Starting phenix.real_space_refine on Sun Aug 24 05:12:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gkg_40183/08_2025/8gkg_40183.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gkg_40183/08_2025/8gkg_40183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gkg_40183/08_2025/8gkg_40183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gkg_40183/08_2025/8gkg_40183.map" model { file = "/net/cci-nas-00/data/ceres_data/8gkg_40183/08_2025/8gkg_40183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gkg_40183/08_2025/8gkg_40183.cif" } resolution = 4.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 10755 2.51 5 N 3095 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17160 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 3432 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 269} Link IDs: {'PTRANS': 12, 'TRANS': 527} Chain breaks: 4 Unresolved non-hydrogen bonds: 985 Unresolved non-hydrogen angles: 1258 Unresolved non-hydrogen dihedrals: 798 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'ARG:plan': 20, 'GLU:plan': 25, 'HIS:plan': 6, 'ASP:plan': 12, 'ASN:plan1': 12, 'PHE:plan': 16, 'TYR:plan': 7, 'GLN:plan1': 7, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 500 Restraints were copied for chains: B, C, D, E Time building chain proxies: 3.48, per 1000 atoms: 0.20 Number of scatterers: 17160 At special positions: 0 Unit cell: (170.008, 172.16, 110.828, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 3260 8.00 N 3095 7.00 C 10755 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: 1.58 Conformation dependent library (CDL) restraints added in 946.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5160 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 0 sheets defined 61.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 132 through 148 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 180 through 196 removed outlier: 4.358A pdb=" N GLU A 185 " --> pdb=" O PRO A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 216 through 225 removed outlier: 3.501A pdb=" N ASN A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.639A pdb=" N ASN A 242 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 306 removed outlier: 4.216A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 328 removed outlier: 4.011A pdb=" N MET A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.950A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.351A pdb=" N GLY A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.570A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.699A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 432 through 440 removed outlier: 3.649A pdb=" N ALA A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 447 removed outlier: 3.555A pdb=" N PHE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 487 through 505 removed outlier: 3.627A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 535 removed outlier: 3.814A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 531 " --> pdb=" O PHE A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 568 removed outlier: 4.250A pdb=" N MET A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 605 Processing helix chain 'A' and resid 629 through 634 removed outlier: 3.547A pdb=" N LEU A 632 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 634 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 679 removed outlier: 3.798A pdb=" N LEU A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 685 removed outlier: 3.886A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 removed outlier: 4.337A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 707 removed outlier: 3.893A pdb=" N LEU A 707 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 130 Processing helix chain 'B' and resid 132 through 148 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.357A pdb=" N GLU B 185 " --> pdb=" O PRO B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.501A pdb=" N ASN B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.640A pdb=" N ASN B 242 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 306 removed outlier: 4.217A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR B 305 " --> pdb=" O HIS B 301 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 328 removed outlier: 4.011A pdb=" N MET B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.950A pdb=" N LEU B 333 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 4.352A pdb=" N GLY B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.570A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.699A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 432 through 440 removed outlier: 3.648A pdb=" N ALA B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LYS B 438 " --> pdb=" O LYS B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 447 removed outlier: 3.555A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 487 through 505 removed outlier: 3.628A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 535 removed outlier: 3.814A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL B 531 " --> pdb=" O PHE B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 568 removed outlier: 4.250A pdb=" N MET B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 605 Processing helix chain 'B' and resid 629 through 634 removed outlier: 3.547A pdb=" N LEU B 632 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 634 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 679 removed outlier: 3.797A pdb=" N LEU B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 685 removed outlier: 3.886A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 702 removed outlier: 4.337A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 707 removed outlier: 3.893A pdb=" N LEU B 707 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 180 through 196 removed outlier: 4.357A pdb=" N GLU C 185 " --> pdb=" O PRO C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.502A pdb=" N ASN C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.640A pdb=" N ASN C 242 " --> pdb=" O ALA C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 306 removed outlier: 4.216A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR C 305 " --> pdb=" O HIS C 301 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 