Starting phenix.real_space_refine on Fri Aug 7 05:50:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oa3_70273/08_2026/9oa3_70273.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oa3_70273/08_2026/9oa3_70273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oa3_70273/08_2026/9oa3_70273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oa3_70273/08_2026/9oa3_70273.map" model { file = "/net/cci-nas-00/data/ceres_data/9oa3_70273/08_2026/9oa3_70273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oa3_70273/08_2026/9oa3_70273.cif" } resolution = 3.02 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 4 5.21 5 S 60 5.16 5 C 12192 2.51 5 N 3448 2.21 5 O 3472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19176 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4793 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 35, 'TRANS': 576} Chain breaks: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.69, per 1000 atoms: 0.24 Number of scatterers: 19176 At special positions: 0 Unit cell: (149.46, 149.46, 87.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 Mg 4 11.99 O 3472 8.00 N 3448 7.00 C 12192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 825.1 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 16 sheets defined 43.8% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 Processing helix chain 'A' and resid 75 through 83 Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 197 through 203 removed outlier: 3.533A pdb=" N GLN A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.708A pdb=" N ALA A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 259 removed outlier: 3.505A pdb=" N THR A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.940A pdb=" N ILE A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 381 through 393 removed outlier: 3.745A pdb=" N GLU A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 removed outlier: 4.053A pdb=" N ASP A 418 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 436 removed outlier: 4.238A pdb=" N PHE A 423 " --> pdb=" O TRP A 419 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 457 removed outlier: 3.660A pdb=" N ASN A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 474 Processing helix chain 'A' and resid 475 through 478 removed outlier: 5.354A pdb=" N GLU A 478 " --> pdb=" O ALA A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 486 through 496 removed outlier: 3.815A pdb=" N LYS A 496 " --> pdb=" O HIS A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 removed outlier: 6.856A pdb=" N ASP A 500 " --> pdb=" O GLN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 528 through 543 removed outlier: 3.960A pdb=" N VAL A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS A 540 " --> pdb=" O LYS A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 552 removed outlier: 3.505A pdb=" N HIS A 550 " --> pdb=" O HIS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 589 through 626 Proline residue: A 612 - end of helix Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 75 through 83 Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 197 through 203 removed outlier: 3.533A pdb=" N GLN B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 220 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.707A pdb=" N ALA B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 259 removed outlier: 3.505A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 removed outlier: 3.939A pdb=" N ILE B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 Processing helix chain 'B' and resid 381 through 393 removed outlier: 3.744A pdb=" N GLU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 removed outlier: 4.053A pdb=" N ASP B 418 " --> pdb=" O ASP B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 436 removed outlier: 4.237A pdb=" N PHE B 423 " --> pdb=" O TRP B 419 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 457 removed outlier: 3.661A pdb=" N ASN B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 474 Processing helix chain 'B' and resid 475 through 478 removed outlier: 5.355A pdb=" N GLU B 478 " --> pdb=" O ALA B 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 475 through 478' Processing helix chain 'B' and resid 479 through 484 Processing helix chain 'B' and resid 486 through 496 removed outlier: 3.816A pdb=" N LYS B 496 " --> pdb=" O HIS B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 501 removed outlier: 6.857A pdb=" N ASP B 500 " --> pdb=" O GLN B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 Processing helix chain 'B' and resid 528 through 543 removed outlier: 3.960A pdb=" N VAL B 532 " --> pdb=" O ILE B 528 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS B 540 " --> pdb=" O LYS B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 552 removed outlier: 3.505A pdb=" N HIS B 550 " --> pdb=" O HIS B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 589 through 626 Proline residue: B 612 - end of helix Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'C' and resid 34 through 38 Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 197 through 203 removed outlier: 3.533A pdb=" N GLN C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.708A pdb=" N ALA C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 259 removed outlier: 3.505A pdb=" N THR C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.940A pdb=" N ILE C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 279 " --> pdb=" O PRO C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 Processing helix chain 'C' and resid 381 through 393 removed outlier: 3.744A pdb=" N GLU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 4.053A pdb=" N ASP C 418 " --> pdb=" O ASP C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 436 removed outlier: 4.237A pdb=" N PHE C 423 " --> pdb=" O TRP C 419 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 457 removed outlier: 3.660A pdb=" N ASN C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 474 Processing helix chain 'C' and resid 475 through 478 removed outlier: 5.355A pdb=" N GLU C 478 " --> pdb=" O ALA C 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 475 through 478' Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'C' and resid 486 through 496 removed outlier: 3.815A pdb=" N LYS C 496 " --> pdb=" O HIS C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 501 removed outlier: 6.856A pdb=" N ASP C 500 " --> pdb=" O GLN C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 510 Processing helix chain 'C' and resid 528 through 543 removed outlier: 3.960A pdb=" N VAL C 532 " --> pdb=" O ILE C 528 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS C 540 " --> pdb=" O LYS C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 552 removed outlier: 3.505A