Starting phenix.real_space_refine on Wed Mar 4 14:26:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6itc_9731/03_2026/6itc_9731.cif Found real_map, /net/cci-nas-00/data/ceres_data/6itc_9731/03_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_9731/03_2026/6itc_9731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6itc_9731/03_2026/6itc_9731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6itc_9731/03_2026/6itc_9731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6itc_9731/03_2026/6itc_9731.map" } 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-dev-5986/lib/python3.9/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: 35 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: 2.84, per 1000 atoms: 0.21 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: 0.93 Conformation dependent library (CDL) restraints added in 408.9 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: 0.42 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: 2.46 Time building geometry restraints manager: 1.20 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: 8348 35.31 - 70.62: 121 70.62 - 105.93: 4 105.93 - 141.24: 2 141.24 - 176.54: 5 Dihedral angle restraints: 8480 sinusoidal: 3474 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 8477 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.310 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 13.871 176.545 5264 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 covalent geometry : bond 0.01579 (14097) covalent geometry : angle 1.48264 (19037) SS BOND : bond 0.01768 ( 3) SS BOND : angle 2.62095 ( 6) hydrogen bonds : bond 0.13092 ( 703) hydrogen bonds : angle 7.20748 ( 2033) Misc. bond : bond 0.00102 ( 1) link_TRANS : bond 0.10153 ( 1) link_TRANS : angle 7.55383 ( 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 : 0.504 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: 0.8249 (mp) REVERT: A 543 ASP cc_start: 0.8185 (t70) cc_final: 0.7933 (t0) REVERT: A 549 PHE cc_start: 0.7942 (m-80) cc_final: 0.7605 (m-80) REVERT: A 555 MET cc_start: 0.7244 (mmt) cc_final: 0.6864 (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: 0.8023 (t80) REVERT: Y 139 MET cc_start: 0.8134 (pmt) cc_final: 0.7639 (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: 0.7095 (tptp) REVERT: V 103 SER cc_start: 0.8691 (m) cc_final: 0.8417 (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: 0.7446 (mp) REVERT: C 81 GLN cc_start: 0.6739 (mm110) cc_final: 0.6289 (mm-40) REVERT: C 98 PHE cc_start: 0.6912 (m-10) cc_final: 0.6616 (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: 0.1157 time to fit residues: 70.7474 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 : 0.484 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 157 ASN A 188 ASN A 283 HIS A 287 ASN A 297 HIS 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.159807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123797 restraints weight = 25349.319| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.73 r_work: 0.3164 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14102 Z= 0.164 Angle : 0.775 9.759 19045 Z= 0.402 Chirality : 0.048 0.322 2129 Planarity : 0.006 0.057 2444 Dihedral : 10.795 164.090 1973 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.21 % Allowed : 13.09 % Favored : 82.70 % 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: -2.71 (0.19), residues: 1719 helix: -0.99 (0.18), residues: 768 sheet: -1.77 (0.28), residues: 279 loop : -2.67 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 109 TYR 0.024 0.002 TYR V 96 PHE 0.032 0.002 PHE Y 276 TRP 0.030 0.002 TRP C 103 HIS 0.008 0.001 HIS G 181 Details of bonding type rmsd covalent geometry : bond 0.00361 (14097) covalent geometry : angle 0.77385 (19037) SS BOND : bond 0.00418 ( 3) SS BOND : angle 2.82060 ( 6) hydrogen bonds : bond 0.04732 ( 703) hydrogen bonds : angle 5.62413 ( 2033) Misc. bond : bond 0.00003 ( 1) link_TRANS : bond 0.00229 ( 1) link_TRANS : angle 0.19009 ( 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 381 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 319 time to evaluate : 0.408 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: 0.7411 (mt-10) cc_final: 0.7197 (mp0) REVERT: A 141 MET cc_start: 0.8680 (mmm) cc_final: 0.8211 (mmm) REVERT: A 427 MET cc_start: 0.8101 (ppp) cc_final: 0.7710 (ppp) REVERT: A 469 GLN cc_start: 0.8356 (pp30) cc_final: 0.8049 (pt0) REVERT: A 501 GLU cc_start: 0.8442 (mp0) cc_final: 0.7789 (mp0) REVERT: A 515 SER cc_start: 0.8943 (t) cc_final: 0.8528 (m) REVERT: A 555 MET cc_start: 0.7271 (mmt) cc_final: 0.6999 (mmm) REVERT: A 573 MET cc_start: 0.5052 (tpp) cc_final: 0.4733 (tpt) REVERT: A 601 ASP cc_start: 0.8348 (t0) cc_final: 0.7810 (t0) REVERT: A 733 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8136 (tt0) REVERT: Y 104 MET cc_start: 0.7273 (tpp) cc_final: 0.6483 (mmt) REVERT: Y 139 MET cc_start: 0.7823 (pmt) cc_final: 0.7260 (pmt) REVERT: Y 142 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6567 (pp30) REVERT: V 4 LEU cc_start: 0.6037 (tp) cc_final: 0.5795 (tp) REVERT: V 6 GLU cc_start: 0.6342 (mp0) cc_final: 0.5910 (mp0) REVERT: V 38 ARG cc_start: 0.7081 (ttm110) cc_final: 0.6408 (ttm170) REVERT: V 39 GLN cc_start: 0.7660 (pp30) cc_final: 0.6902 (tm-30) REVERT: V 64 LYS cc_start: 0.7311 (tptt) cc_final: 0.6928 (tptp) REVERT: V 94 TYR cc_start: 0.7018 (m-80) cc_final: 0.6603 (m-80) REVERT: G 16 VAL cc_start: 0.8293 (t) cc_final: 0.8073 (m) REVERT: G 88 MET cc_start: 0.6836 (mmt) cc_final: 0.6612 (tpp) REVERT: G 109 ARG cc_start: 0.6780 (tpm170) cc_final: 0.6423 (tpm170) REVERT: G 166 LYS cc_start: 0.7027 (mppt) cc_final: 0.6635 (mmtm) REVERT: G 200 TYR cc_start: 0.6165 (p90) cc_final: 0.5721 (p90) REVERT: C 34 MET cc_start: 0.8169 (mmm) cc_final: 0.7893 (mmm) REVERT: C 56 ARG cc_start: 0.6928 (ptm-80) cc_final: 0.6484 (ptm-80) REVERT: C 72 ASP cc_start: 0.7679 (p0) cc_final: 0.7265 (p0) outliers start: 62 outliers final: 29 residues processed: 355 average time/residue: 0.1097 time to fit residues: 57.3285 Evaluate side-chains 286 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 256 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 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 24 MET Chi-restraints excluded: chain Y residue 41 THR 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 62 SER Chi-restraints excluded: chain V residue 68 THR 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: 2.9990 chunk 147 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 121 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 0.0570 chunk 54 optimal weight: 4.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3939 r_free = 0.3939 target = 0.155900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120141 restraints weight = 23911.057| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.86 r_work: 0.3177 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14102 Z= 0.164 Angle : 0.716 8.670 19045 Z= 0.372 Chirality : 0.047 0.295 2129 Planarity : 0.005 0.055 2444 Dihedral : 9.806 168.304 1970 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.60 % Allowed : 15.26 % Favored : 81.14 % 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: -1.94 (0.19), residues: 1719 helix: -0.17 (0.19), residues: 765 sheet: -1.50 (0.28), residues: 296 loop : -2.47 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 109 TYR 0.024 0.002 TYR V 96 PHE 0.033 0.002 PHE Y 276 TRP 0.024 0.002 TRP C 103 HIS 0.007 0.001 HIS G 181 Details of bonding type rmsd covalent geometry : bond 0.00367 (14097) covalent geometry : angle 0.71155 (19037) SS BOND : bond 0.00682 ( 3) SS BOND : angle 4.44968 ( 6) hydrogen bonds : bond 0.04368 ( 703) hydrogen bonds : angle 5.19130 ( 2033) Misc. bond : bond 0.00007 ( 1) link_TRANS : bond 0.00005 ( 1) link_TRANS : angle 0.28822 ( 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 332 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 ILE cc_start: 0.8950 (mm) cc_final: 0.8631 (mt) REVERT: A 484 THR cc_start: 0.8303 (t) cc_final: 0.7902 (p) REVERT: A 515 SER cc_start: 0.9266 (t) cc_final: 0.8795 (m) REVERT: A 539 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8555 (mm) REVERT: A 645 ARG cc_start: 0.7790 (tmt170) cc_final: 0.7396 (tpt170) REVERT: A 702 GLN cc_start: 0.8235 (pp30) cc_final: 0.7721 (tp40) REVERT: A 733 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8275 (tt0) REVERT: A 755 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7805 (tp30) REVERT: Y 77 TYR cc_start: 0.7903 (t80) cc_final: 0.7669 (t80) REVERT: Y 104 MET cc_start: 0.7281 (tpp) cc_final: 0.6563 (mmt) REVERT: Y 142 GLN cc_start: 0.7236 (pp30) cc_final: 0.6686 (pp30) REVERT: V 38 ARG cc_start: 0.7282 (ttm170) cc_final: 0.6715 (ttm170) REVERT: V 39 GLN cc_start: 0.7619 (pp30) cc_final: 0.6950 (tm-30) REVERT: V 64 LYS cc_start: 0.7403 (tptt) cc_final: 0.7023 (tptp) REVERT: V 94 TYR cc_start: 0.6827 (m-80) cc_final: 0.6518 (m-80) REVERT: G 88 MET cc_start: 0.6960 (mmt) cc_final: 0.6539 (tpt) REVERT: G 166 LYS cc_start: 0.7098 (mppt) cc_final: 0.6528 (mmtm) REVERT: G 200 TYR cc_start: 0.6235 (p90) cc_final: 0.5848 (p90) REVERT: C 51 MET cc_start: 0.7594 (tmm) cc_final: 0.7380 (tmm) REVERT: C 56 ARG cc_start: 0.6942 (ptm-80) cc_final: 0.6526 (ptm-80) REVERT: C 72 ASP cc_start: 0.7629 (p0) cc_final: 0.7233 (p0) REVERT: C 98 PHE cc_start: 0.7539 (m-80) cc_final: 0.7289 (m-80) REVERT: C 101 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7180 (tm-30) outliers start: 53 outliers final: 31 residues processed: 310 average time/residue: 0.1035 time to fit residues: 47.7099 Evaluate side-chains 293 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 260 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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 A residue 755 GLU 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 188 VAL Chi-restraints excluded: chain Y residue 305 ASP Chi-restraints excluded: chain Y residue 368 THR 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 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 C residue 30 ASN 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: 9.9990 chunk 51 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 383 ASN Y 101 GLN Y 142 GLN Y 177 ASN E 6 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.153614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117736 restraints weight = 23478.718| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.90 r_work: 0.3149 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 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 = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14102 Z= 0.195 Angle : 0.719 8.785 19045 Z= 0.373 Chirality : 0.048 0.273 2129 Planarity : 0.005 0.056 