Starting phenix.real_space_refine on Sun May 18 16:55:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gkg_40183/05_2025/8gkg_40183.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gkg_40183/05_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_40183/05_2025/8gkg_40183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gkg_40183/05_2025/8gkg_40183.map" model { file = "/net/cci-nas-00/data/ceres_data/8gkg_40183/05_2025/8gkg_40183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gkg_40183/05_2025/8gkg_40183.cif" } resolution = 4.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 7, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 12, 'PHE:plan': 16, 'GLU:plan': 25, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 500 Restraints were copied for chains: C, B, E, D Time building chain proxies: 7.55, per 1000 atoms: 0.44 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: 4.65 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 1.65 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: 4.89 Time building geometry restraints manager: 5.26 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.990 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: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 36.170 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.340 ------------------------------------------------------------------------------- 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 : 5.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP B 692 HIS 0.001 0.000 HIS E 585 PHE 0.017 0.001 PHE C 445 TYR 0.014 0.001 TYR D 594 ARG 0.003 0.000 ARG C 712 Details of bonding type rmsd hydrogen bonds : bond 0.28456 ( 921) hydrogen bonds : angle 8.88618 ( 2688) covalent geometry : bond 0.00221 (17420) covalent geometry : angle 0.54248 (23915) *********************** 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 : 1.949 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: 0.2664 time to fit residues: 125.3659 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 : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 6.9990 chunk 204 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 69 optimal weight: 0.3980 chunk 138 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 211 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 245 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 HIS ** 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 = 0.4439 r_free = 0.4439 target = 0.213764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.179095 restraints weight = 35435.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.179522 restraints weight = 26379.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.181645 restraints weight = 21937.958| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.1549 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= 0.139 Angle : 0.586 5.886 23915 Z= 0.321 Chirality : 0.040 0.132 2905 Planarity : 0.004 0.032 3225 Dihedral : 4.160 18.067 2780 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.28 % Favored : 84.53 % Rotamer: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2650 helix: 0.24 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -3.58 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 692 HIS 0.002 0.001 HIS A 284 PHE 0.016 0.002 PHE E 445 TYR 0.037 0.002 TYR A 594 ARG 0.007 0.000 ARG D 690 Details of bonding type rmsd hydrogen bonds : bond 0.04754 ( 921) hydrogen bonds : angle 5.98397 ( 2688) covalent geometry : bond 0.00275 (17420) covalent geometry : angle 0.58604 (23915) *********************** 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 300 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8646 (m-30) cc_final: 0.8079 (m-30) REVERT: A 240 ASP cc_start: 0.6945 (m-30) cc_final: 0.6723 (m-30) REVERT: A 645 GLN cc_start: 0.6564 (mp10) cc_final: 0.5496 (mp10) REVERT: A 712 ARG cc_start: 0.5039 (tpt90) cc_final: 0.4098 (tpt90) REVERT: B 166 ASP cc_start: 0.8439 (m-30) cc_final: 0.7918 (m-30) REVERT: B 240 ASP cc_start: 0.7516 (m-30) cc_final: 0.7175 (m-30) REVERT: B 282 MET cc_start: 0.7804 (tpt) cc_final: 0.7562 (tpt) REVERT: B 641 ASP cc_start: 0.7792 (m-30) cc_final: 0.7234 (m-30) REVERT: B 706 MET cc_start: 0.5667 (mmm) cc_final: 0.5459 (mmp) REVERT: B 712 ARG cc_start: 0.5495 (tpt90) cc_final: 0.4830 (tpt90) REVERT: C 166 ASP cc_start: 0.8275 (m-30) cc_final: 0.7765 (m-30) REVERT: C 240 ASP cc_start: 0.6802 (m-30) cc_final: 0.6427 (m-30) REVERT: C 645 GLN cc_start: 0.7038 (mp10) cc_final: 0.6358 (mp10) REVERT: D 166 ASP cc_start: 0.8318 (m-30) cc_final: 0.7764 (m-30) REVERT: D 240 ASP cc_start: 0.6955 (m-30) cc_final: 0.6616 (m-30) REVERT: D 449 PHE cc_start: 0.7387 (t80) cc_final: 0.7161 (t80) REVERT: D 706 MET cc_start: 0.6032 (mmm) cc_final: 0.5609 (tpt) REVERT: D 712 ARG cc_start: 0.5720 (tpt90) cc_final: 0.5289 (tpt90) REVERT: E 166 ASP cc_start: 0.8386 (m-30) cc_final: 0.7873 (m-30) REVERT: E 240 ASP cc_start: 0.7430 (m-30) cc_final: 0.7112 (m-30) REVERT: E 594 TYR cc_start: 0.8022 (m-80) cc_final: 0.7665 (m-80) REVERT: E 712 ARG cc_start: 0.5533 (tpt90) cc_final: 0.4861 (tpt90) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2583 time to fit residues: 119.9286 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 : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 184 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 182 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 152 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 HIS ** 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 = 0.4416 r_free = 0.4416 target = 0.211399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.177679 restraints weight = 35976.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.178759 restraints weight = 23818.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.179096 restraints weight = 21981.065| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2043 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= 0.155 Angle : 0.606 5.850 23915 Z= 0.332 Chirality : 0.041 0.162 2905 Planarity : 0.004 0.033 3225 Dihedral : 4.358 18.567 2780 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.74 % Favored : 84.08 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.16), residues: 2650 helix: 0.25 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -3.63 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 692 HIS 0.008 0.002 HIS A 439 PHE 0.020 0.002 PHE D 449 TYR 0.036 0.002 TYR A 594 ARG 0.006 0.001 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 921) hydrogen bonds : angle 5.50665 ( 2688) covalent geometry : bond 0.00299 (17420) covalent geometry : angle 0.60646 (23915) *********************** 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 295 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8595 (m-30) cc_final: 0.8039 (m-30) REVERT: A 240 ASP cc_start: 0.7009 (m-30) cc_final: 0.6784 (m-30) REVERT: A 562 MET cc_start: 0.7064 (ppp) cc_final: 0.6789 (ppp) REVERT: A 594 TYR cc_start: 0.8090 (m-80) cc_final: 0.7681 (m-80) REVERT: A 645 GLN cc_start: 0.6700 (mp10) cc_final: 0.5591 (mp10) REVERT: A 712 ARG cc_start: 0.5305 (tpt90) cc_final: 0.4476 (tpt90) REVERT: B 166 ASP cc_start: 0.8412 (m-30) cc_final: 0.7925 (m-30) REVERT: B 282 MET cc_start: 0.7987 (tpt) cc_final: 0.7751 (tpt) REVERT: B 706 MET cc_start: 0.5797 (mmm) cc_final: 0.5568 (mmp) REVERT: B 712 ARG cc_start: 0.6009 (tpt90) cc_final: 0.5183 (tpt90) REVERT: C 166 ASP cc_start: 0.8243 (m-30) cc_final: 0.7761 (m-30) REVERT: C 240 ASP cc_start: 0.7100 (m-30) cc_final: 0.6691 (m-30) REVERT: C 562 MET cc_start: 0.7158 (ppp) cc_final: 0.6919 (ppp) REVERT: D 166 ASP cc_start: 0.8344 (m-30) cc_final: 0.7777 (m-30) REVERT: D 240 ASP cc_start: 0.7119 (m-30) cc_final: 0.6888 (m-30) REVERT: D 712 ARG cc_start: 0.6100 (tpt90) cc_final: 0.5080 (tpt90) REVERT: E 166 ASP cc_start: 0.8445 (m-30) cc_final: 0.7939 (m-30) REVERT: E 240 ASP cc_start: 0.7546 (m-30) cc_final: 0.7257 (m-30) REVERT: E 324 ILE cc_start: 0.7081 (mt) cc_final: 0.6862 (mt) REVERT: E 488 MET cc_start: 0.6565 (mtt) cc_final: 0.5970 (mtt) REVERT: E 562 MET cc_start: 0.7125 (ppp) cc_final: 0.6919 (ppp) REVERT: E 712 ARG cc_start: 0.5683 (tpt90) cc_final: 0.4949 (tpt90) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2564 time to fit residues: 116.0522 Evaluate side-chains 259 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 198 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 111 optimal weight: 0.0050 chunk 85 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- 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 ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS D 256 HIS ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.212112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.177101 restraints weight = 35261.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.178188 restraints weight = 24012.