328 removed outlier: 4.011A pdb=" N MET C 320 " --> pdb=" O PHE C 316 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.949A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 removed outlier: 4.351A pdb=" N GLY C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.571A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET C 351 " --> pdb=" O LEU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.698A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 432 through 440 removed outlier: 3.649A pdb=" N ALA C 437 " --> pdb=" O TRP C 433 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS C 438 " --> pdb=" O LYS C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 447 removed outlier: 3.555A pdb=" N PHE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS C 446 " --> pdb=" O PHE C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 461 Processing helix chain 'C' and resid 487 through 505 removed outlier: 3.628A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 535 removed outlier: 3.815A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL C 531 " --> pdb=" O PHE C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 568 removed outlier: 4.250A pdb=" N MET C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 605 Processing helix chain 'C' and resid 629 through 634 removed outlier: 3.548A pdb=" N LEU C 632 " --> pdb=" O VAL C 629 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C 634 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 679 removed outlier: 3.797A pdb=" N LEU C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 685 removed outlier: 3.886A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 702 removed outlier: 4.337A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 707 removed outlier: 3.893A pdb=" N LEU C 707 " --> pdb=" O GLU C 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 130 Processing helix chain 'D' and resid 132 through 148 Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 180 through 196 removed outlier: 4.357A pdb=" N GLU D 185 " --> pdb=" O PRO D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 216 through 225 removed outlier: 3.501A pdb=" N ASN D 220 " --> pdb=" O GLN D 216 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 239 through 243 removed outlier: 3.640A pdb=" N ASN D 242 " --> pdb=" O ALA D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 306 removed outlier: 4.216A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 328 removed outlier: 4.011A pdb=" N MET D 320 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.949A pdb=" N LEU D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 removed outlier: 4.352A pdb=" N GLY D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.570A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.699A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 432 through 440 removed outlier: 3.648A pdb=" N ALA D 437 " --> pdb=" O TRP D 433 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 447 removed outlier: 3.554A pdb=" N PHE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS D 446 " --> pdb=" O PHE D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'D' and resid 487 through 505 removed outlier: 3.628A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 535 removed outlier: 3.814A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL D 531 " --> pdb=" O PHE D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 568 removed outlier: 4.250A pdb=" N MET D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 605 Processing helix chain 'D' and resid 629 through 634 removed outlier: 3.547A pdb=" N LEU D 632 " --> pdb=" O VAL D 629 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS D 634 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 679 removed outlier: 3.798A pdb=" N LEU D 657 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 685 removed outlier: 3.886A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 702 removed outlier: 4.338A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 707 removed outlier: 3.894A pdb=" N LEU D 707 " --> pdb=" O GLU D 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 130 Processing helix chain 'E' and resid 132 through 148 Processing helix chain 'E' and resid 172 through 178 Processing helix chain 'E' and resid 180 through 196 removed outlier: 4.357A pdb=" N GLU E 185 " --> pdb=" O PRO E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 205 Processing helix chain 'E' and resid 216 through 225 removed outlier: 3.502A pdb=" N ASN E 220 " --> pdb=" O GLN E 216 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE E 221 " --> pdb=" O THR E 217 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG E 225 " --> pdb=" O ILE E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.639A pdb=" N ASN E 242 " --> pdb=" O ALA E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 272 Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 298 through 306 removed outlier: 4.216A pdb=" N VAL E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR E 305 " --> pdb=" O HIS E 301 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL E 306 " --> pdb=" O ALA E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 328 removed outlier: 4.011A pdb=" N MET E 320 " --> pdb=" O PHE E 316 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 321 " --> pdb=" O VAL E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.949A pdb=" N LEU E 333 " --> pdb=" O ASN E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 342 removed outlier: 4.352A pdb=" N GLY E 341 " --> pdb=" O ARG E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 351 removed outlier: 3.570A pdb=" N ALA E 349 " --> pdb=" O LEU E 345 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET E 351 " --> pdb=" O LEU E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 362 removed outlier: 3.698A pdb=" N TYR E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 432 through 440 removed outlier: 3.648A pdb=" N ALA E 437 " --> pdb=" O TRP E 433 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LYS E 438 " --> pdb=" O LYS E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 447 removed outlier: 3.554A pdb=" N PHE E 445 " --> pdb=" O PHE E 441 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS E 446 " --> pdb=" O PHE E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 461 Processing helix chain 'E' and resid 487 through 505 removed outlier: 3.628A pdb=" N ILE E 492 " --> pdb=" O MET E 488 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP E 493 " --> pdb=" O PHE E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 535 removed outlier: 3.815A pdb=" N VAL E 525 " --> pdb=" O TRP E 521 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL E 531 " --> pdb=" O PHE E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 568 removed outlier: 4.249A pdb=" N MET E 555 " --> pdb=" O LEU E 551 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 563 " --> pdb=" O TRP E 559 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR E 565 " --> pdb=" O ASN E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 605 Processing helix chain 'E' and resid 629 through 634 removed outlier: 3.547A pdb=" N LEU E 632 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS E 634 " --> pdb=" O GLU E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 679 removed outlier: 3.798A pdb=" N LEU E 657 " --> pdb=" O LEU E 653 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE E 659 " --> pdb=" O LEU E 655 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU E 679 " --> pdb=" O ALA E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 685 removed outlier: 3.886A pdb=" N ASN E 683 " --> pdb=" O GLU E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 702 removed outlier: 4.337A pdb=" N ARG E 693 " --> pdb=" O GLU E 689 " (cutoff:3.500A) Processing helix chain 'E' and resid 703 through 707 removed outlier: 3.894A pdb=" N LEU E 707 " --> pdb=" O GLU E 704 " (cutoff:3.500A) 921 hydrogen bonds defined for protein. 2688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 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 - 1.34: 6060 1.34 - 1.46: 3001 1.46 - 1.57: 8264 1.57 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 17420 Sorted by residual: bond pdb=" C VAL E 154 " pdb=" N PRO E 155 " ideal model delta sigma weight residual 1.339 1.378 -0.039 3.40e-02 8.65e+02 1.34e+00 bond pdb=" C VAL B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.339 1.378 -0.039 3.40e-02 8.65e+02 1.32e+00 bond pdb=" C VAL D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 1.339 1.378 -0.039 3.40e-02 8.65e+02 1.32e+00 bond pdb=" C VAL C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.339 1.378 -0.039 3.40e-02 8.65e+02 1.30e+00 bond pdb=" C VAL A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.339 1.378 -0.038 3.40e-02 8.65e+02 1.27e+00 ... (remaining 17415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 22843 1.08 - 2.15: 774 2.15 - 3.23: 179 3.23 - 4.31: 94 4.31 - 5.39: 25 Bond angle restraints: 23915 Sorted by residual: angle pdb=" N ARG C 716 " pdb=" CA ARG C 716 " pdb=" C ARG C 716 " ideal model delta sigma weight residual 107.73 111.83 -4.10 1.34e+00 5.57e-01 9.36e+00 angle pdb=" N ARG E 716 " pdb=" CA ARG E 716 " pdb=" C ARG E 716 " ideal model delta sigma weight residual 107.73 111.83 -4.10 1.34e+00 5.57e-01 9.35e+00 angle pdb=" N ARG D 716 " pdb=" CA ARG D 716 " pdb=" C ARG D 716 " ideal model delta sigma weight residual 107.73 111.82 -4.09 1.34e+00 5.57e-01 9.30e+00 angle pdb=" N ARG A 716 " pdb=" CA ARG A 716 " pdb=" C ARG A 716 " ideal model delta sigma weight residual 107.73 111.81 -4.08 1.34e+00 5.57e-01 9.25e+00 angle pdb=" N ARG B 716 " pdb=" CA ARG B 716 " pdb=" C ARG B 716 " ideal model delta sigma weight residual 107.73 111.77 -4.04 1.34e+00 5.57e-01 9.09e+00 ... (remaining 23910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.17: 9219 12.17 - 24.34: 556 24.34 - 36.50: 345 36.50 - 48.67: 60 48.67 - 60.84: 35 Dihedral angle restraints: 10215 sinusoidal: 2325 harmonic: 7890 Sorted by residual: dihedral pdb=" CA TYR E 254 " pdb=" C TYR E 254 " pdb=" N GLN E 255 " pdb=" CA GLN E 255 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA TYR C 254 " pdb=" C TYR C 254 " pdb=" N GLN C 255 " pdb=" CA GLN C 255 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA TYR D 254 " pdb=" C TYR D 254 " pdb=" N GLN D 255 " pdb=" CA GLN D 255 " ideal model delta harmonic sigma weight residual 180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 10212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1807 0.035 - 0.070: 926 0.070 - 0.104: 150 0.104 - 0.139: 17 0.139 - 0.174: 5 Chirality restraints: 2905 Sorted by residual: chirality pdb=" CB ILE A 644 " pdb=" CA ILE A 644 " pdb=" CG1 ILE A 644 " pdb=" CG2 ILE A 644 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CB ILE E 644 " pdb=" CA ILE E 644 " pdb=" CG1 ILE E 644 " pdb=" CG2 ILE E 644 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CB ILE B 644 " pdb=" CA ILE B 644 " pdb=" CG1 ILE B 644 " pdb=" CG2 ILE B 644 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 2902 not shown) Planarity restraints: 3225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 274 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO C 275 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 275 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 275 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 274 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO A 275 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 275 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 275 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 274 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO E 275 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 275 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 275 " -0.024 5.00e-02 4.00e+02 ... (remaining 3222 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5489 2.81 - 3.34: 17749 3.34 - 3.86: 25065 3.86 - 4.38: 27052 4.38 - 4.90: 42459 Nonbonded interactions: 117814 Sorted by model distance: nonbonded pdb=" NH1 ARG E 712 " pdb=" O SER E 713 " model vdw 2.293 3.120 nonbonded pdb=" NH1 ARG B 712 " pdb=" O SER B 713 " model vdw 2.294 3.120 nonbonded pdb=" NH1 ARG C 712 " pdb=" O SER C 713 " model vdw 2.294 3.120 nonbonded pdb=" NH1 ARG A 712 " pdb=" O SER A 713 " model vdw 2.294 3.120 nonbonded pdb=" NH1 ARG D 712 " pdb=" O SER D 713 " model vdw 2.294 3.120 ... (remaining 117809 