2444 Dihedral : 9.248 171.836 1970 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.82 % Allowed : 16.21 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.58 (0.20), residues: 1719 helix: 0.14 (0.19), residues: 770 sheet: -1.43 (0.28), residues: 291 loop : -2.25 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 122 TYR 0.028 0.002 TYR V 96 PHE 0.039 0.002 PHE Y 276 TRP 0.042 0.002 TRP C 103 HIS 0.007 0.001 HIS G 181 Details of bonding type rmsd covalent geometry : bond 0.00447 (14097) covalent geometry : angle 0.71750 (19037) SS BOND : bond 0.00841 ( 3) SS BOND : angle 2.88347 ( 6) hydrogen bonds : bond 0.04370 ( 703) hydrogen bonds : angle 5.02257 ( 2033) Misc. bond : bond 0.00005 ( 1) link_TRANS : bond 0.00070 ( 1) link_TRANS : angle 0.29208 ( 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 349 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 278 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8341 (mp) REVERT: A 467 GLU cc_start: 0.8717 (pp20) cc_final: 0.8256 (pt0) REVERT: A 573 MET cc_start: 0.5149 (tpp) cc_final: 0.4811 (tpt) REVERT: A 645 ARG cc_start: 0.7959 (tmt170) cc_final: 0.7589 (tpt170) REVERT: A 680 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6536 (tt0) REVERT: A 702 GLN cc_start: 0.8145 (pp30) cc_final: 0.7710 (tp40) REVERT: A 729 ASP cc_start: 0.8930 (t70) cc_final: 0.8051 (m-30) REVERT: A 733 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8509 (tt0) REVERT: A 755 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8110 (tp30) REVERT: Y 101 GLN cc_start: 0.5317 (OUTLIER) cc_final: 0.5061 (pp30) REVERT: Y 104 MET cc_start: 0.7373 (tpp) cc_final: 0.6551 (mmt) REVERT: Y 301 ARG cc_start: 0.8378 (mtm110) cc_final: 0.8115 (mtm-85) REVERT: Y 312 MET cc_start: 0.7003 (mtm) cc_final: 0.6722 (tpp) REVERT: Y 335 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7975 (tm-30) REVERT: Y 417 GLU cc_start: 0.8592 (pp20) cc_final: 0.8373 (pp20) REVERT: V 4 LEU cc_start: 0.6050 (tp) cc_final: 0.5838 (tp) REVERT: V 38 ARG cc_start: 0.7304 (ttm170) cc_final: 0.7047 (ttm170) REVERT: V 39 GLN cc_start: 0.7523 (pp30) cc_final: 0.7267 (tm-30) REVERT: V 64 LYS cc_start: 0.7562 (tptt) cc_final: 0.7186 (tptp) REVERT: V 102 MET cc_start: 0.7173 (pmm) cc_final: 0.6957 (pmm) REVERT: V 109 GLN cc_start: 0.6045 (pm20) cc_final: 0.5816 (pp30) REVERT: G 88 MET cc_start: 0.6861 (mmt) cc_final: 0.6640 (mmt) REVERT: G 123 ILE cc_start: 0.7922 (mp) cc_final: 0.7520 (mp) REVERT: G 200 TYR cc_start: 0.6202 (p90) cc_final: 0.5841 (p90) REVERT: C 51 MET cc_start: 0.7511 (tmm) cc_final: 0.7296 (tmm) REVERT: C 56 ARG cc_start: 0.6914 (ptm-80) cc_final: 0.6346 (ptm-80) REVERT: C 91 TYR cc_start: 0.7593 (m-10) cc_final: 0.7321 (m-10) REVERT: C 101 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7242 (tm-30) REVERT: C 103 TRP cc_start: 0.7607 (m100) cc_final: 0.7406 (m100) outliers start: 71 outliers final: 48 residues processed: 326 average time/residue: 0.1128 time to fit residues: 53.9604 Evaluate side-chains 298 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 247 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 39 ASP 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 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 545 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 A residue 755 GLU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 18 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 101 GLN Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 199 TYR Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 278 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 E residue 12 VAL Chi-restraints excluded: chain E residue 56 ARG 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 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 69 ILE Chi-restraints excluded: chain C residue 78 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 163 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 161 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3937 r_free = 0.3937 target = 0.155841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120694 restraints weight = 30252.832| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 4.52 r_work: 0.3085 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4693 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= 0.140 Angle : 0.669 8.308 19045 Z= 0.343 Chirality : 0.045 0.249 2129 Planarity : 0.004 0.058 2444 Dihedral : 8.755 171.923 1970 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.93 % Allowed : 18.59 % Favored : 77.48 % 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: 0.46 (0.19), residues: 778 sheet: -1.22 (0.29), residues: 286 loop : -2.22 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 50 TYR 0.027 0.002 TYR Y 77 PHE 0.027 0.002 PHE Y 276 TRP 0.021 0.001 TRP C 103 HIS 0.008 0.001 HIS G 181 Details of bonding type rmsd covalent geometry : bond 0.00314 (14097) covalent geometry : angle 0.66861 (19037) SS BOND : bond 0.00790 ( 3) SS BOND : angle 1.94819 ( 6) hydrogen bonds : bond 0.04022 ( 703) hydrogen bonds : angle 4.86291 ( 2033) Misc. bond : bond 0.00003 ( 1) link_TRANS : bond 0.00152 ( 1) link_TRANS : angle 0.19024 ( 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 337 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 279 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.8360 (ptp) cc_final: 0.8071 (ptp) REVERT: A 543 ASP cc_start: 0.8475 (t70) cc_final: 0.8248 (t0) REVERT: A 573 MET cc_start: 0.5187 (tpp) cc_final: 0.4904 (tpt) REVERT: A 631 ILE cc_start: 0.8857 (mt) cc_final: 0.8537 (mt) REVERT: A 645 ARG cc_start: 0.7985 (tmt170) cc_final: 0.7555 (tpt170) REVERT: A 653 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8291 (mmmt) REVERT: A 659 ASP cc_start: 0.8202 (t70) cc_final: 0.7887 (t0) REVERT: A 680 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6548 (tt0) REVERT: A 702 GLN cc_start: 0.8273 (pp30) cc_final: 0.7524 (tp40) REVERT: A 729 ASP cc_start: 0.9001 (t70) cc_final: 0.8103 (m-30) REVERT: A 733 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8600 (tt0) REVERT: A 735 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8487 (ttt-90) REVERT: A 755 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8202 (tp30) REVERT: Y 9 MET cc_start: 0.6740 (mmt) cc_final: 0.6293 (mmt) REVERT: Y 101 GLN cc_start: 0.5379 (OUTLIER) cc_final: 0.4959 (pp30) REVERT: Y 104 MET cc_start: 0.7496 (tpp) cc_final: 0.6410 (mmt) REVERT: Y 301 ARG cc_start: 0.8372 (mtm110) cc_final: 0.8106 (mtm-85) REVERT: Y 312 MET cc_start: 0.7166 (mtm) cc_final: 0.6873 (tpp) REVERT: Y 335 GLN cc_start: 0.8289 (tm-30) cc_final: 0.8033 (tm-30) REVERT: Y 417 GLU cc_start: 0.8614 (pp20) cc_final: 0.8337 (pp20) REVERT: V 64 LYS cc_start: 0.7534 (tptt) cc_final: 0.7022 (tptp) REVERT: G 73 ARG cc_start: 0.6827 (ttp80) cc_final: 0.6174 (ttm-80) REVERT: G 88 MET cc_start: 0.6936 (mmt) cc_final: 0.6564 (tpt) REVERT: G 143 TYR cc_start: 0.8334 (t80) cc_final: 0.7872 (t80) REVERT: G 200 TYR cc_start: 0.6208 (p90) cc_final: 0.5849 (p90) REVERT: G 222 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7486 (tm-30) REVERT: C 56 ARG cc_start: 0.6887 (ptm-80) cc_final: 0.6248 (ptm-80) REVERT: C 81 GLN cc_start: 0.6423 (mm110) cc_final: 0.5944 (mm-40) outliers start: 58 outliers final: 43 residues processed: 320 average time/residue: 0.1221 time to fit residues: 56.2873 Evaluate side-chains 304 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 258 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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 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 557 MET Chi-restraints excluded: chain A residue 597 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 A residue 735 ARG Chi-restraints excluded: chain A residue 755 GLU 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 101 GLN Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 199 TYR 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 78 VAL 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 78 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 126 optimal weight: 8.9990 chunk 99 optimal weight: 0.0030 chunk 18 optimal weight: 0.0970 chunk 109 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 10 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 383 ASN Y 101 GLN B 57 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.158274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121982 restraints weight = 25954.407| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.31 r_work: 0.3181 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 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 = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14102 Z= 0.122 Angle : 0.659 8.569 19045 Z= 0.338 Chirality : 0.045 0.234 2129 Planarity : 0.004 0.054 2444 Dihedral : 8.308 170.919 1970 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.87 % Allowed : 19.81 % Favored : 76.32 % 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: -0.99 (0.21), residues: 1719 helix: 0.69 (0.19), residues: 784 sheet: -0.99 (0.29), residues: 286 loop : -2.17 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 248 TYR 0.029 0.001 TYR Y 77 PHE 0.030 0.001 PHE G 83 TRP 0.040 0.002 TRP C 103 HIS 0.007 0.001 HIS G 181 Details of bonding type rmsd covalent geometry : bond 0.00256 (14097) covalent geometry : angle 0.65877 (19037) SS BOND : bond 0.00153 ( 3) SS BOND : angle 1.66477 ( 6) hydrogen bonds : bond 0.03758 ( 703) hydrogen bonds : angle 4.73736 ( 2033) Misc. bond : bond 0.00000 ( 1) link_TRANS : bond 0.00084 ( 1) link_TRANS : angle 0.12770 ( 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 340 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 283 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8231 (mp) REVERT: A 300 MET cc_start: 0.8259 (ptp) cc_final: 0.7994 (ptp) REVERT: A 403 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.7774 (mtt90) REVERT: A 405 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: A 573 MET cc_start: 0.4965 (tpp) cc_final: 0.4726 (tpt) REVERT: A 631 ILE cc_start: 0.8781 (mt) cc_final: 0.8472 (mt) REVERT: A 645 ARG cc_start: 0.7933 (tmt170) cc_final: 0.7610 (tpt170) REVERT: A 653 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8299 (mmmt) REVERT: A 680 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6673 (tt0) REVERT: A 702 GLN cc_start: 0.8102 (pp30) cc_final: 0.7687 (tp40) REVERT: A 729 ASP cc_start: 0.8916 (t70) cc_final: 0.8071 (m-30) REVERT: A 733 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8526 (tt0) REVERT: Y 9 MET cc_start: 0.6734 (mmt) cc_final: 0.6395 (mmt) REVERT: Y 101 GLN cc_start: 0.5175 (OUTLIER) cc_final: 0.4639 (pp30) REVERT: Y 104 MET cc_start: 0.7568 (tpp) cc_final: 0.6582 (mmt) REVERT: Y 139 MET cc_start: 0.7898 (pmm) cc_final: 0.7436 (pmm) REVERT: Y 301 ARG cc_start: 0.8303 (mtm110) cc_final: 0.8055 (mtm-85) REVERT: Y 312 MET cc_start: 0.7038 (mtm) cc_final: 0.6837 (tpp) REVERT: Y 335 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7968 (tm-30) REVERT: Y 417 GLU cc_start: 0.8566 (pp20) cc_final: 0.8270 (pp20) REVERT: E 13 ARG cc_start: 0.8731 (ttm-80) cc_final: 0.8407 (ttp-110) REVERT: E 16 LYS cc_start: 0.8429 (mttm) cc_final: 0.7775 (mmmt) REVERT: V 39 GLN cc_start: 0.7504 (tm-30) cc_final: 0.7076 (tm-30) REVERT: V 94 TYR cc_start: 0.7160 (m-80) cc_final: 0.6924 (m-80) REVERT: G 88 MET cc_start: 0.6849 (mmt) cc_final: 0.6432 (tpt) REVERT: G 143 TYR cc_start: 0.8270 (t80) cc_final: 0.7859 (t80) REVERT: G 200 TYR cc_start: 0.6223 (p90) cc_final: 0.5889 (p90) REVERT: G 222 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7319 (tm-30) REVERT: C 56 ARG cc_start: 0.6805 (ptm-80) cc_final: 0.6190 (ptm-80) REVERT: C 81 GLN cc_start: 0.6403 (mm110) cc_final: 0.6046 (mm-40) REVERT: C 101 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7242 (tm-30) REVERT: C 103 TRP cc_start: 0.7827 (m100) cc_final: 0.7314 (m100) outliers start: 57 outliers final: 41 residues processed: 324 average time/residue: 0.1119 time to fit residues: 53.2026 Evaluate side-chains 300 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 394 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 405 ASP 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 557 MET Chi-restraints excluded: chain A residue 602 VAL 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 24 MET Chi-restraints excluded: chain Y residue 101 GLN Chi-restraints excluded: chain Y residue 188 VAL 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 68 THR Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER 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 78 VAL 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: 9.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN Y 40 ASN Y 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.153186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116704 restraints weight = 23362.019| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.10 r_work: 0.3118 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14102 Z= 0.181 Angle : 0.704 12.723 19045 Z= 0.360 Chirality : 0.047 0.226 2129 Planarity : 0.005 0.046 2444 Dihedral : 8.269 171.410 1970 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.48 % Allowed : 19.13 % Favored : 76.39 % 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: 0.61 (0.19), residues: 785 sheet: -0.94 (0.29), residues: 288 loop : -2.14 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 70 TYR 0.033 0.002 TYR Y 77 PHE 0.034 0.002 PHE Y 276 TRP 0.031 0.002 TRP C 103 HIS 0.006 0.001 HIS G 181 Details of bonding type rmsd covalent geometry : bond 0.00422 (14097) covalent geometry : angle 0.70254 (19037) SS BOND : bond 0.00322 ( 3) SS BOND : angle 2.26011 ( 6) hydrogen bonds : bond 0.04107 ( 703) hydrogen bonds : angle 4.76986 ( 2033) Misc. bond : bond 0.00001 ( 1) link_TRANS : bond 0.00136 ( 1) link_TRANS : angle 0.29464 ( 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 330 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 264 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8162 (mp) REVERT: A 254 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8981 (mp) REVERT: A 403 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.7863 (mtt90) REVERT: A 405 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8003 (m-30) REVERT: A 573 MET cc_start: 0.5536 (tpp) cc_final: 0.5282 (tpt) REVERT: A 645 ARG cc_start: 0.8015 (tmt170) cc_final: 0.7643 (tpt170) REVERT: A 729 ASP cc_start: 0.9002 (t70) cc_final: 0.8696 (t70) REVERT: A 733 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8574 (tt0) REVERT: A 735 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8524 (ttt-90) REVERT: Y 9 MET cc_start: 0.6717 (mmt) cc_final: 0.6380 (mmt) REVERT: Y 50 LEU cc_start: 0.4651 (OUTLIER) cc_final: 0.4314 (mt) REVERT: Y 101 GLN cc_start: 0.5356 (OUTLIER) cc_final: 0.4895 (pp30) REVERT: Y 139 MET cc_start: 0.7936 (pmm) cc_final: 0.7424 (pmm) REVERT: Y 301 ARG cc_start: 0.8358 (mtm110) cc_final: 0.8104 (mtm-85) REVERT: Y 312 MET cc_start: 0.7075 (mtm) cc_final: 0.6844 (tpp) REVERT: Y 335 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7996 (tm-30) REVERT: Y 417 GLU cc_start: 0.8583 (pp20) cc_final: 0.8289 (pp20) REVERT: E 13 ARG cc_start: 0.8716 (ttm-80) cc_final: 0.8397 (ttp-110) REVERT: E 16 LYS cc_start: 0.8488 (mttm) cc_final: 0.7812 (mmmt) REVERT: V 50 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7532 (tpt-90) REVERT: V 64 LYS cc_start: 0.7568 (tptt) cc_final: 0.7095 (tptp) REVERT: V 82 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7385 (mtp) REVERT: G 73 ARG cc_start: 0.7091 (ttp80) cc_final: 0.6386 (ttm-80) REVERT: G 88 MET cc_start: 0.6807 (mmt) cc_final: 0.6399 (tpt) REVERT: G 143 TYR cc_start: 0.8205 (t80) cc_final: 0.7722 (t80) REVERT: G 200 TYR cc_start: 0.6113 (p90) cc_final: 0.5845 (p90) REVERT: G 222 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7385 (tm-30) REVERT: C 56 ARG cc_start: 0.6833 (ptm-80) cc_final: 0.6215 (ptm-80) REVERT: C 81 GLN cc_start: 0.6408 (mm110) cc_final: 0.5988 (mm-40) REVERT: C 101 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7349 (tm-30) REVERT: C 103 TRP cc_start: 0.7965 (m100) cc_final: 0.7544 (m100) outliers start: 66 outliers final: 50 residues processed: 309 average time/residue: 0.1164 time to fit residues: 52.2480 Evaluate side-chains 311 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 254 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 254 ILE 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 394 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 405 ASP 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 555 MET 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 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 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 50 LEU Chi-restraints excluded: chain Y residue 67 PHE Chi-restraints excluded: chain Y residue 101 GLN Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 188 VAL Chi-restraints excluded: chain Y residue 199 TYR 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 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 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 78 VAL 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: 3.9990 chunk 97 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 0.0770 chunk 95 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 383 ASN 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 = 0.3921 r_free = 0.3921 target = 0.154243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118093 restraints weight = 23924.302| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.16 r_work: 0.3132 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 61 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.5385 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= 0.152 Angle : 0.700 11.399 19045 Z= 0.356 Chirality : 0.046 0.218 2129 Planarity : 0.004 0.047 2444 Dihedral : 8.090 171.736 1970 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.00 % Allowed : 20.22 % Favored : 75.78 % 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: -0.85 (0.21), residues: 1719 helix: 0.74 (0.19), residues: 775 sheet: -0.66 (0.30), residues: 277 loop : -2.10 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 70 TYR 0.026 0.002 TYR Y 77 PHE 0.029 0.002 PHE Y 276 TRP 0.026 0.001 TRP C 103 HIS 0.009 0.001 HIS G 181 Details of bonding type rmsd covalent geometry : bond 0.00350 (14097) covalent geometry : angle 0.69937 (19037) SS BOND : bond 0.00221 ( 3) SS BOND : angle 1.97408 ( 6) hydrogen bonds : bond 0.03920 ( 703) hydrogen bonds : angle 4.68613 ( 2033) Misc. bond : bond 0.00007 ( 1) link_TRANS : bond 0.00106 ( 1) link_TRANS : angle 0.25481 ( 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 314 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 255 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8221 (mp) REVERT: A 157 ASN cc_start: 0.8282 (t0) cc_final: 0.7941 (t0) REVERT: A 254 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8937 (mp) REVERT: A 403 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.7861 (mtt90) REVERT: A 405 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: A 443 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7704 (tm-30) REVERT: A 573 MET cc_start: 0.5586 (tpp) cc_final: 0.5350 (tpt) REVERT: A 645 ARG cc_start: 0.7930 (tmt170) cc_final: 0.7620 (tpt170) REVERT: A 729 ASP cc_start: 0.8936 (t70) cc_final: 0.8182 (m-30) REVERT: A 733 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8648 (tt0) REVERT: A 735 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8507 (ttt-90) REVERT: Y 50 LEU cc_start: 0.4662 (OUTLIER) cc_final: 0.4234 (mt) REVERT: Y 101 GLN cc_start: 0.5359 (OUTLIER) cc_final: 0.5050 (pp30) REVERT: Y 139 MET cc_start: 0.8123 (pmm) cc_final: 0.7631 (pmm) REVERT: Y 301 ARG cc_start: 0.8331 (mtm110) cc_final: 0.8104 (mtm-85) REVERT: Y 312 MET cc_start: 0.7088 (mtm) cc_final: 0.6859 (tpp) REVERT: Y 335 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7995 (tm-30) REVERT: Y 417 GLU cc_start: 0.8513 (pp20) cc_final: 0.8238 (pp20) REVERT: E 16 LYS cc_start: 0.8420 (mttm) cc_final: 0.7780 (mmmt) REVERT: V 34 MET cc_start: 0.7776 (mmm) cc_final: 0.7480 (mmm) REVERT: V 59 TYR cc_start: 0.8263 (m-80) cc_final: 0.7997 (m-80) REVERT: V 64 LYS cc_start: 0.7523 (tptt) cc_final: 0.7046 (tptp) REVERT: G 73 ARG cc_start: 0.7129 (ttp80) cc_final: 0.6449 (ttm-80) REVERT: G 88 MET cc_start: 0.6869 (mmt) cc_final: 0.6457 (tpt) REVERT: G 143 TYR cc_start: 0.8187 (t80) cc_final: 0.7782 (t80) REVERT: G 200 TYR cc_start: 0.6158 (p90) cc_final: 0.5904 (p90) REVERT: G 222 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7420 (tm-30) REVERT: C 56 ARG cc_start: 0.6797 (ptm-80) cc_final: 0.6186 (ptm-80) REVERT: C 81 GLN cc_start: 0.6380 (mm110) cc_final: 0.5961 (mm-40) REVERT: C 101 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7445 (tm-30) REVERT: C 103 TRP cc_start: 0.8009 (m100) cc_final: 0.7657 (m100) outliers start: 59 outliers final: 49 residues processed: 296 average time/residue: 0.1157 time to fit residues: 49.7863 Evaluate side-chains 305 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 250 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 254 ILE 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 394 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 405 ASP 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 557 MET Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 