 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 238 through 242 Processing sheet with id=AB1, first strand: chain 'V' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'V' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'V' and resid 34 through 37 removed outlier: 6.923A pdb=" N MET V 34 " --> pdb=" O ARG V 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG V 50 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TRP V 36 " --> pdb=" O VAL V 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 12 through 22 removed outlier: 5.887A pdb=" N ASN G 149 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS G 166 " --> pdb=" O ASN G 149 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN G 121 " --> pdb=" O PRO G 13 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU G 15 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE G 123 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU G 17 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU G 125 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP G 19 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N GLY G 127 " --> pdb=" O ASP G 19 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP G 21 " --> pdb=" O GLY G 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.749A pdb=" N MET C 34 " --> pdb=" O MET C 51 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 50 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 58 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 11 through 12 708 hydrogen bonds defined for protein. 2033 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: 2.41 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2988 1.32 - 1.45: 3203 1.45 - 1.57: 7774 1.57 - 1.69: 9 1.69 - 1.81: 123 Bond restraints: 14097 Sorted by residual: bond pdb=" F3 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.769 -0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" F1 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.761 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" F2 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.756 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C19 PGV Y 502 " pdb=" O03 PGV Y 502 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C19 PGV Y 501 " pdb=" O03 PGV Y 501 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.99e+01 ... (remaining 14092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 18402 3.60 - 7.21: 535 7.21 - 10.81: 88 10.81 - 14.41: 11 14.41 - 18.01: 1 Bond angle restraints: 19037 Sorted by residual: angle pdb=" C GLN Y 65 " pdb=" CA GLN Y 65 " pdb=" CB GLN Y 65 " ideal model delta sigma weight residual 111.22 100.53 10.69 1.23e+00 6.61e-01 7.56e+01 angle pdb=" N LEU A 666 " pdb=" CA LEU A 666 " pdb=" C LEU A 666 " ideal model delta sigma weight residual 110.88 120.21 -9.33 1.28e+00 6.10e-01 5.31e+01 angle pdb=" N GLU A 668 " pdb=" CA GLU A 668 " pdb=" CB GLU A 668 " ideal model delta sigma weight residual 110.80 100.14 10.66 1.49e+00 4.50e-01 5.12e+01 angle pdb=" C ILE Y 275 " pdb=" N PHE Y 276 " pdb=" CA PHE Y 276 " ideal model delta sigma weight residual 122.38 110.27 12.11 1.81e+00 3.05e-01 4.48e+01 angle pdb=" N GLY Y 251 " pdb=" CA GLY Y 251 " pdb=" C GLY Y 251 " ideal model delta sigma weight residual 115.36 124.00 -8.64 1.33e+00 5.65e-01 4.22e+01 ... (remaining 19032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 8337 35.31 - 70.62: 120 70.62 - 105.93: 4 105.93 - 141.24: 1 141.24 - 176.54: 2 Dihedral angle restraints: 8464 sinusoidal: 3458 harmonic: 5006 Sorted by residual: dihedral pdb=" CA VAL V 101 " pdb=" C VAL V 101 " pdb=" N MET V 102 " pdb=" CA MET V 102 " ideal model delta harmonic sigma weight residual -180.00 -112.12 -67.88 0 5.00e+00 4.00e-02 1.84e+02 dihedral pdb=" CA GLY V 42 " pdb=" C GLY V 42 " pdb=" N LYS V 43 " pdb=" CA LYS V 43 " ideal model delta harmonic sigma weight residual -180.00 -133.68 -46.32 0 5.00e+00 4.00e-02 8.58e+01 dihedral pdb=" CA ARG V 44 " pdb=" C ARG V 44 " pdb=" N ARG V 45 " pdb=" CA ARG V 45 " ideal model delta harmonic sigma weight residual -180.00 -138.29 -41.71 0 5.00e+00 4.00e-02 6.96e+01 ... (remaining 8461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1844 0.118 - 0.237: 261 0.237 - 0.355: 17 0.355 - 0.474: 5 0.474 - 0.592: 2 Chirality restraints: 2129 Sorted by residual: chirality pdb=" CA ARG Y 252 " pdb=" N ARG Y 252 " pdb=" C ARG Y 252 " pdb=" CB ARG Y 252 " both_signs ideal model delta sigma weight residual False 2.51 3.10 -0.59 2.00e-01 2.50e+01 8.76e+00 chirality pdb=" CA GLU Y 250 " pdb=" N GLU Y 250 " pdb=" C GLU Y 250 " pdb=" CB GLU Y 250 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.35e+00 chirality pdb=" CA ASN C 82A" pdb=" N ASN C 82A" pdb=" C ASN C 82A" pdb=" CB ASN C 82A" both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.98e+00 ... (remaining 2126 not shown) Planarity restraints: 2445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 64 " -0.071 2.00e-02 2.50e+03 1.39e-01 1.94e+02 pdb=" C PHE G 64 " 0.241 2.00e-02 2.50e+03 pdb=" O PHE G 64 " -0.097 2.00e-02 2.50e+03 pdb=" N GYS G 66 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG V 44 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ARG V 44 " -0.070 2.00e-02 2.50e+03 pdb=" O ARG V 44 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG V 45 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 290 " 0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C ILE A 290 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE A 290 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 291 " 0.019 2.00e-02 2.50e+03 ... (remaining 2442 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 7 2.24 - 2.90: 5513 2.90 - 3.57: 19597 3.57 - 4.23: 31636 4.23 - 4.90: 54179 Nonbonded interactions: 110932 Sorted by model distance: nonbonded pdb=" NH2 ARG A 528 " pdb=" F1 BEF A1002 " model vdw 1.574 3.070 nonbonded pdb=" O ASN A 662 " pdb=" O ASP A 667 " model vdw 1.787 3.040 nonbonded pdb=" NH2 ARG A 525 " pdb=" F2 BEF A1002 " model vdw 1.823 3.070 nonbonded pdb=" NZ LYS Y 354 " pdb=" OE2 GLU Y 358 " model vdw 1.882 3.120 nonbonded pdb=" O GLN Y 65 " pdb=" CD GLN Y 65 " model