pdb=" N HIS C 550 " --> pdb=" O HIS C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 568 Processing helix chain 'C' and resid 589 through 626 Proline residue: C 612 - end of helix Proline residue: C 623 - end of helix Processing helix chain 'C' and resid 627 through 636 Processing helix chain 'D' and resid 34 through 38 Processing helix chain 'D' and resid 75 through 83 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 197 through 203 removed outlier: 3.533A pdb=" N GLN D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 220 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.708A pdb=" N ALA D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 259 removed outlier: 3.505A pdb=" N THR D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 287 removed outlier: 3.940A pdb=" N ILE D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 279 " --> pdb=" O PRO D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 Processing helix chain 'D' and resid 381 through 393 removed outlier: 3.744A pdb=" N GLU D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 418 removed outlier: 4.053A pdb=" N ASP D 418 " --> pdb=" O ASP D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 436 removed outlier: 4.236A pdb=" N PHE D 423 " --> pdb=" O TRP D 419 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 457 removed outlier: 3.661A pdb=" N ASN D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 474 Processing helix chain 'D' and resid 475 through 478 removed outlier: 5.354A pdb=" N GLU D 478 " --> pdb=" O ALA D 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 475 through 478' Processing helix chain 'D' and resid 479 through 484 Processing helix chain 'D' and resid 486 through 496 removed outlier: 3.816A pdb=" N LYS D 496 " --> pdb=" O HIS D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 501 removed outlier: 6.856A pdb=" N ASP D 500 " --> pdb=" O GLN D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 510 Processing helix chain 'D' and resid 528 through 543 removed outlier: 3.959A pdb=" N VAL D 532 " --> pdb=" O ILE D 528 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS D 540 " --> pdb=" O LYS D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 552 removed outlier: 3.505A pdb=" N HIS D 550 " --> pdb=" O HIS D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 589 through 626 Proline residue: D 612 - end of helix Proline residue: D 623 - end of helix Processing helix chain 'D' and resid 627 through 636 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 18 through 22 current: chain 'A' and resid 57 through 58 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 57 through 58 current: chain 'A' and resid 111 through 119 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 238 removed outlier: 8.075A pdb=" N VAL A 235 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL A 207 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ARG A 237 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 209 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE A 174 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 207 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS A 176 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL A 209 " --> pdb=" O CYS A 176 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N MET A 178 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP A 211 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR A 180 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA A 175 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N MET A 267 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY A 177 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N THR A 360 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 14.569A pdb=" N LEU A 293 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 12.463A pdb=" N ALA A 403 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLY A 295 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL A 405 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN A 297 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N HIS A 407 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU A 299 " --> pdb=" O HIS A 407 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 313 through 315 removed outlier: 3.530A pdb=" N MET A 320 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 503 through 504 Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 18 through 22 current: chain 'B' and resid 57 through 58 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 57 through 58 current: chain 'B' and resid 111 through 119 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 234 through 238 removed outlier: 8.076A pdb=" N VAL B 235 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL B 207 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ARG B 237 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL B 209 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE B 174 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL B 207 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS B 176 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL B 209 " --> pdb=" O CYS B 176 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N MET B 178 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP B 211 " --> pdb=" O MET B 178 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR B 180 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 175 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N MET B 267 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY B 177 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR B 360 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 14.567A pdb=" N LEU B 293 " --> pdb=" O PRO B 401 " (cutoff:3.500A) removed outlier: 12.463A pdb=" N ALA B 403 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLY B 295 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL B 405 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN B 297 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N HIS B 407 " --> pdb=" O GLN B 297 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU B 299 " --> pdb=" O HIS B 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 313 through 315 removed outlier: 3.531A pdb=" N MET B 320 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 503 through 504 Processing sheet with id=AA9, first strand: chain 'C' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 22 current: chain 'C' and resid 57 through 58 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 58 current: chain 'C' and resid 111 through 119 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 234 through 238 removed outlier: 8.076A pdb=" N VAL C 235 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL C 207 