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 group one per residue 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.350 Find NCS groups from input model: 0.180 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 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 0.039 17420 Z= 0.108 Angle : 0.542 5.386 23915 Z= 0.293 Chirality : 0.038 0.174 2905 Planarity : 0.003 0.043 3225 Dihedral : 12.426 60.840 5055 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.30 % Favored : 83.51 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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 aren not related in a simple way. whole: -2.00 (0.17), residues: 2650 helix: 0.09 (0.15), residues: 1345 sheet: None (None), residues: 0 loop : -3.02 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 712 TYR 0.014 0.001 TYR D 594 PHE 0.017 0.001 PHE C 445 TRP 0.005 0.001 TRP B 692 HIS 0.001 0.000 HIS E 585 Details of bonding type rmsd covalent geometry : bond 0.00221 (17420) covalent geometry : angle 0.54248 (23915) hydrogen bonds : bond 0.28456 ( 921) hydrogen bonds : angle 8.88618 ( 2688) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8599 (m-30) cc_final: 0.8122 (m-30) REVERT: A 213 TYR cc_start: 0.4301 (m-10) cc_final: 0.4024 (m-10) REVERT: A 240 ASP cc_start: 0.6976 (m-30) cc_final: 0.6557 (m-30) REVERT: A 562 MET cc_start: 0.7327 (ppp) cc_final: 0.7109 (ppp) REVERT: A 665 THR cc_start: 0.8769 (m) cc_final: 0.8531 (m) REVERT: A 706 MET cc_start: 0.6215 (mmm) cc_final: 0.5884 (mmp) REVERT: B 166 ASP cc_start: 0.8437 (m-30) cc_final: 0.7953 (m-30) REVERT: B 240 ASP cc_start: 0.7496 (m-30) cc_final: 0.7140 (m-30) REVERT: B 562 MET cc_start: 0.7265 (ppp) cc_final: 0.7037 (ppp) REVERT: B 641 ASP cc_start: 0.7905 (m-30) cc_final: 0.7409 (m-30) REVERT: B 661 TYR cc_start: 0.8699 (t80) cc_final: 0.8429 (t80) REVERT: B 706 MET cc_start: 0.5491 (mmm) cc_final: 0.5268 (mmp) REVERT: B 712 ARG cc_start: 0.5524 (tpt90) cc_final: 0.4852 (tpt90) REVERT: C 166 ASP cc_start: 0.8354 (m-30) cc_final: 0.7883 (m-30) REVERT: C 240 ASP cc_start: 0.6896 (m-30) cc_final: 0.6537 (m-30) REVERT: C 440 MET cc_start: 0.7263 (tpt) cc_final: 0.6088 (ttm) REVERT: C 562 MET cc_start: 0.7495 (ppp) cc_final: 0.7265 (ppp) REVERT: C 706 MET cc_start: 0.5955 (mmm) cc_final: 0.5732 (mmp) REVERT: D 166 ASP cc_start: 0.8406 (m-30) cc_final: 0.7874 (m-30) REVERT: D 240 ASP cc_start: 0.6898 (m-30) cc_final: 0.6560 (m-30) REVERT: D 286 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8468 (tm-30) REVERT: D 706 MET cc_start: 0.5769 (mmm) cc_final: 0.5383 (tpt) REVERT: E 166 ASP cc_start: 0.8421 (m-30) cc_final: 0.7884 (m-30) REVERT: E 240 ASP cc_start: 0.7418 (m-30) cc_final: 0.7111 (m-30) REVERT: E 562 MET cc_start: 0.7486 (ppp) cc_final: 0.7259 (ppp) REVERT: E 712 ARG cc_start: 0.5409 (tpt90) cc_final: 0.5084 (tpt90) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.1188 time to fit residues: 56.0010 Evaluate side-chains 263 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS D 256 HIS E 256 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.215568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.173826 restraints weight = 35461.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.178022 restraints weight = 24977.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.181101 restraints weight = 19184.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.183370 restraints weight = 15667.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.184885 restraints weight = 13408.087| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17420 Z= 0.128 Angle : 0.573 5.799 23915 Z= 0.313 Chirality : 0.040 0.129 2905 Planarity : 0.004 0.028 3225 Dihedral : 4.029 18.347 2780 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.49 % Favored : 85.32 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % 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 aren not related in a simple way. whole: -1.99 (0.16), residues: 2650 helix: 0.31 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -3.49 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 690 TYR 0.039 0.001 TYR A 594 PHE 0.017 0.002 PHE E 445 TRP 0.007 0.000 TRP A 692 HIS 0.001 0.001 HIS B 585 Details of bonding type rmsd covalent geometry : bond 0.00254 (17420) covalent geometry : angle 0.57268 (23915) hydrogen bonds : bond 0.04750 ( 921) hydrogen bonds : angle 5.93056 ( 2688) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8601 (m-30) cc_final: 0.8052 (m-30) REVERT: A 240 ASP cc_start: 0.6877 (m-30) cc_final: 0.6636 (m-30) REVERT: A 645 GLN cc_start: 0.6455 (mp10) cc_final: 0.5415 (mp10) REVERT: A 712 ARG cc_start: 0.4899 (tpt90) cc_final: 0.3964 (tpt90) REVERT: B 166 ASP cc_start: 0.8352 (m-30) cc_final: 0.7834 (m-30) REVERT: B 240 ASP cc_start: 0.7438 (m-30) cc_final: 0.7074 (m-30) REVERT: B 282 MET cc_start: 0.7714 (tpt) cc_final: 0.7492 (tpt) REVERT: B 641 ASP cc_start: 0.7811 (m-30) cc_final: 0.7274 (m-30) REVERT: B 706 MET cc_start: 0.5695 (mmm) cc_final: 0.5483 (mmp) REVERT: B 712 ARG cc_start: 0.5274 (tpt90) cc_final: 0.4722 (tpt90) REVERT: C 166 ASP cc_start: 0.8191 (m-30) cc_final: 0.7713 (m-30) REVERT: C 240 ASP cc_start: 0.7026 (m-30) cc_final: 0.6614 (m-30) REVERT: C 645 GLN cc_start: 0.6969 (mp10) cc_final: 0.6327 (mp10) REVERT: D 166 ASP cc_start: 0.8224 (m-30) cc_final: 0.7680 (m-30) REVERT: D 240 ASP cc_start: 0.6921 (m-30) cc_final: 0.6623 (m-30) REVERT: D 706 MET cc_start: 0.6060 (mmm) cc_final: 0.5642 (tpt) REVERT: D 712 ARG cc_start: 0.5497 (tpt90) cc_final: 0.5213 (tpt90) REVERT: E 166 ASP cc_start: 0.8327 (m-30) cc_final: 0.7805 (m-30) REVERT: E 240 ASP cc_start: 0.7381 (m-30) cc_final: 0.7070 (m-30) REVERT: E 594 TYR cc_start: 0.8060 (m-80) cc_final: 0.7721 (m-80) REVERT: E 712 ARG cc_start: 0.5354 (tpt90) cc_final: 0.4814 (tpt90) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1175 time to fit residues: 54.5637 Evaluate side-chains 262 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 109 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 241 optimal weight: 8.9990 chunk 133 optimal weight: 0.0050 chunk 5 optimal weight: 0.0980 chunk 14 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.217682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.175188 restraints weight = 36279.