vdw 2.045 3.270 ... (remaining 110927 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.270 Find NCS groups from input model: 0.060 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 0.016 0.293 14102 Z= 0.672 Angle : 1.485 18.015 19045 Z= 0.794 Chirality : 0.083 0.592 2129 Planarity : 0.009 0.072 2444 Dihedral : 13.301 176.545 5248 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.96 % Favored : 90.92 % Rotamer: Outliers : 1.02 % Allowed : 7.12 % Favored : 91.86 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -4.38 (0.16), residues: 1719 helix: -2.86 (0.13), residues: 776 sheet: -2.03 (0.29), residues: 270 loop : -3.14 (0.20), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG C 56 TYR 0.051 0.005 TYR A 174 PHE 0.049 0.006 PHE A 203 TRP 0.033 0.005 TRP G 57 HIS 0.026 0.004 HIS Y 424 Details of bonding type rmsd/Z covalent geometry : bond 0.01579 / 0.67 (14097) covalent geometry : angle 1.48264 / 0.79 (19037) SS BOND : bond 0.01768 / 0.92 ( 3) SS BOND : angle 2.62095 / 1.35 ( 6) hydrogen bonds : bond 0.13092 / 8.33 ( 703) hydrogen bonds : angle 7.20748 / 5.12 ( 2033) Misc. bond : bond 0.00102 / 0.05 ( 1) link_TRANS : bond 0.10153 / 5.34 ( 1) link_TRANS : angle 7.55383 / 4.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 417 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8559 (mt) cc_final: 0.8358 (mt) REVERT: A 501 GLU cc_start: 0.8076 (mp0) cc_final: 0.7694 (mp0) REVERT: A 539 LEU cc_start: 0.8549 (mm) cc_final: 0.8245 (mp) REVERT: A 543 ASP cc_start: 0.8185 (t70) cc_final: 0.7928 (t0) REVERT: A 549 PHE cc_start: 0.7942 (m-80) cc_final: 0.7604 (m-80) REVERT: A 555 MET cc_start: 0.7244 (mmt) cc_final: 0.6863 (mmm) REVERT: A 601 ASP cc_start: 0.7630 (t0) cc_final: 0.7210 (t0) REVERT: Y 67 PHE cc_start: 0.8333 (t80) cc_final: 0.8024 (t80) REVERT: Y 139 MET cc_start: 0.8134 (pmt) cc_final: 0.7636 (pmt) REVERT: Y 142 GLN cc_start: 0.6868 (pp30) cc_final: 0.6646 (pp30) REVERT: V 64 LYS cc_start: 0.7349 (tptt) cc_final: 0.7090 (tptp) REVERT: V 103 SER cc_start: 0.8691 (m) cc_final: 0.8418 (p) REVERT: G 18 LEU cc_start: 0.7640 (tt) cc_final: 0.7197 (tp) REVERT: G 55 VAL cc_start: 0.7963 (m) cc_final: 0.7731 (p) REVERT: G 123 ILE cc_start: 0.8021 (mp) cc_final: 0.7447 (mp) REVERT: C 81 GLN cc_start: 0.6739 (mm110) cc_final: 0.6291 (mm-40) REVERT: C 98 PHE cc_start: 0.6912 (m-10) cc_final: 0.6615 (m-80) REVERT: C 101 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6681 (tm-30) outliers start: 15 outliers final: 2 residues processed: 427 average time/residue: 0.1215 time to fit residues: 75.2365 Evaluate side-chains 268 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 602 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 117 ASN A 157 ASN A 188 ASN A 287 ASN A 297 HIS A 346 GLN A 359 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 HIS A 529 GLN A 613 GLN A 747 ASN A 753 GLN Y 101 GLN Y 142 GLN Y 143 ASN ** Y 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 267 ASN Y 308 HIS Y 355 ASN Y 424 HIS G 25 HIS C 76 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.159306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.122900 restraints weight = 25379.277| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.55 r_work: 0.3166 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14102 Z= 0.176 Angle : 0.794 10.767 19045 Z= 0.412 Chirality : 0.048 0.334 2129 Planarity : 0.006 0.057 2444 Dihedral : 9.749 164.226 1957 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.07 % Allowed : 13.43 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.18), residues: 1719 helix: -1.04 (0.17), residues: 767 sheet: -1.78 (0.28), residues: 279 loop : -2.73 (0.21), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 109 TYR 0.023 0.002 TYR V 96 PHE 0.034 0.002 PHE Y 276 TRP 0.026 0.002 TRP C 103 HIS 0.008 0.001 HIS G 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (14097) covalent geometry : angle 0.79174 / 0.41 (19037) SS BOND : bond 0.00361 / 0.18 ( 3) SS BOND : angle 3.12028 / 1.59 ( 6) hydrogen bonds : bond 0.04950 / 3.22 ( 703) hydrogen bonds : angle 5.69740 / 4.05 ( 2033) Misc. bond : bond 0.00017 / 0.01 ( 1) link_TRANS : bond 0.00502 / 0.26 ( 1) link_TRANS : angle 0.12861 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 325 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7168 (mp0) REVERT: A 141 MET cc_start: 0.8651 (mmm) cc_final: 0.8184 (mmm) REVERT: A 427 MET cc_start: 0.8109 (ppp) cc_final: 0.7691 (ppp) REVERT: A 467 GLU cc_start: 0.8566 (pp20) cc_final: 0.8118 (pt0) REVERT: A 469 GLN cc_start: 0.8353 (pp30) cc_final: 0.8020 (pt0) REVERT: A 501 GLU cc_start: 0.8428 (mp0) cc_final: 0.7784 (mp0) REVERT: A 515 SER cc_start: 0.8897 (t) cc_final: 0.8513 (m) REVERT: A 549 PHE cc_start: 0.8157 (m-80) cc_final: 0.7926 (m-80) REVERT: A 557 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8161 (mtm) REVERT: A 573 MET cc_start: 0.4995 (tpp) cc_final: 0.4652 (tpt) REVERT: A 601 ASP cc_start: 0.8338 (t0) cc_final: 0.7842 (t0) REVERT: A 733 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8123 (tt0) REVERT: Y 104 MET cc_start: 0.7052 (tpp) cc_final: 0.6417 (mmt) REVERT: Y 139 MET cc_start: 0.7856 (pmt) cc_final: 0.7345 (pmt) REVERT: Y 142 GLN cc_start: 0.6830 (OUTLIER) cc_final: 0.6522 (pp30) REVERT: E 39 PHE cc_start: 0.8608 (t80) cc_final: 0.8397 (t80) REVERT: V 4 LEU cc_start: 0.6052 (tp) cc_final: 0.5791 (tp) REVERT: V 6 GLU cc_start: 0.6270 (mp0) cc_final: 0.5917 (mp0) REVERT: V 38 ARG cc_start: 0.6980 (ttm110) cc_final: 0.6769 (ttm110) REVERT: V 39 GLN cc_start: 0.7700 (pp30) cc_final: 0.7456 (pp30) REVERT: V 64 LYS cc_start: 0.7319 (tptt) cc_final: 0.6933 (tptp) REVERT: G 88 MET cc_start: 0.6835 (mmt) cc_final: 0.6556 (tpp) REVERT: G 166 LYS cc_start: 0.7036 (mppt) cc_final: 0.6427 (mmtm) REVERT: G 200 TYR cc_start: 0.6167 (p90) cc_final: 0.5726 (p90) REVERT: C 34 MET cc_start: 0.8155 (mmm) cc_final: 0.7880 (mmm) REVERT: C 56 ARG cc_start: 0.6919 (ptm-80) cc_final: 0.6480 (ptm-80) REVERT: C 72 ASP cc_start: 0.7645 (p0) cc_final: 0.7323 (p0) outliers start: 60 outliers final: 31 residues processed: 357 average time/residue: 0.1181 time to fit residues: 61.9506 Evaluate side-chains 280 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 776 MET Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 24 MET Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 142 GLN Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 413 MET Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 121 optimal weight: 0.3980 chunk 130 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 0.0570 chunk 54 optimal weight: 8.