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ARG C 237 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL C 209 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE C 174 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 207 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS C 176 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL C 209 " --> pdb=" O CYS C 176 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N MET C 178 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP C 211 " --> pdb=" O MET C 178 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR C 180 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C 175 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N MET C 267 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY C 177 " --> pdb=" O MET C 267 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N THR C 360 " --> pdb=" O GLY C 296 " (cutoff:3.500A) removed outlier: 14.568A pdb=" N LEU C 293 " --> pdb=" O PRO C 401 " (cutoff:3.500A) removed outlier: 12.462A pdb=" N ALA C 403 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLY C 295 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL C 405 " --> pdb=" O GLY C 295 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN C 297 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N HIS C 407 " --> pdb=" O GLN C 297 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU C 299 " --> pdb=" O HIS C 407 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 315 removed outlier: 3.531A pdb=" N MET C 320 " --> pdb=" O ASP C 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 503 through 504 Processing sheet with id=AB4, first strand: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 57 through 58 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 58 current: chain 'D' and resid 111 through 119 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 234 through 238 removed outlier: 8.076A pdb=" N VAL D 235 " --> pdb=" O ALA D 205 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL D 207 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ARG D 237 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL D 209 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE D 174 " --> pdb=" O ALA D 205 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL D 207 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS D 176 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL D 209 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N MET D 178 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASP D 211 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR D 180 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA D 175 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N MET D 267 " --> pdb=" O ALA D 175 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY D 177 " --> pdb=" O MET D 267 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N THR D 360 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 14.569A pdb=" N LEU D 293 " --> pdb=" O PRO D 401 " (cutoff:3.500A) removed outlier: 12.463A pdb=" N ALA D 403 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLY D 295 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N VAL D 405 " --> pdb=" O GLY D 295 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN D 297 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N HIS D 407 " --> pdb=" O GLN D 297 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU D 299 " --> pdb=" O HIS D 407 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 313 through 315 removed outlier: 3.530A pdb=" N MET D 320 " --> pdb=" O ASP D 315 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 503 through 504 692 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6444 1.35 - 1.46: 4484 1.46 - 1.58: 8600 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 19632 Sorted by residual: bond pdb=" CB LYS C 413 " pdb=" CG LYS C 413 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CB LYS D 413 " pdb=" CG LYS D 413 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CB LYS B 413 " pdb=" CG LYS B 413 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB LYS A 413 " pdb=" CG LYS A 413 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CA THR B 153 " pdb=" CB THR B 153 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.62e-02 3.81e+03 1.08e+00 ... (remaining 19627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 26223 1.93 - 3.86: 389 3.86 - 5.79: 60 5.79 - 7.73: 16 7.73 - 9.66: 8 Bond angle restraints: 26696 Sorted by residual: angle pdb=" CB MET C 601 " pdb=" CG MET C 601 " pdb=" SD MET C 601 " ideal model delta sigma weight residual 112.70 122.36 -9.66 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CB MET D 601 " pdb=" CG MET D 601 " pdb=" SD MET D 601 " ideal model delta sigma weight residual 112.70 122.33 -9.63 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CB MET B 601 " pdb=" CG MET B 601 " pdb=" SD MET B 601 " ideal model delta sigma weight residual 112.70 122.30 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CB MET A 601 " pdb=" CG MET A 601 " pdb=" SD MET A 601 " ideal model delta sigma weight residual 112.70 122.28 -9.58 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CA LYS D 413 " pdb=" CB LYS D 413 " pdb=" CG LYS D 413 " ideal model delta sigma weight residual 114.10 120.05 -5.95 2.00e+00 2.50e-01 8.85e+00 ... (remaining 26691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 10502 17.13 - 34.27: 852 34.27 - 51.40: 270 51.40 - 68.53: 32 68.53 - 85.67: 36 Dihedral angle restraints: 11692 sinusoidal: 4652 harmonic: 7040 Sorted by residual: dihedral pdb=" CA LEU A 379 " pdb=" C LEU A 379 " pdb=" N LYS A 380 " pdb=" CA LYS A 380 " ideal model delta harmonic sigma weight residual -180.00 -162.17 -17.83 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LEU C 379 " pdb=" C LEU C 379 " pdb=" N LYS C 380 " pdb=" CA LYS C 380 " ideal model delta harmonic sigma weight residual 180.00 -162.17 -17.83 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LEU D 379 " pdb=" C LEU D 379 " pdb=" N LYS D 380 " pdb=" CA LYS D 380 " ideal model delta harmonic sigma weight residual -180.00 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 11689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2384 0.049 - 0.098: 484 0.098 - 0.148: 92 0.148 - 0.197: 0 0.197 - 0.246: 4 Chirality restraints: 2964 Sorted by residual: chirality pdb=" CB THR A 153 " pdb=" CA THR A 153 " pdb=" OG1 THR A 153 " pdb=" CG2 THR A 153 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB THR B 153 " pdb=" CA THR B 153 " pdb=" OG1 THR B 153 " pdb=" CG2 THR B 153 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB THR C 153 " pdb=" CA THR C 153 " pdb=" OG1 THR C 153 " pdb=" CG2 THR C 153 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2961 