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.179682 restraints weight = 25153.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.182943 restraints weight = 19099.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.185300 restraints weight = 15480.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.187181 restraints weight = 13151.388| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17420 Z= 0.107 Angle : 0.543 5.644 23915 Z= 0.291 Chirality : 0.040 0.145 2905 Planarity : 0.003 0.026 3225 Dihedral : 3.862 18.342 2780 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.13 % Favored : 84.68 % Rotamer: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % 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 aren not related in a simple way. whole: -1.69 (0.17), residues: 2650 helix: 0.68 (0.14), residues: 1450 sheet: None (None), residues: 0 loop : -3.63 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 690 TYR 0.037 0.001 TYR A 594 PHE 0.013 0.001 PHE A 449 TRP 0.009 0.001 TRP A 692 HIS 0.008 0.001 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00222 (17420) covalent geometry : angle 0.54314 (23915) hydrogen bonds : bond 0.03811 ( 921) hydrogen bonds : angle 5.14744 ( 2688) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8514 (m-30) cc_final: 0.7929 (m-30) REVERT: A 240 ASP cc_start: 0.6848 (m-30) cc_final: 0.6554 (m-30) REVERT: A 562 MET cc_start: 0.7036 (ppp) cc_final: 0.6812 (ppp) REVERT: A 594 TYR cc_start: 0.8141 (m-80) cc_final: 0.7737 (m-80) REVERT: B 166 ASP cc_start: 0.8277 (m-30) cc_final: 0.7784 (m-30) REVERT: B 240 ASP cc_start: 0.7464 (m-30) cc_final: 0.7228 (m-30) REVERT: B 282 MET cc_start: 0.7867 (tpt) cc_final: 0.7616 (tpt) REVERT: B 594 TYR cc_start: 0.7989 (m-80) cc_final: 0.7777 (m-80) REVERT: B 706 MET cc_start: 0.5688 (mmm) cc_final: 0.5480 (mmp) REVERT: B 712 ARG cc_start: 0.5583 (tpt90) cc_final: 0.5006 (tpt90) REVERT: C 166 ASP cc_start: 0.8185 (m-30) cc_final: 0.7685 (m-30) REVERT: C 240 ASP cc_start: 0.7117 (m-30) cc_final: 0.6698 (m-30) REVERT: C 562 MET cc_start: 0.7288 (ppp) cc_final: 0.7067 (ppp) REVERT: C 645 GLN cc_start: 0.6934 (mp10) cc_final: 0.6250 (mp10) REVERT: D 166 ASP cc_start: 0.8299 (m-30) cc_final: 0.7795 (m-30) REVERT: D 240 ASP cc_start: 0.6946 (m-30) cc_final: 0.6650 (m-30) REVERT: D 706 MET cc_start: 0.6110 (mmm) cc_final: 0.5732 (tpt) REVERT: D 712 ARG cc_start: 0.5737 (tpt90) cc_final: 0.5163 (tpt90) REVERT: E 166 ASP cc_start: 0.8322 (m-30) cc_final: 0.7825 (m-30) REVERT: E 240 ASP cc_start: 0.7423 (m-30) cc_final: 0.7168 (m-30) REVERT: E 712 ARG cc_start: 0.5384 (tpt90) cc_final: 0.4588 (tpt90) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1286 time to fit residues: 57.8957 Evaluate side-chains 257 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 208 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 227 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.209209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.174254 restraints weight = 35745.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.174726 restraints weight = 26350.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.176003 restraints weight = 23667.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.177084 restraints weight = 18695.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.178443 restraints weight = 16407.296| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17420 Z= 0.183 Angle : 0.632 5.836 23915 Z= 0.349 Chirality : 0.042 0.161 2905 Planarity : 0.004 0.041 3225 Dihedral : 4.571 21.441 2780 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.26 % Favored : 83.55 % Rotamer: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % 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 aren not related in a simple way. whole: -2.02 (0.16), residues: 2650 helix: 0.42 (0.14), residues: 1415 sheet: None (None), residues: 0 loop : -3.69 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 712 TYR 0.026 0.002 TYR A 594 PHE 0.021 0.002 PHE A 449 TRP 0.010 0.001 TRP A 692 HIS 0.005 0.001 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00349 (17420) covalent geometry : angle 0.63238 (23915) hydrogen bonds : bond 0.04162 ( 921) hydrogen bonds : angle 5.47699 ( 2688) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8586 (m-30) cc_final: 0.8044 (m-30) REVERT: A 562 MET cc_start: 0.7071 (ppp) cc_final: 0.6765 (ppp) REVERT: B 166 ASP cc_start: 0.8453 (m-30) cc_final: 0.7963 (m-30) REVERT: B 282 MET cc_start: 0.8140 (tpt) cc_final: 0.7909 (tpt) REVERT: B 562 MET cc_start: 0.7006 (ppp) cc_final: 0.6770 (ppp) REVERT: B 706 MET cc_start: 0.5858 (mmm) cc_final: 0.5563 (mmp) REVERT: B 712 ARG cc_start: 0.5994 (tpt90) cc_final: 0.5181 (tpt90) REVERT: C 166 ASP cc_start: 0.8386 (m-30) cc_final: 0.7916 (m-30) REVERT: C 240 ASP cc_start: 0.7167 (m-30) cc_final: 0.6881 (m-30) REVERT: C 562 MET cc_start: 0.6983 (ppp) cc_final: 0.6740 (ppp) REVERT: D 166 ASP cc_start: 0.8371 (m-30) cc_final: 0.7808 (m-30) REVERT: D 240 ASP cc_start: 0.7196 (m-30) cc_final: 0.6938 (m-30) REVERT: D 712 ARG cc_start: 0.6082 (tpt90) cc_final: 0.4975 (tpt90) REVERT: E 166 ASP cc_start: 0.8482 (m-30) cc_final: 0.7968 (m-30) REVERT: E 240 ASP cc_start: 0.7479 (m-30) cc_final: 0.7187 (m-30) REVERT: E 324 ILE cc_start: 0.7199 (mt) cc_final: 0.6982 (mt) REVERT: E 488 MET cc_start: 0.6562 (mtt) cc_final: 0.5944 (mtt) REVERT: E 562 MET cc_start: 0.7070 (ppp) cc_final: 0.6808 (ppp) REVERT: E 712 ARG cc_start: 0.5808 (tpt90) cc_final: 0.5190 (tpt90) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1319 time to fit residues: 61.3908 Evaluate side-chains 270 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 260 optimal weight: 5.9990 chunk 189 optimal weight: 0.4980 chunk 133 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 111 optimal weight: 0.0000 chunk 244 optimal weight: 0.5980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.211908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.175548 restraints weight = 35985.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.177173 restraints weight = 24684.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.178814 restraints weight = 19830.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.180029 restraints weight = 15792.