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 101 GLN Y 143 ASN ** Y 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.155536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119595 restraints weight = 23861.315| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.91 r_work: 0.3169 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14102 Z= 0.171 Angle : 0.737 9.305 19045 Z= 0.382 Chirality : 0.047 0.296 2129 Planarity : 0.005 0.066 2444 Dihedral : 8.943 160.590 1954 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.87 % Allowed : 15.33 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.19), residues: 1719 helix: -0.26 (0.18), residues: 766 sheet: -1.54 (0.28), residues: 292 loop : -2.51 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 75 TYR 0.024 0.002 TYR V 96 PHE 0.034 0.002 PHE Y 276 TRP 0.025 0.002 TRP C 103 HIS 0.007 0.001 HIS G 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (14097) covalent geometry : angle 0.73191 / 0.38 (19037) SS BOND : bond 0.01090 / 0.57 ( 3) SS BOND : angle 4.82566 / 2.71 ( 6) hydrogen bonds : bond 0.04431 / 2.88 ( 703) hydrogen bonds : angle 5.21535 / 3.72 ( 2033) Misc. bond : bond 0.00008 / 0.00 ( 1) link_TRANS : bond 0.00400 / 0.21 ( 1) link_TRANS : angle 0.37010 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 276 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ASN cc_start: 0.8789 (m-40) cc_final: 0.8589 (m-40) REVERT: A 384 ILE cc_start: 0.8989 (mm) cc_final: 0.8672 (mt) REVERT: A 515 SER cc_start: 0.9334 (t) cc_final: 0.8871 (m) REVERT: A 539 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 645 ARG cc_start: 0.7807 (tmt170) cc_final: 0.7408 (tpt170) REVERT: A 702 GLN cc_start: 0.8274 (pp30) cc_final: 0.7881 (tp40) REVERT: A 733 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8208 (tt0) REVERT: Y 72 MET cc_start: 0.7980 (tpt) cc_final: 0.7723 (tpt) REVERT: Y 77 TYR cc_start: 0.7917 (t80) cc_final: 0.7711 (t80) REVERT: Y 104 MET cc_start: 0.7261 (tpp) cc_final: 0.6477 (mmt) REVERT: Y 142 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6722 (pp30) REVERT: E 2 GLN cc_start: 0.6851 (mm-40) cc_final: 0.6252 (pp30) REVERT: V 61 ASP cc_start: 0.6897 (m-30) cc_final: 0.6685 (m-30) REVERT: V 64 LYS cc_start: 0.7363 (tptt) cc_final: 0.7014 (tptp) REVERT: G 78 MET cc_start: 0.5989 (ptp) cc_final: 0.5585 (pmm) REVERT: G 88 MET cc_start: 0.6935 (mmt) cc_final: 0.6542 (tpt) REVERT: G 122 ARG cc_start: 0.7425 (mtt-85) cc_final: 0.7139 (mtt-85) REVERT: G 166 LYS cc_start: 0.7105 (mppt) cc_final: 0.6570 (mmtm) REVERT: G 200 TYR cc_start: 0.6201 (p90) cc_final: 0.5813 (p90) REVERT: C 51 MET cc_start: 0.7662 (tmm) cc_final: 0.7437 (tmm) REVERT: C 56 ARG cc_start: 0.6961 (ptm-80) cc_final: 0.6543 (ptm-80) REVERT: C 72 ASP cc_start: 0.7763 (p0) cc_final: 0.7270 (p0) REVERT: C 98 PHE cc_start: 0.7578 (m-80) cc_final: 0.7322 (m-80) REVERT: C 101 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7204 (tm-30) outliers start: 57 outliers final: 32 residues processed: 311 average time/residue: 0.1160 time to fit residues: 53.8444 Evaluate side-chains 282 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 24 MET Chi-restraints excluded: chain Y residue 141 ILE Chi-restraints excluded: chain Y residue 142 GLN Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 305 ASP Chi-restraints excluded: chain Y residue 368 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 ASN Y 101 GLN Y 143 ASN Y 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.155131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118497 restraints weight = 23308.496| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.99 r_work: 0.3152 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14102 Z= 0.169 Angle : 0.700 8.349 19045 Z= 0.363 Chirality : 0.047 0.266 2129 Planarity : 0.005 0.063 2444 Dihedral : 8.609 164.529 1954 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 4.68 % Allowed : 16.42 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.20), residues: 1719 helix: 0.06 (0.19), residues: 780 sheet: -1.38 (0.28), residues: 285 loop : -2.32 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 75 TYR 0.027 0.002 TYR V 96 PHE 0.036 0.002 PHE Y 276 TRP 0.043 0.002 TRP C 103 HIS 0.007 0.001 HIS G 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (14097) covalent geometry : angle 0.69814 / 0.36 (19037) SS BOND : bond 0.00750 / 0.37 ( 3) SS BOND : angle 2.90045 / 1.62 ( 6) hydrogen bonds : bond 0.04240 / 2.74 ( 703) hydrogen bonds : angle 5.03830 / 3.60 ( 2033) Misc. bond : bond 0.00004 / 0.00 ( 1) link_TRANS : bond 0.00119 / 0.06 ( 1) link_TRANS : angle 0.29031 / 0.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 282 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8287 (mp) REVERT: A 384 ILE cc_start: 0.9080 (mm) cc_final: 0.8873 (mt) REVERT: A 539 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8701 (mm) REVERT: A 631 ILE cc_start: 0.8845 (mt) cc_final: 0.8510 (mt) REVERT: A 645 ARG cc_start: 0.7950 (tmt170) cc_final: 0.7555 (tpt170) REVERT: A 680 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6480 (tt0) REVERT: A 702 GLN cc_start: 0.8207 (pp30) cc_final: 0.7404 (tp40) REVERT: A 729 ASP cc_start: 0.8899 (t70) cc_final: 0.7949 (m-30) REVERT: A 733 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8389 (tt0) REVERT: Y 72 MET cc_start: 0.8046 (tpt) cc_final: 0.7792 (tpt) REVERT: Y 104 MET cc_start: 0.7388 (tpp) cc_final: 0.6452 (mmt) REVERT: Y 142 GLN cc_start: 0.6789 (pp30) cc_final: 0.6486 (pp30) REVERT: Y 301 ARG cc_start: 0.8346 (mtm110) cc_final: 0.8068 (mtm-85) REVERT: Y 312 MET cc_start: 0.7000 (mtm) cc_final: 0.6753 (tpp) REVERT: Y 335 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7980 (tm-30) REVERT: Y 413 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8275 (ptm) REVERT: Y 417 GLU cc_start: 0.8558 (pp20) cc_final: 0.8329 (pp20) REVERT: E 2 GLN cc_start: 0.6906 (mm-40) cc_final: 0.6384 (pp30) REVERT: V 39 GLN cc_start: 0.7440 (tm-30) cc_final: 0.7228 (tm-30) REVERT: V 64 LYS cc_start: 0.7484 (tptt) cc_final: 0.7194 (tptp) REVERT: V 109 GLN cc_start: 0.6624 (pm20) cc_final: 0.6246 (pm20) REVERT: G 73 ARG cc_start: 0.6830 (ttp80) cc_final: 0.6295 (ttm-80) REVERT: G 78 MET cc_start: 0.6225 (ptp) cc_final: 0.5589 (pmm) REVERT: G 88 MET cc_start: 0.6873 (mmt) cc_final: 0.6506 (tpt) REVERT: G 123 ILE cc_start: 0.7655 (mp) cc_final: 0.7236 (mp) REVERT: G 200 TYR cc_start: 0.6175 (p90) cc_final: 0.5812 (p90) REVERT: C 34 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7983 (mmm) REVERT: C 51 MET cc_start: 0.7548 (tmm) cc_final: 0.7319 (tmm) REVERT: C 56 ARG cc_start: 0.6896 (ptm-80) cc_final: 0.6326 (ptm-80) REVERT: C 72 ASP cc_start: 0.7805 (p0) cc_final: 0.7152 (p0) REVERT: C 81 GLN cc_start: 0.6618 (mm110) cc_final: 0.6175 (mm-40) outliers start: 69 outliers final: 41 residues processed: 328 average time/residue: 0.1228 time to fit residues: 59.4397 Evaluate side-chains 299 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 24 MET Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 179 ILE Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 305 ASP Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Y residue 413 MET Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 163 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 63 optimal weight: 0.0670 chunk 36 optimal weight: 0.9990 chunk 151 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 161 optimal weight: 30.0000 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 383 ASN Y 101 GLN Y 143 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.157121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121752 restraints weight = 30423.500| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 4.65 r_work: 0.3082 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14102 Z= 0.134 Angle : 0.664 8.639 19045 Z= 0.341 Chirality : 0.045 0.255 2129 Planarity : 0.004 0.060 2444 Dihedral : 8.341 163.461 1954 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.40 % Favored : 93.54 % Rotamer: Outliers : 4.27 % Allowed : 17.57 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.26 (0.20), residues: 1719 helix: 0.42 (0.19), residues: 775 sheet: -1.24 (0.29), residues: 286 loop : -2.15 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 75 TYR 0.028 0.002 TYR V 96 PHE 0.028 0.002 PHE Y 276 TRP 0.020 0.001 TRP C 103 HIS 0.008 0.001 HIS G 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (14097) covalent geometry : angle 0.66298 / 0.34 (19037) SS BOND : bond 0.00339 / 0.18 ( 3) SS BOND : angle 1.99508 / 1.09 ( 6) hydrogen bonds : bond 0.03991 / 2.60 ( 703) hydrogen bonds : angle 4.90007 / 3.50 ( 2033) Misc. bond : bond 0.00001 / 0.00 ( 1) link_TRANS : bond 0.00121 / 0.06 ( 1) link_TRANS : angle 0.20752 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 277 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8140 (mp) REVERT: A 300 MET cc_start: 0.8333 (ptp) cc_final: 0.8051 (ptp) REVERT: A 539 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8756 (mm) REVERT: A 645 ARG cc_start: 0.7980 (tmt170) cc_final: 0.7547 (tpt170) REVERT: A 653 LYS cc_start: 0.8544 (mtmt) cc_final: 0.8312 (mmmt) REVERT: A 680 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6470 (tt0) REVERT: A 702 GLN cc_start: 0.8320 (pp30) cc_final: 0.7501 (tp40) REVERT: A 729 ASP cc_start: 0.8995 (t70) cc_final: 0.8057 (m-30) REVERT: A 733 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8504 (tt0) REVERT: Y 104 MET cc_start: 0.7535 (tpp) cc_final: 0.6587 (mmt) REVERT: Y 142 GLN cc_start: 0.7181 (pp30) cc_final: 0.6236 (pp30) REVERT: Y 143 ASN cc_start: 0.7875 (m-40) cc_final: 0.7439 (m-40) REVERT: Y 301 ARG cc_start: 0.8366 (mtm110) cc_final: 0.8109 (mtm-85) REVERT: Y 312 MET cc_start: 0.7231 (mtm) cc_final: 0.6954 (tpp) REVERT: Y 335 GLN cc_start: 0.8266 (tm-30) cc_final: 0.8049 (tm-30) REVERT: Y 417 GLU cc_start: 0.8598 (pp20) cc_final: 0.8316 (pp20) REVERT: E 2 GLN cc_start: 0.6947 (mm-40) cc_final: 0.6532 (pp30) REVERT: V 39 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7562 (tm-30) REVERT: V 64 LYS cc_start: 0.7491 (tptt) cc_final: 0.7119 (tptp) REVERT: V 102 MET cc_start: 0.7346 (pmm) cc_final: 0.7054 (mtp) REVERT: G 73 ARG cc_start: 0.6954 (ttp80) cc_final: 0.6360 (ttm-80) REVERT: G 88 MET cc_start: 0.6934 (mmt) cc_final: 0.6516 (tpt) REVERT: G 143 TYR cc_start: 0.8387 (t80) cc_final: 0.7944 (t80) REVERT: G 200 TYR cc_start: 0.6146 (p90) cc_final: 0.5801 (p90) REVERT: G 222 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7611 (tm-30) REVERT: C 19 ARG cc_start: 0.7424 (tmm-80) cc_final: 0.6866 (tpt-90) REVERT: C 56 ARG cc_start: 0.6889 (ptm-80) cc_final: 0.6290 (ptm-80) REVERT: C 72 ASP cc_start: 0.7391 (p0) cc_final: 0.6931 (p0) REVERT: C 81 GLN cc_start: 0.6633 (mm110) cc_final: 0.6141 (mm-40) REVERT: C 98 PHE cc_start: 0.7608 (m-10) cc_final: 0.7281 (m-80) REVERT: C 101 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7434 (tm-30) outliers start: 63 outliers final: 47 residues processed: 317 average time/residue: 0.1218 time to fit residues: 56.5200 Evaluate side-chains 306 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 24 MET Chi-restraints excluded: chain Y residue 67 PHE Chi-restraints excluded: chain Y residue 179 ILE Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 194 ILE Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain V residue 58 MET Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 79 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 126 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 ASN Y 101 GLN B 57 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.157754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121249 restraints weight = 26008.751| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.81 