602 VAL 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 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 50 LEU Chi-restraints excluded: chain Y residue 67 PHE Chi-restraints excluded: chain Y residue 101 GLN Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 188 VAL 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 68 THR Chi-restraints excluded: chain V residue 76 ASN Chi-restraints excluded: chain V residue 78 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 18 LEU 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 78 VAL 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: 0.0980 chunk 139 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS A 383 ASN Y 101 GLN V 39 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 = 0.3937 r_free = 0.3937 target = 0.155603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111852 restraints weight = 32615.610| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.91 r_work: 0.3152 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5541 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= 0.135 Angle : 0.686 11.257 19045 Z= 0.348 Chirality : 0.045 0.211 2129 Planarity : 0.004 0.043 2444 Dihedral : 7.842 171.087 1970 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.80 % Allowed : 20.62 % 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: -0.75 (0.21), residues: 1719 helix: 0.82 (0.19), residues: 782 sheet: -0.51 (0.31), residues: 275 loop : -2.12 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 19 TYR 0.027 0.001 TYR Y 77 PHE 0.026 0.001 PHE Y 276 TRP 0.024 0.002 TRP C 103 HIS 0.009 0.001 HIS G 181 Details of bonding type rmsd covalent geometry : bond 0.00301 (14097) covalent geometry : angle 0.68497 (19037) SS BOND : bond 0.00187 ( 3) SS BOND : angle 1.80306 ( 6) hydrogen bonds : bond 0.03770 ( 703) hydrogen bonds : angle 4.63637 ( 2033) Misc. bond : bond 0.00006 ( 1) link_TRANS : bond 0.00105 ( 1) link_TRANS : angle 0.29068 ( 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 316 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 260 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8200 (mp) REVERT: A 99 GLU cc_start: 0.7576 (tt0) cc_final: 0.7169 (tt0) REVERT: A 300 MET cc_start: 0.8087 (ptp) cc_final: 0.7675 (ptp) REVERT: A 403 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.7840 (mtt90) REVERT: A 573 MET cc_start: 0.5579 (tpp) cc_final: 0.5367 (tpt) REVERT: A 645 ARG cc_start: 0.7899 (tmt170) cc_final: 0.7612 (tpt170) REVERT: A 729 ASP cc_start: 0.8920 (t70) cc_final: 0.8159 (m-30) REVERT: A 733 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8627 (tt0) REVERT: A 735 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8471 (ttt-90) REVERT: Y 50 LEU cc_start: 0.4568 (OUTLIER) cc_final: 0.4280 (mt) REVERT: Y 101 GLN cc_start: 0.5305 (OUTLIER) cc_final: 0.5052 (pp30) REVERT: Y 139 MET cc_start: 0.8090 (pmm) cc_final: 0.7673 (pmm) REVERT: Y 301 ARG cc_start: 0.8297 (mtm110) cc_final: 0.8039 (mtm-85) REVERT: Y 335 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7969 (tm-30) REVERT: Y 417 GLU cc_start: 0.8477 (pp20) cc_final: 0.8165 (pp20) REVERT: E 13 ARG cc_start: 0.8714 (ttm-80) cc_final: 0.8390 (ttp-110) REVERT: E 16 LYS cc_start: 0.8405 (mttm) cc_final: 0.7772 (mmmt) REVERT: V 19 ARG cc_start: 0.6765 (tpp80) cc_final: 0.6557 (tpp80) REVERT: V 34 MET cc_start: 0.7759 (mmm) cc_final: 0.7423 (mmm) REVERT: V 64 LYS cc_start: 0.7515 (tptt) cc_final: 0.7021 (tptp) REVERT: V 82 MET cc_start: 0.7666 (mtm) cc_final: 0.7436 (mtp) REVERT: G 73 ARG cc_start: 0.7103 (ttp80) cc_final: 0.6417 (ttm-80) REVERT: G 88 MET cc_start: 0.6836 (mmt) cc_final: 0.6444 (tpt) REVERT: G 143 TYR cc_start: 0.8200 (t80) cc_final: 0.7850 (t80) REVERT: G 200 TYR cc_start: 0.6171 (p90) cc_final: 0.5908 (p90) REVERT: G 222 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7336 (tm-30) REVERT: C 56 ARG cc_start: 0.6769 (ptm-80) cc_final: 0.6396 (ptm-80) REVERT: C 81 GLN cc_start: 0.6455 (mm110) cc_final: 0.6027 (mm-40) REVERT: C 82 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5281 (mt) REVERT: C 101 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7354 (tm-30) REVERT: C 103 TRP cc_start: 0.8025 (m100) cc_final: 0.7646 (m100) outliers start: 56 outliers final: 46 residues processed: 298 average time/residue: 0.1188 time to fit residues: 51.1909 Evaluate side-chains 302 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 251 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 350 MET 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 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 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 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 67 PHE Chi-restraints excluded: chain Y residue 101 GLN Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 188 VAL 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 39 GLN 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 101 VAL Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 64 PHE Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 82 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 138 optimal weight: 0.0020 chunk 149 optimal weight: 20.0000 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 383 ASN Y 66 ASN Y 101 GLN Y 387 ASN V 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.154834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.119793 