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.180613 restraints weight = 13874.816| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17420 Z= 0.123 Angle : 0.586 7.138 23915 Z= 0.314 Chirality : 0.041 0.236 2905 Planarity : 0.003 0.038 3225 Dihedral : 4.355 18.651 2780 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.42 % Favored : 85.36 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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 aren not related in a simple way. whole: -1.73 (0.16), residues: 2650 helix: 0.71 (0.14), residues: 1410 sheet: None (None), residues: 0 loop : -3.61 (0.16), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 690 TYR 0.027 0.002 TYR A 594 PHE 0.015 0.001 PHE A 449 TRP 0.011 0.001 TRP A 692 HIS 0.005 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00249 (17420) covalent geometry : angle 0.58558 (23915) hydrogen bonds : bond 0.03563 ( 921) hydrogen bonds : angle 5.15644 ( 2688) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8535 (m-30) cc_final: 0.8010 (m-30) REVERT: A 562 MET cc_start: 0.7030 (ppp) cc_final: 0.6723 (ppp) REVERT: A 645 GLN cc_start: 0.6570 (mp10) cc_final: 0.5449 (mp10) REVERT: A 712 ARG cc_start: 0.5321 (tpt170) cc_final: 0.4976 (tpt90) REVERT: B 166 ASP cc_start: 0.8448 (m-30) cc_final: 0.7968 (m-30) REVERT: B 712 ARG cc_start: 0.5671 (tpt90) cc_final: 0.4820 (tpt90) REVERT: C 166 ASP cc_start: 0.8228 (m-30) cc_final: 0.7738 (m-30) REVERT: C 240 ASP cc_start: 0.7176 (m-30) cc_final: 0.6741 (m-30) REVERT: C 562 MET cc_start: 0.6871 (ppp) cc_final: 0.6609 (ppp) REVERT: C 712 ARG cc_start: 0.5572 (tpt170) cc_final: 0.5115 (tpt90) REVERT: D 166 ASP cc_start: 0.8402 (m-30) cc_final: 0.7864 (m-30) REVERT: D 240 ASP cc_start: 0.7222 (m-30) cc_final: 0.6932 (m-30) REVERT: D 706 MET cc_start: 0.6474 (mmp) cc_final: 0.5969 (tpt) REVERT: D 712 ARG cc_start: 0.6005 (tpt90) cc_final: 0.4859 (tpt90) REVERT: E 166 ASP cc_start: 0.8447 (m-30) cc_final: 0.7917 (m-30) REVERT: E 240 ASP cc_start: 0.7477 (m-30) cc_final: 0.7188 (m-30) REVERT: E 324 ILE cc_start: 0.7041 (mt) cc_final: 0.6835 (mt) REVERT: E 488 MET cc_start: 0.6474 (mtt) cc_final: 0.5876 (mtt) REVERT: E 562 MET cc_start: 0.7018 (ppp) cc_final: 0.6800 (ppp) REVERT: E 712 ARG cc_start: 0.5679 (tpt90) cc_final: 0.5136 (tpt90) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.1303 time to fit residues: 62.4252 Evaluate side-chains 268 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 0.0270 chunk 3 optimal weight: 0.0030 chunk 71 optimal weight: 4.9990 chunk 142 optimal weight: 0.6980 chunk 249 optimal weight: 0.5980 chunk 169 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.3448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.218596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.176669 restraints weight = 35714.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.181159 restraints weight = 24558.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.184484 restraints weight = 18482.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.186797 restraints weight = 14885.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.188725 restraints weight = 12579.380| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17420 Z= 0.101 Angle : 0.556 6.129 23915 Z= 0.294 Chirality : 0.040 0.246 2905 Planarity : 0.003 0.030 3225 Dihedral : 3.959 20.611 2780 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.58 % Favored : 86.11 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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 aren not related in a simple way. whole: -1.46 (0.17), residues: 2650 helix: 1.01 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -3.64 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 690 TYR 0.027 0.001 TYR D 594 PHE 0.013 0.001 PHE B 526 TRP 0.015 0.001 TRP A 692 HIS 0.004 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00213 (17420) covalent geometry : angle 0.55620 (23915) hydrogen bonds : bond 0.03045 ( 921) hydrogen bonds : angle 4.58362 ( 2688) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8434 (m-30) cc_final: 0.7870 (m-30) REVERT: A 562 MET cc_start: 0.7006 (ppp) cc_final: 0.6727 (ppp) REVERT: A 594 TYR cc_start: 0.7973 (m-80) cc_final: 0.7517 (m-80) REVERT: A 645 GLN cc_start: 0.6467 (mp10) cc_final: 0.5321 (mp10) REVERT: B 166 ASP cc_start: 0.8305 (m-30) cc_final: 0.7809 (m-30) REVERT: B 488 MET cc_start: 0.6562 (mtt) cc_final: 0.5862 (mtt) REVERT: B 635 LEU cc_start: 0.8724 (pp) cc_final: 0.8336 (pp) REVERT: B 712 ARG cc_start: 0.5611 (tpt90) cc_final: 0.4662 (tpt90) REVERT: C 166 ASP cc_start: 0.8271 (m-30) cc_final: 0.7817 (m-30) REVERT: C 240 ASP cc_start: 0.7039 (m-30) cc_final: 0.6684 (m-30) REVERT: C 665 THR cc_start: 0.9061 (m) cc_final: 0.8857 (m) REVERT: D 166 ASP cc_start: 0.8330 (m-30) cc_final: 0.7836 (m-30) REVERT: D 240 ASP cc_start: 0.7310 (m-30) cc_final: 0.6999 (m-30) REVERT: D 594 TYR cc_start: 0.8225 (m-80) cc_final: 0.7826 (m-80) REVERT: D 706 MET cc_start: 0.6568 (mmp) cc_final: 0.6279 (mmm) REVERT: D 712 ARG cc_start: 0.6019 (tpt90) cc_final: 0.4920 (tpt90) REVERT: E 166 ASP cc_start: 0.8363 (m-30) cc_final: 0.7854 (m-30) REVERT: E 240 ASP cc_start: 0.7372 (m-30) cc_final: 0.7056 (m-30) REVERT: E 488 MET cc_start: 0.6700 (mtt) cc_final: 0.6137 (mtt) REVERT: E 712 ARG cc_start: 0.5572 (tpt90) cc_final: 0.4933 (tpt90) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.1331 time to fit residues: 62.3147 Evaluate side-chains 265 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 235 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 99 optimal weight: 0.0370 chunk 222 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 overall best weight: 2.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 ASN ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.209440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.174457 restraints weight = 36373.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.175956 restraints weight = 27260.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.177243 restraints weight = 22931.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.178506 restraints weight = 18135.