r_work: 0.3160 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14102 Z= 0.133 Angle : 0.659 8.458 19045 Z= 0.340 Chirality : 0.045 0.244 2129 Planarity : 0.004 0.062 2444 Dihedral : 8.116 165.083 1954 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 5.02 % Allowed : 17.77 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.20), residues: 1719 helix: 0.63 (0.19), residues: 780 sheet: -1.16 (0.29), residues: 280 loop : -2.13 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 248 TYR 0.026 0.001 TYR V 96 PHE 0.034 0.002 PHE G 83 TRP 0.036 0.002 TRP C 103 HIS 0.006 0.001 HIS G 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (14097) covalent geometry : angle 0.65839 / 0.34 (19037) SS BOND : bond 0.00307 / 0.15 ( 3) SS BOND : angle 1.72110 / 0.93 ( 6) hydrogen bonds : bond 0.03869 / 2.52 ( 703) hydrogen bonds : angle 4.78129 / 3.41 ( 2033) Misc. bond : bond 0.00006 / 0.00 ( 1) link_TRANS : bond 0.00124 / 0.07 ( 1) link_TRANS : angle 0.14369 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 282 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8146 (mp) REVERT: A 300 MET cc_start: 0.8251 (ptp) cc_final: 0.7957 (ptp) REVERT: A 403 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7718 (mtt90) REVERT: A 631 ILE cc_start: 0.8859 (mt) cc_final: 0.8553 (mt) REVERT: A 645 ARG cc_start: 0.7972 (tmt170) cc_final: 0.7622 (tpt170) REVERT: A 653 LYS cc_start: 0.8507 (mtmt) cc_final: 0.8291 (mmmt) REVERT: A 659 ASP cc_start: 0.8143 (t70) cc_final: 0.7838 (t0) REVERT: A 680 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6612 (tt0) REVERT: A 702 GLN cc_start: 0.8141 (pp30) cc_final: 0.7693 (tp40) REVERT: A 729 ASP cc_start: 0.8938 (t70) cc_final: 0.8055 (m-30) REVERT: A 733 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8547 (tt0) REVERT: Y 104 MET cc_start: 0.7537 (tpp) cc_final: 0.6586 (mmt) REVERT: Y 142 GLN cc_start: 0.7026 (pp30) cc_final: 0.6081 (pp30) REVERT: Y 143 ASN cc_start: 0.7796 (m-40) cc_final: 0.7362 (m-40) REVERT: Y 301 ARG cc_start: 0.8297 (mtm110) cc_final: 0.8063 (mtm-85) REVERT: Y 312 MET cc_start: 0.7085 (mtm) cc_final: 0.6850 (tpp) REVERT: Y 335 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7984 (tm-30) REVERT: Y 417 GLU cc_start: 0.8536 (pp20) cc_final: 0.8253 (pp20) REVERT: E 2 GLN cc_start: 0.6981 (mm-40) cc_final: 0.6530 (pp30) REVERT: E 13 ARG cc_start: 0.8726 (ttm-80) cc_final: 0.8414 (ttp-110) REVERT: E 16 LYS cc_start: 0.8438 (mttm) cc_final: 0.7779 (mmmt) REVERT: V 39 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7535 (tm-30) REVERT: V 64 LYS cc_start: 0.7520 (tptt) cc_final: 0.7191 (tptp) REVERT: G 73 ARG cc_start: 0.7017 (ttp80) cc_final: 0.6396 (ttm-80) REVERT: G 88 MET cc_start: 0.6862 (mmt) cc_final: 0.6459 (tpt) REVERT: G 143 TYR cc_start: 0.8292 (t80) cc_final: 0.7828 (t80) REVERT: G 200 TYR cc_start: 0.6096 (p90) cc_final: 0.5795 (p90) REVERT: G 222 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7466 (tm-30) REVERT: C 56 ARG cc_start: 0.6830 (ptm-80) cc_final: 0.6206 (ptm-80) REVERT: C 72 ASP cc_start: 0.7430 (p0) cc_final: 0.7025 (p0) REVERT: C 81 GLN cc_start: 0.6557 (mm110) cc_final: 0.6212 (mm-40) REVERT: C 98 PHE cc_start: 0.7505 (m-10) cc_final: 0.7280 (m-80) REVERT: C 103 TRP cc_start: 0.7824 (m100) cc_final: 0.7295 (m100) outliers start: 74 outliers final: 52 residues processed: 336 average time/residue: 0.1208 time to fit residues: 59.5979 Evaluate side-chains 309 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 256 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 24 MET Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 67 PHE Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 194 ILE Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 368 THR Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 PHE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 79 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 161 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 130 optimal weight: 40.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 283 HIS A 383 ASN Y 40 ASN Y 101 GLN B 57 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.155823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119531 restraints weight = 23349.550| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.01 r_work: 0.3152 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14102 Z= 0.160 Angle : 0.692 12.613 19045 Z= 0.351 Chirality : 0.046 0.220 2129 Planarity : 0.004 0.055 2444 Dihedral : 8.039 168.505 1954 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.68 % Allowed : 18.52 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.02 (0.20), residues: 1719 helix: 0.63 (0.19), residues: 780 sheet: -0.85 (0.30), residues: 267 loop : -2.18 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.024 0.002 TYR V 96 PHE 0.030 0.002 PHE Y 276 TRP 0.028 0.001 TRP C 103 HIS 0.007 0.001 HIS G 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (14097) covalent geometry : angle 0.69096 / 0.35 (19037) SS BOND : bond 0.00342 / 0.17 ( 3) SS BOND : angle 1.91933 / 1.04 ( 6) hydrogen bonds : bond 0.04032 / 2.63 ( 703) hydrogen bonds : angle 4.75598 / 3.40 ( 2033) Misc. bond : bond 0.00003 / 0.00 ( 1) link_TRANS : bond 0.00126 / 0.07 ( 1) link_TRANS : angle 0.33919 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 264 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8164 (mp) REVERT: A 300 MET cc_start: 0.8230 (ptp) cc_final: 0.7922 (ptp) REVERT: A 403 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7730 (mtt90) REVERT: A 555 MET cc_start: 0.7521 (tpt) cc_final: 0.7272 (mmp) REVERT: A 600 ASP cc_start: 0.8127 (m-30) cc_final: 0.7397 (t70) REVERT: A 645 ARG cc_start: 0.7982 (tmt170) cc_final: 0.7614 (tpt170) REVERT: A 659 ASP cc_start: 0.8197 (t70) cc_final: 0.7896 (t0) REVERT: A 702 GLN cc_start: 0.8080 (pp30) cc_final: 0.7548 (tp40) REVERT: A 729 ASP cc_start: 0.8898 (t70) cc_final: 0.8612 (t70) REVERT: A 733 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8562 (tt0) REVERT: A 735 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8472 (ttt-90) REVERT: Y 9 MET cc_start: 0.6675 (mmt) cc_final: 