restraints weight = 30262.305| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 4.66 r_work: 0.3060 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14102 Z= 0.151 Angle : 0.690 11.203 19045 Z= 0.351 Chirality : 0.046 0.206 2129 Planarity : 0.004 0.069 2444 Dihedral : 7.758 170.780 1970 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.87 % Allowed : 20.90 % Favored : 75.24 % 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: -0.75 (0.21), residues: 1719 helix: 0.82 (0.19), residues: 782 sheet: -0.47 (0.31), residues: 275 loop : -2.14 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.022 0.002 TYR Y 130 PHE 0.029 0.002 PHE Y 276 TRP 0.025 0.001 TRP C 103 HIS 0.008 0.001 HIS G 181 Details of bonding type rmsd covalent geometry : bond 0.00346 (14097) covalent geometry : angle 0.68896 (19037) SS BOND : bond 0.00235 ( 3) SS BOND : angle 1.91286 ( 6) hydrogen bonds : bond 0.03827 ( 703) hydrogen bonds : angle 4.63391 ( 2033) Misc. bond : bond 0.00004 ( 1) link_TRANS : bond 0.00115 ( 1) link_TRANS : angle 0.30948 ( 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 316 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 259 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8208 (mp) REVERT: A 99 GLU cc_start: 0.7784 (tt0) cc_final: 0.7414 (tt0) REVERT: A 300 MET cc_start: 0.8175 (ptp) cc_final: 0.7773 (ptp) REVERT: A 403 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.7755 (mmm-85) REVERT: A 481 THR cc_start: 0.9515 (OUTLIER) cc_final: 0.9198 (p) REVERT: A 573 MET cc_start: 0.5725 (tpp) cc_final: 0.5497 (tpt) REVERT: A 600 ASP cc_start: 0.8359 (m-30) cc_final: 0.7526 (t70) REVERT: A 645 ARG cc_start: 0.7933 (tmt170) cc_final: 0.7609 (tpt170) REVERT: A 729 ASP cc_start: 0.9072 (t70) cc_final: 0.8331 (m-30) REVERT: A 733 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8715 (tt0) REVERT: Y 50 LEU cc_start: 0.4572 (OUTLIER) cc_final: 0.4275 (mt) REVERT: Y 139 MET cc_start: 0.8161 (pmm) cc_final: 0.7694 (pmm) REVERT: Y 301 ARG cc_start: 0.8430 (mtm110) cc_final: 0.8143 (mtm-85) REVERT: Y 335 GLN cc_start: 0.8312 (tm-30) cc_final: 0.8062 (tm-30) REVERT: Y 417 GLU cc_start: 0.8571 (pp20) cc_final: 0.8265 (pp20) REVERT: E 16 LYS cc_start: 0.8452 (mttm) cc_final: 0.7807 (mmmt) REVERT: V 19 ARG cc_start: 0.6675 (tpp80) cc_final: 0.6345 (tpp80) REVERT: V 34 MET cc_start: 0.7835 (mmm) cc_final: 0.7523 (mmm) REVERT: V 64 LYS cc_start: 0.7561 (tptt) cc_final: 0.7097 (tptp) REVERT: G 73 ARG cc_start: 0.7170 (ttp80) cc_final: 0.6505 (ttt180) REVERT: G 88 MET cc_start: 0.6906 (mmt) cc_final: 0.6479 (tpt) REVERT: G 143 TYR cc_start: 0.8170 (t80) cc_final: 0.7893 (t80) REVERT: G 200 TYR cc_start: 0.6171 (p90) cc_final: 0.5920 (p90) REVERT: G 222 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7507 (tm-30) REVERT: C 56 ARG cc_start: 0.6832 (ptm-80) cc_final: 0.6453 (ptm-80) REVERT: C 81 GLN cc_start: 0.6432 (mm110) cc_final: 0.5995 (mm-40) REVERT: C 82 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5448 (mt) REVERT: C 103 TRP cc_start: 0.8148 (m100) cc_final: 0.7796 (m100) outliers start: 57 outliers final: 47 residues processed: 298 average time/residue: 0.1221 time to fit residues: 52.3445 Evaluate side-chains 306 residues out of total 1473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 350 MET 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 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 557 MET 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 21 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 228 ILE Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Y residue 413 MET Chi-restraints excluded: chain V residue 39 GLN 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 101 VAL Chi-restraints excluded: chain V residue 114 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 82 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 43 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 153 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 383 ASN Y 101 GLN V 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.154277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118082 restraints weight = 23279.191| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.09 r_work: 0.3136 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5704 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= 0.159 Angle : 0.696 11.214 19045 Z= 0.354 Chirality : 0.046 0.202 2129 Planarity : 0.004 0.065 2444 Dihedral : 7.706 170.604 1970 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.21 % Allowed : 20.90 % Favored : 74.90 % 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: -0.74 (0.21), residues: 1719 helix: 0.83 (0.19), residues: 781 sheet: -0.44 (0.31), residues: 276 loop : -2.14 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 70 TYR 0.022 0.002 TYR Y 130 PHE 0.030 0.002 PHE Y 276 TRP 0.026 0.002 TRP C 103 HIS 0.014 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00370 (14097) covalent geometry : angle 0.69556 (19037) SS BOND : bond 0.00283 ( 3) SS BOND : angle 1.98827 ( 6) hydrogen bonds : bond 0.03880 ( 703) hydrogen bonds : angle 4.62659 ( 2033) Misc. bond : bond 0.00003 ( 1) link_TRANS : bond 0.00126 ( 1) link_TRANS : angle 0.31611 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3455.33 seconds wall clock time: 59 minutes 46.13 seconds (3586.13 seconds total)