not shown) Planarity restraints: 3460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 484 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO D 485 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 485 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 485 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 484 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO C 485 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 485 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 485 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 484 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 485 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.022 5.00e-02 4.00e+02 ... (remaining 3457 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 40 2.65 - 3.21: 17885 3.21 - 3.77: 29916 3.77 - 4.34: 43070 4.34 - 4.90: 69500 Nonbonded interactions: 160411 Sorted by model distance: nonbonded pdb=" OD1 ASP D 270 " pdb="MG MG D 701 " model vdw 2.088 2.170 nonbonded pdb=" OD1 ASP C 270 " pdb="MG MG C 701 " model vdw 2.088 2.170 nonbonded pdb=" OD1 ASP A 270 " pdb="MG MG A 701 " model vdw 2.088 2.170 nonbonded pdb=" OD1 ASP B 270 " pdb="MG MG B 701 " model vdw 2.089 2.170 nonbonded pdb=" OD2 ASP C 270 " pdb="MG MG C 701 " model vdw 2.281 2.170 ... (remaining 160406 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.130 Find NCS groups from input model: 0.160 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.002 0.034 19632 Z= 0.120 Angle : 0.634 9.658 26696 Z= 0.344 Chirality : 0.041 0.246 2964 Planarity : 0.004 0.039 3460 Dihedral : 14.648 85.668 7148 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.80 % Allowed : 15.40 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.18), residues: 2408 helix: 0.48 (0.19), residues: 896 sheet: -1.86 (0.23), residues: 464 loop : 0.21 (0.21), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 15 TYR 0.008 0.001 TYR B 266 PHE 0.009 0.001 PHE B 139 TRP 0.008 0.001 TRP A 321 HIS 0.004 0.001 HIS B 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (19632) covalent geometry : angle 0.63431 / 0.34 (26696) hydrogen bonds : bond 0.17529 / 12.02 ( 692) hydrogen bonds : angle 6.66738 / 4.53 ( 1944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 261 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7890 (mt-10) REVERT: A 320 MET cc_start: 0.8127 (tpt) cc_final: 0.7791 (tpt) REVERT: A 338 LEU cc_start: 0.1638 (OUTLIER) cc_final: 0.0990 (pp) REVERT: A 351 ILE cc_start: 0.8840 (mt) cc_final: 0.8585 (tt) REVERT: A 588 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7185 (ttp80) REVERT: A 616 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7825 (tm-30) REVERT: B 249 SER cc_start: 0.8846 (m) cc_final: 0.8634 (m) REVERT: B 320 MET cc_start: 0.8108 (tpt) cc_final: 0.7773 (tpt) REVERT: B 338 LEU cc_start: 0.1662 (OUTLIER) cc_final: 0.0978 (pp) REVERT: B 351 ILE cc_start: 0.8818 (mt) cc_final: 0.8572 (tt) REVERT: B 588 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7215 (ttp80) REVERT: C 262 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7895 (mt-10) REVERT: C 320 MET cc_start: 0.8090 (tpt) cc_final: 0.7805 (tpt) REVERT: C 338 LEU cc_start: 0.1642 (OUTLIER) cc_final: 0.0964 (pp) REVERT: C 351 ILE cc_start: 0.8813 (mt) cc_final: 0.8558 (tt) REVERT: C 588 ARG cc_start: 0.7764 (ttp80) cc_final: 0.7166 (ttp80) REVERT: D 262 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7887 (mt-10) REVERT: D 320 MET cc_start: 0.8099 (tpt) cc_final: 0.7801 (tpt) REVERT: D 338 LEU cc_start: 0.1693 (OUTLIER) cc_final: 0.1005 (pp) REVERT: D 351 ILE cc_start: 0.8866 (mt) cc_final: 0.8616 (tt) REVERT: D 588 ARG cc_start: 0.7774 (ttp80) cc_final: 0.7177 (ttp80) REVERT: D 616 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7813 (tm-30) outliers start: 16 outliers final: 7 residues processed: 273 average time/residue: 0.1415 time to fit residues: 60.6839 Evaluate side-chains 237 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 226 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 613 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 HIS B 331 HIS C 331 HIS D 331 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.154783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.103978 restraints weight = 23789.853| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.59 r_work: 0.3119 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 19632 Z= 0.311 Angle : 0.678 8.442 26696 Z= 0.336 Chirality : 0.048 0.208 2964 Planarity : 0.005 0.034 3460 Dihedral : 5.257 66.515 2699 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.05 % Allowed : 13.70 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.18), residues: 2408 helix: 0.70 (0.18), residues: 884 sheet: -1.96 (0.24), residues: 460 loop : -0.16 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 99 TYR 0.013 0.002 TYR C 263 PHE 0.016 0.002 PHE D 378 TRP 0.013 0.002 TRP B 146 HIS 0.006 0.001 HIS C 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.31 (19632) covalent geometry : angle 0.67766 / 0.34 (26696) hydrogen bonds : bond 0.04774 / 3.22 ( 692) hydrogen bonds : angle 4.97513 / 3.43 ( 1944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 200 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8330 (t0) cc_final: 0.7945 (t0) REVERT: A 262 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: A 338 LEU cc_start: 0.1860 (OUTLIER) cc_final: 0.1217 (pp) REVERT: A 351 ILE cc_start: 0.8883 (mt) cc_final: 0.8514 (tt) REVERT: A 588 ARG cc_start: 0.7692 (ttp80) cc_final: 0.6776 (ttp-170) REVERT: A 601 MET cc_start: 0.8403 (mmp) cc_final: 0.8157 (mmp) REVERT: A 616 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7944 (tm-30) REVERT: B 338 LEU cc_start: 0.1886 (OUTLIER) cc_final: 0.1242 (pp) REVERT: B 351 ILE cc_start: 0.8876 (mt) cc_final: 0.8509 (tt) REVERT: B 453 LYS cc_start: 0.7098 (tppt) cc_final: 0.6701 (tppt) REVERT: B 588 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7364 (ttp80) REVERT: B 601 MET cc_start: 0.8420 (mmp) cc_final: 0.8185 (mmp) REVERT: B 613 GLU cc_start: 0.7764 (pp20) cc_final: 0.7406 (pm20) REVERT: B 616 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7956 (tm-30) REVERT: C 262 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: C 338 LEU cc_start: 0.1835 (OUTLIER) cc_final: 0.1201 (pp) REVERT: C 351 ILE cc_start: 0.8857 (mt) cc_final: 0.8468 (tt) REVERT: C 588 ARG cc_start: 0.7676 (ttp80) cc_final: 0.6758 (ttp-170) REVERT: C 601 MET cc_start: 0.8438 (mmp) cc_final: 0.8198 (mmp) REVERT: C 616 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7986 (tm-30) REVERT: D 211 ASP cc_start: 0.8323 (t0) cc_final: 0.7951 (t0) REVERT: D 262 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: D 338 LEU cc_start: 0.1850 (OUTLIER) cc_final: 0.1210 (pp) REVERT: D 351 ILE cc_start: 0.8833 (mt) cc_final: 0.8452 (tt) REVERT: D 588 ARG cc_start: 0.7702 (ttp80) cc_final: 0.6770 (ttp-170) REVERT: D 601 MET cc_start: 0.8445 (mmp) cc_final: 0.8211 (mmp) REVERT: D 616 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7981 (tm-30) outliers start: 61 outliers final: 30 residues processed: 244 average time/residue: 0.1303 time to fit residues: 50.8295 Evaluate side-chains 222 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 366 GLN Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 366 GLN Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 566 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 194 optimal weight: 5.9990 chunk 205 optimal weight: 0.7980 chunk 242 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.158506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.108192 restraints weight = 23772.481| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.60 r_work: 0.3179 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19632 Z= 0.117 Angle : 0.536 7.365 26696 Z= 0.263 Chirality : 0.043 0.236 2964 Planarity : 0.004 0.037 3460 Dihedral : 4.272 26.690 2689 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.50 % Allowed : 13.85 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.18), residues: 2408 helix: 1.15 (0.19), residues: 884 sheet: -1.70 (0.26), residues: 436 loop : -0.15 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 15 TYR 0.008 0.001 TYR A 253 PHE 0.022 0.002 PHE A 223 TRP 0.010 0.001 TRP A 321 HIS 0.003 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (19632) covalent geometry : angle 0.53551 / 0.26 (26696) hydrogen bonds : bond 0.03272 / 2.23 ( 692) hydrogen bonds : angle 4.47836 / 3.08 ( 1944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7598 (mt-10) REVERT: A 338 LEU cc_start: 0.1237 (OUTLIER) cc_final: 0.0720 (pp) REVERT: A 351 ILE cc_start: 0.8732 (mt) cc_final: 0.8288 (tt) REVERT: A 561 ASP cc_start: 0.8330 (m-30) cc_final: 0.8086 (p0) REVERT: A 588 ARG cc_start: 0.7614 (ttp80) cc_final: 0.6715 (ttp-170) REVERT: A 601 MET cc_start: 0.8423 (mmp) cc_final: 0.8122 (mmp) REVERT: A 616 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7885 (tm-30) REVERT: A 624 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7543 (tm130) REVERT: B 249 SER cc_start: 0.8979 (m) cc_final: 0.8745 (m) REVERT: B 338 LEU cc_start: 0.1207 (OUTLIER) cc_final: 0.0700 (pp) REVERT: B 351 ILE cc_start: 0.8724 (mt) cc_final: 0.8285 (tt) REVERT: B 561 ASP cc_start: 0.8337 (m-30) cc_final: 0.8074 (p0) REVERT: B 588 ARG cc_start: 0.7622 (ttp80) cc_final: 0.6724 (ttp-170) REVERT: B 601 MET cc_start: 0.8364 (mmp) cc_final: 0.8059 (mmp) REVERT: B 613 GLU cc_start: 0.7853 (pp20) cc_final: 0.7509 (pm20) REVERT: B 616 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 624 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7528 (tm130) REVERT: C 262 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7610 (mt-10) REVERT: C 338 LEU cc_start: 0.1209 (OUTLIER) cc_final: 0.0698 (pp) REVERT: C 351 ILE cc_start: 0.8724 (mt) cc_final: 0.8287 (tt) REVERT: C 561 ASP cc_start: 0.8345 (m-30) cc_final: 0.8021 (p0) REVERT: C 588 ARG cc_start: 0.7592 (ttp80) cc_final: 0.6699 (ttp-170) REVERT: C 601 MET cc_start: 0.8352 (mmp) cc_final: 0.8035 (mmp) REVERT: C 616 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7919 (tm-30) REVERT: C 624 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7487 (tm130) REVERT: D 262 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7609 (mt-10) REVERT: D 338 LEU cc_start: 0.1183 (OUTLIER) cc_final: 0.0674 (pp) REVERT: D 351 ILE cc_start: 0.8721 (mt) cc_final: 0.8283 (tt) REVERT: D 561 ASP cc_start: 0.8347 (m-30) cc_final: 0.8073 (p0) REVERT: D 588 ARG cc_start: 0.7595 (ttp80) cc_final: 0.6696 (ttp-170) REVERT: D 601 MET cc_start: 0.8353 (mmp) cc_final: 0.8036 (mmp) REVERT: D 616 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7917 (tm-30) REVERT: D 624 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7485 (tm130) outliers start: 50 outliers final: 21 residues processed: 261 average time/residue: 0.1459 time to fit residues: 59.4849 Evaluate side-chains 228 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 624 GLN Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 624 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 223 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 233 optimal weight: 20.0000 chunk 239 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 210 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.158054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107773 restraints weight = 23655.358| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.59 r_work: 0.3168 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19632 Z= 0.133 Angle : 0.536 7.080 26696 Z= 0.264 Chirality : 0.043 0.229 2964 Planarity : 0.004 0.036 3460 Dihedral : 4.203 27.070 2689 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.30 % Allowed : 15.00 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.18), residues: 2408 helix: 1.32 (0.19), residues: 884 sheet: -1.68 (0.26), residues: 436 loop : -0.15 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 365 TYR 0.008 0.001 TYR B 473 PHE 0.023 0.002 PHE D 223 TRP 0.011 0.001 TRP B 321 HIS 0.003 0.001 HIS D 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (19632) covalent geometry : angle 0.53647 / 0.26 (26696) hydrogen bonds : bond 0.03191 / 2.16 ( 692) hydrogen bonds : angle 4.38045 / 3.01 ( 1944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: A 338 LEU cc_start: 0.1483 (OUTLIER) cc_final: 0.0957 (pp) REVERT: A 351 ILE cc_start: 0.8739 (mt) cc_final: 0.8311 (tt) REVERT: A 561 ASP cc_start: 0.8342 (m-30) cc_final: 0.8044 (p0) REVERT: A 588 ARG cc_start: 0.7669 (ttp80) cc_final: 0.6930 (ttp80) REVERT: A 601 MET cc_start: 0.8372 (mmp) cc_final: 0.7780 (mmm) REVERT: A 624 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7499 (tm130) REVERT: B 338 LEU cc_start: 0.1538 (OUTLIER) cc_final: 0.1006 (pp) REVERT: B 351 ILE cc_start: 0.8744 (mt) cc_final: 0.8319 (tt) REVERT: B 561 ASP cc_start: 0.8348 (m-30) cc_final: 0.8047 (p0) REVERT: B 588 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7366 (ttp-170) REVERT: B 601 MET cc_start: 0.8383 (mmp) cc_final: 0.7770 (mmm) REVERT: B 613 GLU cc_start: 0.7841 (pp20) cc_final: 0.7433 (pm20) REVERT: B 624 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7499 (tm130) REVERT: C 262 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: C 338 LEU cc_start: 0.1598 (OUTLIER) cc_final: 0.1080 (pp) REVERT: C 351 ILE cc_start: 0.8735 (mt) cc_final: 0.8311 (tt) REVERT: C 561 ASP cc_start: 0.8382 (m-30) cc_final: 0.8055 (p0) REVERT: C 588 ARG cc_start: 0.7617 (ttp80) cc_final: 0.6867 (ttp80) REVERT: C 601 