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.178956 restraints weight = 15822.440| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17420 Z= 0.177 Angle : 0.653 6.844 23915 Z= 0.356 Chirality : 0.043 0.247 2905 Planarity : 0.004 0.047 3225 Dihedral : 4.578 21.653 2780 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.96 % Favored : 83.77 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % 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 aren not related in a simple way. whole: -1.84 (0.16), residues: 2650 helix: 0.60 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -3.67 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 567 TYR 0.027 0.002 TYR A 594 PHE 0.025 0.002 PHE E 449 TRP 0.014 0.001 TRP A 692 HIS 0.007 0.001 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00341 (17420) covalent geometry : angle 0.65271 (23915) hydrogen bonds : bond 0.03775 ( 921) hydrogen bonds : angle 5.15141 ( 2688) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8471 (m-30) cc_final: 0.7910 (m-30) REVERT: A 562 MET cc_start: 0.6940 (ppp) cc_final: 0.6575 (ppp) REVERT: B 166 ASP cc_start: 0.8421 (m-30) cc_final: 0.7946 (m-30) REVERT: B 261 PHE cc_start: 0.8098 (m-10) cc_final: 0.7706 (m-80) REVERT: B 282 MET cc_start: 0.8106 (tpt) cc_final: 0.7800 (tpt) REVERT: B 712 ARG cc_start: 0.5836 (tpt90) cc_final: 0.4817 (tpt90) REVERT: C 166 ASP cc_start: 0.8374 (m-30) cc_final: 0.7908 (m-30) REVERT: C 240 ASP cc_start: 0.7195 (m-30) cc_final: 0.6888 (m-30) REVERT: C 562 MET cc_start: 0.7138 (ppp) cc_final: 0.6890 (ppp) REVERT: D 166 ASP cc_start: 0.8469 (m-30) cc_final: 0.7926 (m-30) REVERT: D 562 MET cc_start: 0.6939 (ppp) cc_final: 0.6725 (ppp) REVERT: D 712 ARG cc_start: 0.6083 (tpt90) cc_final: 0.4789 (tpt90) REVERT: E 166 ASP cc_start: 0.8480 (m-30) cc_final: 0.7927 (m-30) REVERT: E 240 ASP cc_start: 0.7355 (m-30) cc_final: 0.7101 (m-30) REVERT: E 712 ARG cc_start: 0.5900 (tpt90) cc_final: 0.5265 (tpt90) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.1291 time to fit residues: 61.2438 Evaluate side-chains 271 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 148 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 251 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 198 optimal weight: 7.9990 chunk 2 optimal weight: 30.0000 chunk 196 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.213768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.178262 restraints weight = 36329.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.179477 restraints weight = 27641.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.181617 restraints weight = 21374.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.182242 restraints weight = 16715.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.184271 restraints weight = 15084.176| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17420 Z= 0.117 Angle : 0.593 7.218 23915 Z= 0.316 Chirality : 0.041 0.251 2905 Planarity : 0.003 0.044 3225 Dihedral : 4.343 19.972 2780 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.11 % Favored : 85.62 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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 aren not related in a simple way. whole: -1.66 (0.17), residues: 2650 helix: 0.72 (0.14), residues: 1455 sheet: None (None), residues: 0 loop : -3.67 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 690 TYR 0.029 0.001 TYR A 594 PHE 0.018 0.001 PHE A 124 TRP 0.016 0.001 TRP A 692 HIS 0.003 0.001 HIS E 256 Details of bonding type rmsd covalent geometry : bond 0.00241 (17420) covalent geometry : angle 0.59331 (23915) hydrogen bonds : bond 0.03261 ( 921) hydrogen bonds : angle 4.83493 ( 2688) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8477 (m-30) cc_final: 0.7925 (m-30) REVERT: A 449 PHE cc_start: 0.7542 (t80) cc_final: 0.7272 (t80) REVERT: A 562 MET cc_start: 0.6913 (ppp) cc_final: 0.6629 (ppp) REVERT: A 594 TYR cc_start: 0.7996 (m-80) cc_final: 0.7620 (m-80) REVERT: B 166 ASP cc_start: 0.8460 (m-30) cc_final: 0.7971 (m-30) REVERT: B 261 PHE cc_start: 0.8198 (m-10) cc_final: 0.7990 (m-80) REVERT: B 712 ARG cc_start: 0.5824 (tpt90) cc_final: 0.4905 (tpt90) REVERT: C 166 ASP cc_start: 0.8376 (m-30) cc_final: 0.7893 (m-30) REVERT: C 240 ASP cc_start: 0.7132 (m-30) cc_final: 0.6878 (m-30) REVERT: C 565 TYR cc_start: 0.7431 (m-80) cc_final: 0.7212 (m-80) REVERT: D 166 ASP cc_start: 0.8559 (m-30) cc_final: 0.8019 (m-30) REVERT: D 240 ASP cc_start: 0.7437 (m-30) cc_final: 0.7189 (m-30) REVERT: D 712 ARG cc_start: 0.6226 (tpt90) cc_final: 0.4944 (tpt90) REVERT: E 166 ASP cc_start: 0.8483 (m-30) cc_final: 0.7927 (m-30) REVERT: E 240 ASP cc_start: 0.7271 (m-30) cc_final: 0.7006 (m-30) REVERT: E 706 MET cc_start: 0.6428 (mmm) cc_final: 0.6101 (tpt) REVERT: E 712 ARG cc_start: 0.5946 (tpt90) cc_final: 0.5255 (tpt90) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1251 time to fit residues: 58.9781 Evaluate side-chains 267 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 92 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 166 optimal weight: 0.1980 chunk 34 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.206933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.171610 restraints weight = 36483.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.173620 restraints weight = 26734.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.174546 restraints weight = 20967.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.175859 restraints weight = 17169.