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.179210 restraints weight = 19729.557| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.2364 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= 0.129 Angle : 0.576 7.086 23915 Z= 0.312 Chirality : 0.040 0.141 2905 Planarity : 0.004 0.034 3225 Dihedral : 4.303 18.841 2780 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.75 % Favored : 85.06 % Rotamer: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.16), residues: 2650 helix: 0.62 (0.14), residues: 1385 sheet: None (None), residues: 0 loop : -3.66 (0.16), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 692 HIS 0.002 0.001 HIS C 585 PHE 0.017 0.001 PHE B 526 TYR 0.028 0.002 TYR A 594 ARG 0.005 0.000 ARG A 690 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 921) hydrogen bonds : angle 5.18973 ( 2688) covalent geometry : bond 0.00255 (17420) covalent geometry : angle 0.57565 (23915) *********************** 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 301 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8545 (m-30) cc_final: 0.7994 (m-30) REVERT: A 240 ASP cc_start: 0.7074 (m-30) cc_final: 0.6867 (m-30) REVERT: A 562 MET cc_start: 0.7049 (ppp) cc_final: 0.6746 (ppp) REVERT: A 645 GLN cc_start: 0.6593 (mp10) cc_final: 0.5460 (mp10) REVERT: A 712 ARG cc_start: 0.5440 (tpt90) cc_final: 0.4282 (tpt90) REVERT: B 166 ASP cc_start: 0.8376 (m-30) cc_final: 0.7910 (m-30) REVERT: B 282 MET cc_start: 0.8023 (tpt) cc_final: 0.7797 (tpt) REVERT: B 562 MET cc_start: 0.6925 (ppp) cc_final: 0.6717 (ppp) REVERT: B 712 ARG cc_start: 0.5659 (tpt90) cc_final: 0.4754 (tpt90) REVERT: C 166 ASP cc_start: 0.8257 (m-30) cc_final: 0.7791 (m-30) REVERT: C 240 ASP cc_start: 0.7188 (m-30) cc_final: 0.6778 (m-30) REVERT: C 562 MET cc_start: 0.7057 (ppp) cc_final: 0.6757 (ppp) REVERT: D 166 ASP cc_start: 0.8376 (m-30) cc_final: 0.7837 (m-30) REVERT: D 240 ASP cc_start: 0.7255 (m-30) cc_final: 0.6994 (m-30) REVERT: D 712 ARG cc_start: 0.6099 (tpt90) cc_final: 0.5073 (tpt90) REVERT: E 166 ASP cc_start: 0.8395 (m-30) cc_final: 0.7902 (m-30) REVERT: E 240 ASP cc_start: 0.7503 (m-30) cc_final: 0.7232 (m-30) REVERT: E 488 MET cc_start: 0.6572 (mtt) cc_final: 0.5996 (mtt) REVERT: E 562 MET cc_start: 0.7019 (ppp) cc_final: 0.6749 (ppp) REVERT: E 712 ARG cc_start: 0.5733 (tpt90) cc_final: 0.4985 (tpt90) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2623 time to fit residues: 120.4216 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 : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 238 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 117 optimal weight: 0.0010 overall best weight: 1.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 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 = 0.4426 r_free = 0.4426 target = 0.212134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.176579 restraints weight = 36448.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.178625 restraints weight = 26734.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.180055 restraints weight = 21165.609| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2556 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= 0.136 Angle : 0.595 8.158 23915 Z= 0.321 Chirality : 0.041 0.141 2905 Planarity : 0.004 0.037 3225 Dihedral : 4.371 19.103 2780 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.58 % Favored : 84.23 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.16), residues: 2650 helix: 0.61 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -3.68 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 692 HIS 0.006 0.001 HIS B 256 PHE 0.018 0.002 PHE B 597 TYR 0.027 0.002 TYR D 594 ARG 0.008 0.000 ARG B 690 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 921) hydrogen bonds : angle 5.16793 ( 2688) covalent geometry : bond 0.00272 (17420) covalent geometry : angle 0.59484 (23915) *********************** 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 305 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8539 (m-30) cc_final: 0.7957 (m-30) REVERT: A 562 MET cc_start: 0.7004 (ppp) cc_final: 0.6693 (ppp) REVERT: A 594 TYR cc_start: 0.7979 (m-80) cc_final: 0.7526 (m-80) REVERT: A 645 GLN cc_start: 0.6631 (mp10) cc_final: 0.5462 (mp10) REVERT: A 712 ARG cc_start: 0.5483 (tpt90) cc_final: 0.4368 (tpt90) REVERT: B 166 ASP cc_start: 0.8421 (m-30) cc_final: 0.7950 (m-30) REVERT: B 282 MET cc_start: 0.7950 (tpt) cc_final: 0.7748 (tpt) REVERT: B 488 MET cc_start: 0.6718 (mtt) cc_final: 0.5955 (mtt) REVERT: B 712 ARG cc_start: 0.5771 (tpt90) cc_final: 0.4784 (tpt90) REVERT: C 166 ASP cc_start: 0.8345 (m-30) cc_final: 0.7884 (m-30) REVERT: C 240 ASP cc_start: 0.7329 (m-30) cc_final: 0.7050 (m-30) REVERT: C 562 MET cc_start: 0.7026 (ppp) cc_final: 0.6729 (ppp) REVERT: C 712 ARG cc_start: 0.5592 (tpt170) cc_final: 0.5128 (tpt90) REVERT: D 166 ASP cc_start: 0.8418 (m-30) cc_final: 0.7866 (m-30) REVERT: D 240 ASP cc_start: 0.7374 (m-30) cc_final: 0.7106 (m-30) REVERT: D 712 ARG cc_start: 