MET cc_start: 0.8366 (mmp) cc_final: 0.7768 (mmm) REVERT: C 624 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7510 (tm130) REVERT: D 262 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7588 (mt-10) REVERT: D 338 LEU cc_start: 0.1375 (OUTLIER) cc_final: 0.0903 (pp) REVERT: D 351 ILE cc_start: 0.8738 (mt) cc_final: 0.8313 (tt) REVERT: D 561 ASP cc_start: 0.8364 (m-30) cc_final: 0.8036 (p0) REVERT: D 588 ARG cc_start: 0.7669 (ttp80) cc_final: 0.6931 (ttp80) REVERT: D 601 MET cc_start: 0.8369 (mmp) cc_final: 0.7774 (mmm) REVERT: D 624 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7514 (tm130) outliers start: 46 outliers final: 23 residues processed: 238 average time/residue: 0.1422 time to fit residues: 53.3767 Evaluate side-chains 227 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 624 GLN Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 624 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 168 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 182 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 210 optimal weight: 0.0270 chunk 229 optimal weight: 5.9990 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 366 GLN C 366 GLN D 366 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.157249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.107112 restraints weight = 23682.781| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.59 r_work: 0.3156 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19632 Z= 0.142 Angle : 0.534 7.436 26696 Z= 0.262 Chirality : 0.043 0.230 2964 Planarity : 0.004 0.035 3460 Dihedral : 4.170 26.756 2689 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.30 % Allowed : 14.85 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 2408 helix: 1.40 (0.19), residues: 884 sheet: -1.62 (0.26), residues: 428 loop : -0.15 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 15 TYR 0.008 0.001 TYR B 253 PHE 0.025 0.002 PHE A 223 TRP 0.010 0.001 TRP C 321 HIS 0.003 0.001 HIS C 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (19632) covalent geometry : angle 0.53353 / 0.26 (26696) hydrogen bonds : bond 0.03188 / 2.15 ( 692) hydrogen bonds : angle 4.33615 / 2.98 ( 1944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: A 338 LEU cc_start: 0.1540 (OUTLIER) cc_final: 0.1037 (pp) REVERT: A 351 ILE cc_start: 0.8746 (mt) cc_final: 0.8310 (tt) REVERT: A 561 ASP cc_start: 0.8345 (m-30) cc_final: 0.8116 (p0) REVERT: A 588 ARG cc_start: 0.7675 (ttp80) cc_final: 0.7398 (ttp-170) REVERT: A 601 MET cc_start: 0.8392 (mmp) cc_final: 0.7773 (mmm) REVERT: A 624 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7448 (tm130) REVERT: B 338 LEU cc_start: 0.1592 (OUTLIER) cc_final: 0.1058 (pp) REVERT: B 351 ILE cc_start: 0.8755 (mt) cc_final: 0.8324 (tt) REVERT: B 561 ASP cc_start: 0.8347 (m-30) cc_final: 0.8079 (p0) REVERT: B 588 ARG cc_start: 0.7685 (ttp80) cc_final: 0.7411 (ttp-170) REVERT: B 601 MET cc_start: 0.8398 (mmp) cc_final: 0.7761 (mmm) REVERT: B 613 GLU cc_start: 0.7816 (pp20) cc_final: 0.7406 (pm20) REVERT: B 624 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7447 (tm130) REVERT: C 262 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: C 338 LEU cc_start: 0.1598 (OUTLIER) cc_final: 0.1059 (pp) REVERT: C 351 ILE cc_start: 0.8749 (mt) cc_final: 0.8319 (tt) REVERT: C 561 ASP cc_start: 0.8344 (m-30) cc_final: 0.8078 (p0) REVERT: C 588 ARG cc_start: 0.7662 (ttp80) cc_final: 0.7389 (ttp-170) REVERT: C 601 MET cc_start: 0.8389 (mmp) cc_final: 0.7757 (mmm) REVERT: C 624 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7461 (tm130) REVERT: D 262 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: D 338 LEU cc_start: 0.1572 (OUTLIER) cc_final: 0.1042 (pp) REVERT: D 351 ILE cc_start: 0.8745 (mt) cc_final: 0.8315 (tt) REVERT: D 561 ASP cc_start: 0.8350 (m-30) cc_final: 0.8114 (p0) REVERT: D 588 ARG cc_start: 0.7657 (ttp80) cc_final: 0.7382 (ttp-170) REVERT: D 601 MET cc_start: 0.8421 (mmp) cc_final: 0.7782 (mmm) REVERT: D 624 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7449 (tm130) outliers start: 46 outliers final: 27 residues processed: 236 average time/residue: 0.1457 time to fit residues: 54.0443 Evaluate side-chains 231 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 366 GLN Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 624 GLN Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 366 GLN Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 624 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 127 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 100 optimal weight: 0.0670 chunk 96 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 159 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.161651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123348 restraints weight = 23007.926| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.02 r_work: 0.3179 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19632 Z= 0.174 Angle : 0.552 8.051 26696 Z= 0.271 Chirality : 0.044 0.216 2964 Planarity : 0.004 0.035 3460 Dihedral : 4.248 26.800 2689 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.15 % Allowed : 15.35 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.18), residues: 2408 helix: 1.37 (0.19), residues: 884 sheet: -1.67 (0.26), residues: 428 loop : -0.17 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 15 TYR 0.008 0.001 TYR B 253 PHE 0.026 0.002 PHE A 223 TRP 0.010 0.001 TRP B 321 HIS 0.003 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (19632) covalent geometry : angle 0.55182 / 0.27 (26696) hydrogen bonds : bond 0.03365 / 2.27 ( 692) hydrogen bonds : angle 4.39197 / 3.02 ( 1944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: A 338 LEU cc_start: 0.2614 (OUTLIER) cc_final: 0.1937 (pp) REVERT: A 351 ILE cc_start: 0.8996 (mt) cc_final: 0.8664 (tt) REVERT: A 588 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7720 (ttp-170) REVERT: A 601 MET cc_start: 0.8410 (mmp) cc_final: 0.7775 (mmm) REVERT: A 624 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7508 (tm130) REVERT: B 338 LEU cc_start: 0.2644 (OUTLIER) cc_final: 0.1982 (pp) REVERT: B 351 ILE cc_start: 0.8998 (mt) cc_final: 0.8666 (tt) REVERT: B 588 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7724 (ttp-170) REVERT: B 613 GLU cc_start: 0.7805 (pp20) cc_final: 0.7442 (pm20) REVERT: B 624 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7524 (tm130) REVERT: C 262 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: C 338 LEU cc_start: 0.2613 (OUTLIER) cc_final: 0.1959 (pp) REVERT: C 351 ILE cc_start: 0.8992 (mt) cc_final: 0.8657 (tt) REVERT: C 588 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7719 (ttp-170) REVERT: C 601 MET cc_start: 0.8443 (mmp) cc_final: 0.7785 (mmm) REVERT: C 624 