0.6138 (mmt) REVERT: Y 104 MET cc_start: 0.7476 (tpp) cc_final: 0.6578 (mmt) REVERT: Y 142 GLN cc_start: 0.7135 (pp30) cc_final: 0.6166 (pp30) REVERT: Y 143 ASN cc_start: 0.7847 (m-40) cc_final: 0.7280 (m-40) REVERT: Y 301 ARG cc_start: 0.8331 (mtm110) cc_final: 0.8073 (mtm-85) REVERT: Y 312 MET cc_start: 0.7013 (mtm) cc_final: 0.6788 (tpp) REVERT: Y 335 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7900 (tm-30) REVERT: Y 417 GLU cc_start: 0.8567 (pp20) cc_final: 0.8270 (pp20) REVERT: E 2 GLN cc_start: 0.6987 (mm-40) cc_final: 0.6525 (pp30) REVERT: E 13 ARG cc_start: 0.8730 (ttm-80) cc_final: 0.8408 (ttp-110) REVERT: E 16 LYS cc_start: 0.8428 (mttm) cc_final: 0.7785 (mmmt) REVERT: V 4 LEU cc_start: 0.4888 (pt) cc_final: 0.4174 (tp) REVERT: V 39 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7634 (tm-30) REVERT: V 64 LYS cc_start: 0.7525 (tptt) cc_final: 0.7232 (tptp) REVERT: V 82 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7471 (mtp) REVERT: V 102 MET cc_start: 0.7341 (pmm) cc_final: 0.6723 (ptm) REVERT: G 73 ARG cc_start: 0.6986 (ttp80) cc_final: 0.6368 (ttm-80) REVERT: G 88 MET cc_start: 0.6966 (mmt) cc_final: 0.6503 (tpt) REVERT: G 106 TYR cc_start: 0.5673 (m-80) cc_final: 0.5142 (m-80) REVERT: G 143 TYR cc_start: 0.8193 (t80) cc_final: 0.7693 (t80) REVERT: G 200 TYR cc_start: 0.6094 (p90) cc_final: 0.5818 (p90) REVERT: G 222 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7370 (tm-30) REVERT: C 34 MET cc_start: 0.8453 (mmm) cc_final: 0.7889 (mmm) REVERT: C 56 ARG cc_start: 0.6840 (ptm-80) cc_final: 0.6459 (ptm-80) REVERT: C 72 ASP cc_start: 0.7308 (p0) cc_final: 0.6867 (p0) REVERT: C 81 GLN cc_start: 0.6613 (mm110) cc_final: 0.6175 (mm-40) REVERT: C 98 PHE cc_start: 0.7450 (m-10) cc_final: 0.7200 (m-80) REVERT: C 103 TRP cc_start: 0.7937 (m100) cc_final: 0.7513 (m100) outliers start: 69 outliers final: 57 residues processed: 311 average time/residue: 0.1272 time to fit residues: 57.1323 Evaluate side-chains 311 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 251 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 67 PHE Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 194 ILE Chi-restraints excluded: chain Y residue 199 TYR Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 368 THR Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain V residue 58 MET Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 82 MET Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 PHE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 79 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 64 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 26 optimal weight: 0.0010 chunk 108 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 ASN Y 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.156473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120283 restraints weight = 23643.523| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.07 r_work: 0.3159 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14102 Z= 0.142 Angle : 0.681 10.990 19045 Z= 0.345 Chirality : 0.045 0.217 2129 Planarity : 0.004 0.053 2444 Dihedral : 7.880 170.623 1954 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.34 % Allowed : 19.54 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.20), residues: 1719 helix: 0.72 (0.19), residues: 782 sheet: -0.83 (0.30), residues: 271 loop : -2.10 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.027 0.002 TYR V 96 PHE 0.028 0.002 PHE Y 276 TRP 0.025 0.001 TRP C 103 HIS 0.007 0.001 HIS G 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (14097) covalent geometry : angle 0.68098 / 0.35 (19037) SS BOND : bond 0.00273 / 0.14 ( 3) SS BOND : angle 1.66817 / 0.91 ( 6) hydrogen bonds : bond 0.03919 / 2.55 ( 703) hydrogen bonds : angle 4.70183 / 3.37 ( 2033) Misc. bond : bond 0.00009 / 0.00 ( 1) link_TRANS : bond 0.00117 / 0.06 ( 1) link_TRANS : angle 0.30689 / 0.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 265 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8164 (mp) REVERT: A 157 ASN cc_start: 0.8196 (t0) cc_final: 0.7979 (t0) REVERT: A 300 MET cc_start: 0.8201 (ptp) cc_final: 0.7887 (ptp) REVERT: A 403 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7701 (mtt90) REVERT: A 555 MET cc_start: 0.7530 (tpt) cc_final: 0.7263 (mmp) REVERT: A 600 ASP cc_start: 0.8078 (m-30) cc_final: 0.7458 (t70) REVERT: A 645 ARG cc_start: 0.7911 (tmt170) cc_final: 0.7601 (tpt170) REVERT: A 702 GLN cc_start: 0.8066 (pp30) cc_final: 0.7568 (tp40) REVERT: A 729 ASP cc_start: 0.8874 (t70) cc_final: 0.8106 (m-30) REVERT: A 733 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8583 (tt0) REVERT: A 735 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8494 (ttt-90) REVERT: Y 9 MET cc_start: 0.6741 (mmt) cc_final: 0.6354 (mmt) REVERT: Y 50 LEU cc_start: 0.4623 (OUTLIER) cc_final: 0.4278 (mt) REVERT: Y 104 MET cc_start: 0.7444 (tpp) cc_final: 0.6556 (mmt) REVERT: Y 142 GLN cc_start: 0.7126 (pp30) cc_final: 0.6159 (pp30) REVERT: Y 143 ASN cc_start: 0.7941 (m-40) cc_final: 0.7402 (m-40) REVERT: Y 301 ARG cc_start: 0.8324 (mtm110) cc_final: 0.8080 (mtm-85) REVERT: Y 312 MET cc_start: 0.7004 (mtm) cc_final: 0.6785 (tpp) REVERT: Y 335 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7896 (tm-30) REVERT: Y 417 GLU cc_start: 0.8537 (pp20) cc_final: 0.8266 (pp20) REVERT: E 2 GLN cc_start: 0.6954 (mm-40) cc_final: 0.6523 (pp30) REVERT: E 13 ARG cc_start: 0.8732 (ttm-80) cc_final: 0.8411 (ttp-110) REVERT: E 16 LYS cc_start: 0.8383 (mttm) cc_final: 0.7761 (mmmt) REVERT: V 4 LEU cc_start: 0.4864 (pt) cc_final: 0.4124 (tp) REVERT: V 34 MET cc_start: 0.7841 (mmm) cc_final: 0.7427 (mmm) REVERT: V 39 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7617 (tm-30) REVERT: V 64 LYS cc_start: 0.7523 (tptt) cc_final: 0.7246 (tptp) REVERT: V 82 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7430 (mtp) REVERT: V 102 MET cc_start: 0.7338 (pmm) cc_final: 0.6722 (ptm) REVERT: G 73 ARG cc_start: 0.7026 (ttp80) cc_final: 0.6378 (ttm-80) REVERT: G 88 MET cc_start: 0.6981 (mmt) cc_final: 0.6518 (tpt) REVERT: G 106 TYR cc_start: 0.5688 (m-80) cc_final: 