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.176596 restraints weight = 14866.531| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17420 Z= 0.181 Angle : 0.676 7.854 23915 Z= 0.368 Chirality : 0.043 0.235 2905 Planarity : 0.004 0.045 3225 Dihedral : 4.819 23.684 2780 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.91 % Favored : 82.87 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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 aren not related in a simple way. whole: -2.05 (0.16), residues: 2650 helix: 0.37 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -3.71 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 464 TYR 0.029 0.002 TYR A 594 PHE 0.028 0.002 PHE A 449 TRP 0.012 0.001 TRP A 692 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00347 (17420) covalent geometry : angle 0.67647 (23915) hydrogen bonds : bond 0.03924 ( 921) hydrogen bonds : angle 5.25854 ( 2688) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8508 (m-30) cc_final: 0.8011 (m-30) REVERT: A 562 MET cc_start: 0.7129 (ppp) cc_final: 0.6796 (ppp) REVERT: A 594 TYR cc_start: 0.8041 (m-80) cc_final: 0.7676 (m-80) REVERT: A 710 TRP cc_start: 0.6531 (t60) cc_final: 0.6294 (t60) REVERT: A 712 ARG cc_start: 0.5890 (tpt170) cc_final: 0.4184 (tpt90) REVERT: B 166 ASP cc_start: 0.8543 (m-30) cc_final: 0.8054 (m-30) REVERT: B 282 MET cc_start: 0.8039 (tpt) cc_final: 0.7825 (tpt) REVERT: B 449 PHE cc_start: 0.7595 (t80) cc_final: 0.7305 (t80) REVERT: B 565 TYR cc_start: 0.8194 (m-80) cc_final: 0.7759 (m-80) REVERT: B 712 ARG cc_start: 0.5941 (tpt90) cc_final: 0.5096 (tpt90) REVERT: C 166 ASP cc_start: 0.8444 (m-30) cc_final: 0.7994 (m-30) REVERT: C 240 ASP cc_start: 0.6925 (m-30) cc_final: 0.6567 (m-30) REVERT: C 565 TYR cc_start: 0.7644 (m-80) cc_final: 0.7431 (m-80) REVERT: D 166 ASP cc_start: 0.8507 (m-30) cc_final: 0.7940 (m-30) REVERT: D 712 ARG cc_start: 0.6094 (tpt90) cc_final: 0.4822 (tpt90) REVERT: E 166 ASP cc_start: 0.8536 (m-30) cc_final: 0.7943 (m-30) REVERT: E 240 ASP cc_start: 0.7308 (m-30) cc_final: 0.7041 (m-30) REVERT: E 324 ILE cc_start: 0.7116 (mt) cc_final: 0.6907 (mt) REVERT: E 449 PHE cc_start: 0.7762 (t80) cc_final: 0.7388 (t80) REVERT: E 562 MET cc_start: 0.7265 (ppp) cc_final: 0.7033 (ppp) REVERT: E 712 ARG cc_start: 0.5942 (tpt90) cc_final: 0.5394 (tpt90) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1319 time to fit residues: 62.4464 Evaluate side-chains 268 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 127 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 173 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.214465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.178951 restraints weight = 35126.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.180848 restraints weight = 25420.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.181963 restraints weight = 21203.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.182873 restraints weight = 16965.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.184252 restraints weight = 14912.203| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17420 Z= 0.111 Angle : 0.595 6.651 23915 Z= 0.315 Chirality : 0.042 0.262 2905 Planarity : 0.003 0.040 3225 Dihedral : 4.416 20.782 2780 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.00 % Favored : 85.74 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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 aren not related in a simple way. whole: -1.66 (0.17), residues: 2650 helix: 0.70 (0.14), residues: 1455 sheet: None (None), residues: 0 loop : -3.62 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 690 TYR 0.027 0.001 TYR A 594 PHE 0.016 0.001 PHE E 449 TRP 0.019 0.001 TRP A 692 HIS 0.004 0.001 HIS E 256 Details of bonding type rmsd covalent geometry : bond 0.00229 (17420) covalent geometry : angle 0.59460 (23915) hydrogen bonds : bond 0.03234 ( 921) hydrogen bonds : angle 4.77768 ( 2688) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8498 (m-30) cc_final: 0.7880 (m-30) REVERT: A 464 ARG cc_start: 0.5258 (ttp-170) cc_final: 0.4989 (ttp80) REVERT: A 562 MET cc_start: 0.6936 (ppp) cc_final: 0.6569 (ppp) REVERT: A 594 TYR cc_start: 0.7986 (m-80) cc_final: 0.7609 (m-80) REVERT: B 166 ASP cc_start: 0.8459 (m-30) cc_final: 0.7975 (m-30) REVERT: B 449 PHE cc_start: 0.7540 (t80) cc_final: 0.7119 (t80) REVERT: B 562 MET cc_start: 0.7095 (ppp) cc_final: 0.6893 (ppp) REVERT: B 565 TYR cc_start: 0.8163 (m-80) cc_final: 0.7707 (m-80) REVERT: B 712 ARG cc_start: 0.5825 (tpt90) cc_final: 0.5096 (tpt90) REVERT: C 166 ASP cc_start: 0.8365 (m-30) cc_final: 0.7930 (m-30) REVERT: C 240 ASP cc_start: 0.7169 (m-30) cc_final: 0.6925 (m-30) REVERT: C 488 MET cc_start: 0.5148 (mtt) cc_final: 0.4623 (mtt) REVERT: D 166 ASP cc_start: 0.8511 (m-30) cc_final: 0.8006 (m-30) REVERT: D 449 PHE cc_start: 0.7372 (t80) cc_final: 0.7020 (t80) REVERT: D 706 MET cc_start: 0.6642 (mmp) cc_final: 0.6422 (mmm) REVERT: E 166 ASP cc_start: 0.8415 (m-30) cc_final: 0.7904 (m-30) REVERT: E 240 ASP cc_start: 0.7227 (m-30) cc_final: 0.6941 (m-30) REVERT: E 261 PHE cc_start: 0.8351 (m-10) cc_final: 0.8136 (m-80) REVERT: E 706 MET cc_start: 0.6509 (mmm) cc_final: 0.6195 (tpt) REVERT: E 712 ARG cc_start: 0.5929 (tpt90) cc_final: 0.5074 (tpt90) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1298 time to fit residues: 61.3276 Evaluate side-chains 265 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 161 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 157 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 3 optimal weight: 50.0000 chunk 251 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.209844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.174178 restraints weight = 36128.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.176454 restraints weight = 27551.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.177789 restraints weight = 21580.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.178685 restraints weight = 17506.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.179266 restraints weight = 15548.574| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17420 Z= 0.154 Angle : 0.641 7.446 23915 Z= 0.345 Chirality : 0.043 0.230 2905 Planarity : 0.004 0.074 3225 Dihedral : 4.611 21.444 2780 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.19 % Favored : 83.58 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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 aren not related in a simple way. whole: -1.85 (0.17), residues: 2650 helix: 0.55 (0.14), residues: 1455 sheet: None (None), residues: 0 loop : -3.72 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 712 TYR 0.028 0.002 TYR A 594 PHE 0.025 0.002 PHE C 449 TRP 0.015 0.001 TRP A 692 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00302 (17420) covalent geometry : angle 0.64148 (23915) hydrogen bonds : bond 0.03577 ( 921) hydrogen bonds : angle 5.02457 ( 2688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2882.13 seconds wall clock time: 50 minutes 16.36 seconds (3016.36 seconds total)