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7561 (tm130) REVERT: D 262 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: D 338 LEU cc_start: 0.2625 (OUTLIER) cc_final: 0.1969 (pp) REVERT: D 351 ILE cc_start: 0.8999 (mt) cc_final: 0.8666 (tt) REVERT: D 588 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7721 (ttp-170) REVERT: D 601 MET cc_start: 0.8455 (mmp) cc_final: 0.7797 (mmm) REVERT: D 624 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7518 (tm130) outliers start: 43 outliers final: 28 residues processed: 230 average time/residue: 0.1433 time to fit residues: 51.9371 Evaluate side-chains 232 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 624 GLN Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 624 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 86 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.161337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.122415 restraints weight = 23153.212| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.86 r_work: 0.3184 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19632 Z= 0.168 Angle : 0.548 8.431 26696 Z= 0.270 Chirality : 0.043 0.194 2964 Planarity : 0.004 0.033 3460 Dihedral : 4.290 26.324 2689 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.50 % Allowed : 15.25 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.18), residues: 2408 helix: 1.40 (0.18), residues: 884 sheet: -1.71 (0.26), residues: 428 loop : -0.20 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 15 TYR 0.008 0.001 TYR B 253 PHE 0.028 0.002 PHE A 223 TRP 0.010 0.001 TRP A 321 HIS 0.003 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (19632) covalent geometry : angle 0.54771 / 0.27 (26696) hydrogen bonds : bond 0.03357 / 2.26 ( 692) hydrogen bonds : angle 4.37659 / 3.01 ( 1944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: A 338 LEU cc_start: 0.2691 (OUTLIER) cc_final: 0.2007 (pp) REVERT: A 351 ILE cc_start: 0.8995 (mt) cc_final: 0.8635 (tt) REVERT: A 588 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7696 (ttp-170) REVERT: A 601 MET cc_start: 0.8405 (mmp) cc_final: 0.7743 (mmm) REVERT: A 624 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7550 (tm130) REVERT: B 338 LEU cc_start: 0.2707 (OUTLIER) cc_final: 0.2026 (pp) REVERT: B 351 ILE cc_start: 0.8983 (mt) cc_final: 0.8617 (tt) REVERT: B 588 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7703 (ttp-170) REVERT: B 613 GLU cc_start: 0.7817 (pp20) cc_final: 0.7400 (pm20) REVERT: B 624 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7544 (tm130) REVERT: C 262 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: C 338 LEU cc_start: 0.2405 (OUTLIER) cc_final: 0.1751 (pp) REVERT: C 351 ILE cc_start: 0.8964 (mt) cc_final: 0.8604 (tt) REVERT: C 588 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7701 (ttp-170) REVERT: C 601 MET cc_start: 0.8407 (mmp) cc_final: 0.7736 (mmm) REVERT: C 624 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7572 (tm130) REVERT: D 262 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: D 338 LEU cc_start: 0.2396 (OUTLIER) cc_final: 0.1744 (pp) REVERT: D 351 ILE cc_start: 0.8950 (mt) cc_final: 0.8613 (tt) REVERT: D 588 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7704 (ttp-170) REVERT: D 601 MET cc_start: 0.8418 (mmp) cc_final: 0.7749 (mmm) REVERT: D 624 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7558 (tm130) outliers start: 50 outliers final: 34 residues processed: 234 average time/residue: 0.1442 time to fit residues: 52.8229 Evaluate side-chains 237 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 624 GLN Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 624 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 159 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 232 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.162534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123876 restraints weight = 23029.387| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.88 r_work: 0.3215 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19632 Z= 0.128 Angle : 0.529 8.510 26696 Z= 0.260 Chirality : 0.042 0.167 2964 Planarity : 0.004 0.034 3460 Dihedral : 4.171 26.398 2689 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.40 % Allowed : 16.05 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 2408 helix: 1.53 (0.19), residues: 884 sheet: -1.64 (0.27), residues: 428 loop : -0.15 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 15 TYR 0.008 0.001 TYR B 253 PHE 0.029 0.002 PHE A 223 TRP 0.010 0.001 TRP D 321 HIS 0.002 0.000 HIS A 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (19632) covalent geometry : angle 0.52868 / 0.26 (26696) hydrogen bonds : bond 0.03017 / 2.04 ( 692) hydrogen bonds : angle 4.29062 / 2.95 ( 1944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: A 338 LEU cc_start: 0.2567 (OUTLIER) cc_final: 0.1964 (pp) REVERT: A 351 ILE cc_start: 0.8952 (mt) cc_final: 0.8598 (tt) REVERT: A 588 ARG cc_start: 0.7908 (ttp80) cc_final: 0.7667 (ttp-170) REVERT: A 601 MET cc_start: 0.8393 (mmp) cc_final: 0.7729 (mmm) REVERT: A 624 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7511 (tm130) REVERT: B 338 LEU cc_start: 0.2580 (OUTLIER) cc_final: 0.1965 (pp) REVERT: B 351 ILE cc_start: 0.8954 (mt) cc_final: 0.8598 (tt) REVERT: B 588 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7694 (ttp-170) REVERT: B 613 GLU cc_start: 0.7791 (pp20) cc_final: 0.7478 (pm20) REVERT: B 624 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7505 (tm130) REVERT: C 262 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: C 338 LEU cc_start: 0.2552 (OUTLIER) cc_final: 0.1944 (pp) REVERT: C 351 ILE cc_start: 0.8956 (mt) cc_final: 0.8606 (tt) REVERT: C 588 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7687 (ttp-170) REVERT: C 601 MET cc_start: 0.8431 (mmp) cc_final: 0.7770 (mmm) REVERT: C 624 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7529 (tm130) REVERT: D 262 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: D 338 LEU cc_start: 0.2543 (OUTLIER) cc_final: 0.1940 (pp) REVERT: D 351 ILE cc_start: 0.8960 (mt) cc_final: 0.8611 (tt) REVERT: D 588 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7678 (ttp-170) REVERT: D 601 MET cc_start: 0.8435 (mmp) cc_final: 0.7771 (mmm) REVERT: D 624 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7508 (tm130) outliers start: 48 outliers final: 34 residues processed: 247 average time/residue: 0.1374 time to fit residues: 53.7938 Evaluate side-chains 254 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 268 ASP Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 624 GLN Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 624 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 200 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 