0.5197 (m-80) REVERT: G 143 TYR cc_start: 0.8257 (t80) cc_final: 0.7740 (t80) REVERT: G 200 TYR cc_start: 0.6080 (p90) cc_final: 0.5831 (p90) REVERT: G 222 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7339 (tm-30) REVERT: C 34 MET cc_start: 0.8472 (mmm) cc_final: 0.7874 (mmm) REVERT: C 56 ARG cc_start: 0.6813 (ptm-80) cc_final: 0.5718 (ptm-80) REVERT: C 72 ASP cc_start: 0.7345 (p0) cc_final: 0.6954 (p0) REVERT: C 81 GLN cc_start: 0.6701 (mm110) cc_final: 0.6212 (mm-40) REVERT: C 98 PHE cc_start: 0.7510 (m-10) cc_final: 0.7270 (m-80) REVERT: C 103 TRP cc_start: 0.7987 (m100) cc_final: 0.7641 (m100) outliers start: 64 outliers final: 50 residues processed: 310 average time/residue: 0.1233 time to fit residues: 55.4312 Evaluate side-chains 307 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 253 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 67 PHE Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 194 ILE Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 368 THR Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Y residue 413 MET Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 82 MET Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 PHE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 79 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 110 optimal weight: 0.0170 chunk 139 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 101 GLN Y 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.155725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116361 restraints weight = 32344.744| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.61 r_work: 0.3097 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14102 Z= 0.176 Angle : 0.716 11.032 19045 Z= 0.363 Chirality : 0.047 0.212 2129 Planarity : 0.004 0.050 2444 Dihedral : 7.802 173.424 1954 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.41 % Allowed : 19.74 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.20), residues: 1719 helix: 0.67 (0.19), residues: 782 sheet: -0.78 (0.30), residues: 274 loop : -2.08 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 70 TYR 0.022 0.002 TYR V 96 PHE 0.032 0.002 PHE Y 276 TRP 0.026 0.002 TRP C 103 HIS 0.007 0.001 HIS G 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (14097) covalent geometry : angle 0.71550 / 0.36 (19037) SS BOND : bond 0.00334 / 0.17 ( 3) SS BOND : angle 1.95623 / 1.09 ( 6) hydrogen bonds : bond 0.04108 / 2.66 ( 703) hydrogen bonds : angle 4.69811 / 3.36 ( 2033) Misc. bond : bond 0.00007 / 0.00 ( 1) link_TRANS : bond 0.00145 / 0.08 ( 1) link_TRANS : angle 0.39692 / 0.23 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 260 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8169 (mp) REVERT: A 300 MET cc_start: 0.8292 (ptp) cc_final: 0.7953 (ptp) REVERT: A 403 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.7843 (mtt90) REVERT: A 600 ASP cc_start: 0.8287 (m-30) cc_final: 0.7551 (t70) REVERT: A 645 ARG cc_start: 0.7889 (tmt170) cc_final: 0.7580 (tpt170) REVERT: A 702 GLN cc_start: 0.8144 (pp30) cc_final: 0.7703 (tp40) REVERT: A 729 ASP cc_start: 0.8930 (t70) cc_final: 0.8631 (t70) REVERT: A 733 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8606 (tt0) REVERT: Y 9 MET cc_start: 0.6802 (mmt) cc_final: 0.6476 (mmt) REVERT: Y 50 LEU cc_start: 0.4697 (OUTLIER) cc_final: 0.4431 (mt) REVERT: Y 104 MET cc_start: 0.7469 (tpp) cc_final: 0.6604 (mmt) REVERT: Y 139 MET cc_start: 0.8223 (pmm) cc_final: 0.7914 (pmm) REVERT: Y 142 GLN cc_start: 0.7108 (pp30) cc_final: 0.6163 (pp30) REVERT: Y 143 ASN cc_start: 0.7863 (m-40) cc_final: 0.7303 (m-40) REVERT: Y 301 ARG cc_start: 0.8418 (mtm110) cc_final: 0.8151 (mtm-85) REVERT: Y 312 MET cc_start: 0.7026 (mtm) cc_final: 0.6786 (tpp) REVERT: Y 335 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7947 (tm-30) REVERT: Y 417 GLU cc_start: 0.8598 (pp20) cc_final: 0.8300 (pp20) REVERT: E 2 GLN cc_start: 0.6944 (mm-40) cc_final: 0.6499 (pp30) REVERT: E 13 ARG cc_start: 0.8811 (ttm-80) cc_final: 0.8480 (ttp-110) REVERT: E 16 LYS cc_start: 0.8451 (mttm) cc_final: 0.7822 (mmmt) REVERT: V 4 LEU cc_start: 0.4917 (pt) cc_final: 0.4175 (tp) REVERT: V 39 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7708 (tm-30) REVERT: V 61 ASP cc_start: 0.7511 (m-30) cc_final: 0.7248 (m-30) REVERT: V 64 LYS cc_start: 0.7590 (tptt) cc_final: 0.7248 (tptp) REVERT: V 82 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7339 (mtp) REVERT: G 73 ARG cc_start: 0.7064 (ttp80) cc_final: 0.6380 (ttm-80) REVERT: G 88 MET cc_start: 0.7030 (mmt) cc_final: 0.6541 (tpt) REVERT: G 106 TYR cc_start: 0.5609 (m-80) cc_final: 0.4965 (m-80) REVERT: G 143 TYR cc_start: 0.8121 (t80) cc_final: 0.7774 (t80) REVERT: G 200 TYR cc_start: 0.6161 (p90) cc_final: 0.5891 (p90) REVERT: G 222 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7417 (tm-30) REVERT: C 34 MET cc_start: 0.8631 (mmm) cc_final: 0.8050 (mmm) REVERT: C 56 ARG cc_start: 0.6832 (ptm-80) cc_final: 0.5720 (ptm-80) REVERT: C 72 ASP cc_start: 0.7250 (p0) cc_final: 0.6801 (p0) REVERT: C 81 GLN cc_start: 0.6531 (mm110) cc_final: 0.6061 (mm-40) REVERT: C 82 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.5493 (mt) REVERT: C 98 PHE cc_start: 0.7643 (m-10) cc_final: 0.7322 (m-80) REVERT: C 103 TRP cc_start: 0.8076 (m100) cc_final: 0.7718 (m100) outliers start: 65 outliers final: 54 residues processed: 307 average time/residue: 0.1229 time to fit residues: 55.1621 Evaluate side-chains 308 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 250 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 67 PHE Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 194 ILE Chi-restraints excluded: chain Y residue 199 TYR Chi-restraints excluded: chain Y residue 217 LEU Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 368 THR Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Y residue 413 MET Chi-restraints excluded: chain V residue 62 SER Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 82 MET Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 PHE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 79 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 127 optimal weight: 7.9990 chunk 138 optimal weight: 0.2980 chunk 149 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 ASN A 288 HIS Y 66 ASN Y 101 GLN B 57 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.159083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123089 restraints weight = 30016.298| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 4.66 r_work: 0.3104 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14102 Z= 0.129 Angle : 0.677 10.804 19045 Z= 0.342 Chirality : 0.045 0.200 2129 Planarity : 0.004 0.051 2444 Dihedral : 7.545 175.133 1954 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.87 % Allowed : 20.76 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1719 helix: 0.86 (0.19), residues: 782 sheet: -0.72 (0.30), residues: 274 loop : -1.97 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.025 0.001 TYR V 96 PHE 0.024 0.001 PHE Y 276 TRP 0.024 0.001 TRP C 103 HIS 0.008 0.001 HIS G 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (14097) covalent geometry : angle 0.67685 / 0.34 (19037) SS BOND : bond 0.00247 / 0.12 ( 3) SS BOND : angle 1.40601 / 0.76 ( 6) hydrogen bonds : bond 0.03706 / 2.41 ( 703) hydrogen bonds : angle 4.63221 / 3.32 ( 2033) Misc. bond : bond 0.00014 / 0.01 ( 1) link_TRANS : bond 0.00123 / 0.06 ( 1) link_TRANS : angle 0.30625 / 0.18 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8206 (mp) REVERT: A 99 GLU cc_start: 0.7758 (tt0) cc_final: 0.7391 (tt0) REVERT: A 300 MET cc_start: 0.8246 (ptp) cc_final: 0.7985 (ptp) REVERT: A 403 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.7904 (mtt90) REVERT: A 427 MET cc_start: 0.8540 (ppp) cc_final: 0.8271 (ppp) REVERT: A 481 THR cc_start: 0.9487 (OUTLIER) cc_final: 0.9168 (p) REVERT: A 600 ASP cc_start: 0.8228 (m-30) cc_final: 0.7496 (t70) REVERT: A 645 ARG cc_start: 0.7812 (tmt170) cc_final: 0.7578 (tpt170) REVERT: A 702 GLN cc_start: 0.8289 (pp30) cc_final: 0.7830 (tp40) REVERT: A 729 ASP cc_start: 0.8862 (t70) cc_final: 0.8125 (m-30) REVERT: A 733 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8604 (tt0) REVERT: Y 50 LEU cc_start: 0.4689 (OUTLIER) cc_final: 0.4428 (mt) REVERT: Y 104 MET cc_start: 0.7494 (tpp) cc_final: 0.6520 (mmt) REVERT: Y 142 GLN cc_start: 0.7141 (pp30) cc_final: 0.6200 (pp30) REVERT: Y 143 ASN cc_start: 0.7685 (m-40) cc_final: 0.7236 (m-40) REVERT: Y 301 ARG cc_start: 0.8350 (mtm110) cc_final: 0.8089 (mtm-85) REVERT: Y 335 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7960 (tm-30) REVERT: Y 417 GLU cc_start: 0.8588 (pp20) cc_final: 0.8268 (pp20) REVERT: E 2 GLN cc_start: 0.7048 (mm-40) cc_final: 0.6540 (pp30) REVERT: E 10 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7752 (mm-30) REVERT: E 13 ARG cc_start: 0.8756 (ttm-80) cc_final: 0.8543 (ttp-110) REVERT: E 16 LYS cc_start: 0.8426 (mttm) cc_final: 0.7800 (mmmt) REVERT: V 4 LEU cc_start: 0.5100 (pt) cc_final: 0.4195 (tp) REVERT: V 34 MET cc_start: 0.7974 (mmm) cc_final: 0.7558 (mmm) REVERT: V 39 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7669 (tm-30) REVERT: V 64 LYS cc_start: 0.7590 (tptt) cc_final: 0.7243 (tptp) REVERT: V 82 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7382 (mtp) REVERT: V 102 MET cc_start: 0.7368 (pmm) cc_final: 0.6828 (ptm) REVERT: G 73 ARG cc_start: 0.7116 (ttp80) cc_final: 0.6434 (ttm-80) REVERT: G 88 MET cc_start: 0.7094 (mmt) cc_final: 0.6571 (tpt) REVERT: G 100 PHE cc_start: 0.5529 (m-10) cc_final: 0.5239 (m-10) REVERT: G 143 TYR cc_start: 0.8170 (t80) cc_final: 0.7709 (t80) REVERT: G 222 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7505 (tm-30) REVERT: C 19 ARG cc_start: 0.7173 (tmt170) cc_final: 0.6643 (tmt170) REVERT: C 34 MET cc_start: 0.8637 (mmm) cc_final: 0.8103 (mmm) REVERT: C 56 ARG cc_start: 0.6764 (ptm-80) cc_final: 0.6333 (ptm-80) REVERT: C 72 ASP cc_start: 0.7252 (p0) cc_final: 0.6682 (p0) REVERT: C 81 GLN cc_start: 0.6381 (mm110) cc_final: 0.5982 (mm-40) REVERT: C 82 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.5815 (mt) REVERT: C 98 PHE cc_start: 0.7732 (m-10) cc_final: 0.7478 (m-80) REVERT: C 103 TRP cc_start: 0.8216 (m100) cc_final: 0.7843 (m100) outliers start: 57 outliers final: 44 residues processed: 320 average time/residue: 0.1261 time to fit residues: 58.7006 Evaluate side-chains 306 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 50 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 194 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 368 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 82 MET Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 PHE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 79 TYR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 43 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 163 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 ASN Y 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.159152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122377 restraints weight = 23215.615| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.00 r_work: 0.3199 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14102 Z= 0.130 Angle : 0.691 10.964 19045 Z= 0.349 Chirality : 0.045 0.197 2129 Planarity : 0.004 0.049 2444 Dihedral : 7.446 174.540 1954 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.39 % Allowed : 21.03 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.21), residues: 1719 helix: 0.95 (0.19), residues: 782 sheet: -0.71 (0.30), residues: 274 loop : -1.94 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.023 0.002 TYR V 96 PHE 0.029 0.002 PHE G 83 TRP 0.024 0.001 TRP C 103 HIS 0.011 0.001 HIS G 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (14097) covalent geometry : angle 0.69100 / 0.35 (19037) SS BOND : bond 0.00244 / 0.12 ( 3) SS BOND : angle 1.43468 / 0.78 ( 6) hydrogen bonds : bond 0.03674 / 2.39 ( 703) hydrogen bonds : angle 4.59120 / 3.29 ( 2033) Misc. bond : bond 0.00013 / 0.01 ( 1) link_TRANS : bond 0.00122 / 0.06 ( 1) link_TRANS : angle 0.30742 / 0.18 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3746.23 seconds wall clock time: 64 minutes 55.23 seconds (3895.23 seconds total)