206 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 569 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.161836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123733 restraints weight = 22892.953| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.95 r_work: 0.3196 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19632 Z= 0.146 Angle : 0.541 9.064 26696 Z= 0.265 Chirality : 0.043 0.139 2964 Planarity : 0.004 0.034 3460 Dihedral : 4.210 26.015 2689 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.50 % Allowed : 16.10 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 2408 helix: 1.53 (0.18), residues: 884 sheet: -1.60 (0.27), residues: 428 loop : -0.15 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 15 TYR 0.008 0.001 TYR B 253 PHE 0.030 0.002 PHE A 223 TRP 0.010 0.001 TRP D 321 HIS 0.002 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (19632) covalent geometry : angle 0.54122 / 0.27 (26696) hydrogen bonds : bond 0.03169 / 2.13 ( 692) hydrogen bonds : angle 4.32065 / 2.97 ( 1944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: A 338 LEU cc_start: 0.2609 (OUTLIER) cc_final: 0.1981 (pp) REVERT: A 351 ILE cc_start: 0.8978 (mt) cc_final: 0.8613 (tt) REVERT: A 588 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7715 (ttp-170) REVERT: A 601 MET cc_start: 0.8441 (mmp) cc_final: 0.7772 (mmm) REVERT: A 624 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7527 (tm130) REVERT: B 338 LEU cc_start: 0.2534 (OUTLIER) cc_final: 0.1906 (pp) REVERT: B 351 ILE cc_start: 0.8937 (mt) cc_final: 0.8601 (tt) REVERT: B 588 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7736 (ttp-170) REVERT: B 613 GLU cc_start: 0.7867 (pp20) cc_final: 0.7424 (pm20) REVERT: B 624 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7524 (tm130) REVERT: C 262 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: C 338 LEU cc_start: 0.2480 (OUTLIER) cc_final: 0.1871 (pp) REVERT: C 351 ILE cc_start: 0.8940 (mt) cc_final: 0.8601 (tt) REVERT: C 588 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7717 (ttp-170) REVERT: C 601 MET cc_start: 0.8444 (mmp) cc_final: 0.7779 (mmm) REVERT: C 624 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7534 (tm130) REVERT: D 262 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: D 338 LEU cc_start: 0.2419 (OUTLIER) cc_final: 0.1814 (pp) REVERT: D 351 ILE cc_start: 0.8944 (mt) cc_final: 0.8604 (tt) REVERT: D 588 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7720 (ttp-170) REVERT: D 601 MET cc_start: 0.8452 (mmp) cc_final: 0.7782 (mmm) REVERT: D 624 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7539 (tm130) outliers start: 50 outliers final: 33 residues processed: 243 average time/residue: 0.1451 time to fit residues: 54.6093 Evaluate side-chains 248 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 624 GLN Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 624 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 193 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 234 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120950 restraints weight = 23237.025| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.07 r_work: 0.3146 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 19632 Z= 0.250 Angle : 0.619 9.619 26696 Z= 0.302 Chirality : 0.045 0.147 2964 Planarity : 0.004 0.033 3460 Dihedral : 4.529 25.610 2689 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.05 % Allowed : 16.70 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.18), residues: 2408 helix: 1.32 (0.18), residues: 884 sheet: -1.68 (0.26), residues: 452 loop : -0.25 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 15 TYR 0.011 0.002 TYR C 253 PHE 0.032 0.002 PHE B 223 TRP 0.012 0.002 TRP B 146 HIS 0.004 0.001 HIS C 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.25 (19632) covalent geometry : angle 0.61907 / 0.30 (26696) hydrogen bonds : bond 0.03838 / 2.59 ( 692) hydrogen bonds : angle 4.52218 / 3.11 ( 1944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: A 338 LEU cc_start: 0.2955 (OUTLIER) cc_final: 0.2187 (pp) REVERT: A 351 ILE cc_start: 0.9016 (mt) cc_final: 0.8733 (tt) REVERT: A 624 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7605 (tm130) REVERT: B 200 VAL cc_start: 0.9183 (t) cc_final: 0.8917 (p) REVERT: B 338 LEU cc_start: 0.3156 (OUTLIER) cc_final: 0.2401 (pp) REVERT: B 351 ILE cc_start: 0.9016 (mt) cc_final: 0.8730 (tt) REVERT: B 588 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7791 (ttp-170) REVERT: B 613 GLU cc_start: 0.7863 (pp20) cc_final: 0.7487 (pm20) REVERT: B 624 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7596 (tm130) REVERT: C 262 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: C 338 LEU cc_start: 0.3138 (OUTLIER) cc_final: 0.2387 (pp) REVERT: C 351 ILE cc_start: 0.9012 (mt) cc_final: 0.8726 (tt) REVERT: C 624 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7597 (tm130) REVERT: D 200 VAL cc_start: 0.9183 (t) cc_final: 0.8934 (p) REVERT: D 262 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: D 338 LEU cc_start: 0.3115 (OUTLIER) cc_final: 0.2375 (pp) REVERT: D 351 ILE cc_start: 0.9016 (mt) cc_final: 0.8733 (tt) REVERT: D 624 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7578 (tm130) outliers start: 41 outliers final: 29 residues processed: 220 average time/residue: 0.1434 time to fit residues: 49.7098 Evaluate side-chains 225 residues out of total 2000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain B residue 33 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 443 MET Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 624 GLN Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 624 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 202 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120566 restraints weight = 23209.718| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.07 r_work: 0.3137 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19632 Z= 0.229 Angle : 0.606 9.487 26696 Z= 0.296 Chirality : 0.045 0.142 2964 Planarity : 0.004 0.033 3460 Dihedral : 4.551 26.319 2689 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.05 % Allowed : 16.80 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2408 helix: 1.33 (0.18), residues: 884 sheet: -1.87 (0.25), residues: 448 loop : -0.29 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.009 0.002 TYR D 263 PHE 0.032 0.002 PHE A 223 TRP 0.010 0.002 TRP B 321 HIS 0.003 0.001 HIS D 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (19632) covalent geometry : angle 0.60609 / 0.30 (26696) hydrogen bonds : bond 0.03709 / 2.50 ( 692) hydrogen bonds : angle 4.49615 / 3.10 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4405.46 seconds wall clock time: 76 minutes 27.54 seconds (4587.54 seconds total)