0.6043 (tpt90) cc_final: 0.4908 (tpt90) REVERT: E 166 ASP cc_start: 0.8381 (m-30) cc_final: 0.7880 (m-30) REVERT: E 240 ASP cc_start: 0.7500 (m-30) cc_final: 0.7220 (m-30) REVERT: E 449 PHE cc_start: 0.7733 (t80) cc_final: 0.7520 (t80) REVERT: E 488 MET cc_start: 0.6460 (mtt) cc_final: 0.5838 (mtt) REVERT: E 561 ASN cc_start: 0.7268 (t0) cc_final: 0.6713 (t0) REVERT: E 562 MET cc_start: 0.6942 (ppp) cc_final: 0.6739 (ppp) REVERT: E 712 ARG cc_start: 0.5781 (tpt90) cc_final: 0.5162 (tpt90) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2835 time to fit residues: 133.3376 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 : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 56 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 126 optimal weight: 1.9990 chunk 216 optimal weight: 30.0000 chunk 191 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 chunk 250 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.4413 r_free = 0.4413 target = 0.210863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.177416 restraints weight = 35483.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.178230 restraints weight = 26701.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.180237 restraints weight = 21563.564| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17420 Z= 0.132 Angle : 0.599 6.317 23915 Z= 0.323 Chirality : 0.041 0.238 2905 Planarity : 0.004 0.038 3225 Dihedral : 4.395 19.783 2780 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.68 % Favored : 85.13 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.16), residues: 2650 helix: 0.66 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -3.68 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 692 HIS 0.006 0.001 HIS B 256 PHE 0.021 0.002 PHE E 449 TYR 0.028 0.002 TYR D 594 ARG 0.005 0.001 ARG E 567 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 921) hydrogen bonds : angle 5.04424 ( 2688) covalent geometry : bond 0.00262 (17420) covalent geometry : angle 0.59934 (23915) *********************** 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 298 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8542 (m-30) cc_final: 0.7978 (m-30) REVERT: A 562 MET cc_start: 0.6846 (ppp) cc_final: 0.6538 (ppp) REVERT: A 712 ARG cc_start: 0.5384 (tpt90) cc_final: 0.4115 (tpt90) REVERT: B 166 ASP cc_start: 0.8529 (m-30) cc_final: 0.8051 (m-30) REVERT: B 712 ARG cc_start: 0.5827 (tpt90) cc_final: 0.4859 (tpt90) REVERT: C 166 ASP cc_start: 0.8379 (m-30) cc_final: 0.7916 (m-30) REVERT: C 240 ASP cc_start: 0.7167 (m-30) cc_final: 0.6920 (m-30) REVERT: C 562 MET cc_start: 0.7037 (ppp) cc_final: 0.6734 (ppp) REVERT: D 166 ASP cc_start: 0.8553 (m-30) cc_final: 0.8003 (m-30) REVERT: D 240 ASP cc_start: 0.7408 (m-30) cc_final: 0.7169 (m-30) REVERT: D 594 TYR cc_start: 0.8156 (m-80) cc_final: 0.7763 (m-80) REVERT: D 712 ARG cc_start: 0.6080 (tpt90) cc_final: 0.4831 (tpt90) REVERT: E 166 ASP cc_start: 0.8434 (m-30) cc_final: 0.7927 (m-30) REVERT: E 240 ASP cc_start: 0.7396 (m-30) cc_final: 0.7160 (m-30) REVERT: E 562 MET cc_start: 0.7029 (ppp) cc_final: 0.6776 (ppp) REVERT: E 712 ARG cc_start: 0.5846 (tpt90) cc_final: 0.5162 (tpt90) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2759 time to fit residues: 124.2627 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 : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 79 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 191 optimal weight: 10.0000 chunk 237 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 chunk 253 optimal weight: 0.0980 chunk 26 optimal weight: 0.8980 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 ** 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 = 0.4425 r_free = 0.4425 target = 0.211565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.176225 restraints weight = 35732.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.178262 restraints weight = 26304.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.179586 restraints weight = 21594.642| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17420 Z= 0.137 Angle : 0.609 6.697 23915 Z= 0.329 Chirality : 0.042 0.224 2905 Planarity : 0.004 0.038 3225 Dihedral : 4.459 20.122 2780 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.17 % Favored : 84.64 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.16), residues: 2650 helix: 0.56 (0.14), residues: 1455 sheet: None (None), residues: 0 loop : -3.74 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 692 HIS 0.006 0.001 HIS B 256 PHE 0.021 0.002 PHE B 449 TYR 0.028 0.002 TYR A 594 ARG 0.006 0.001 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 921) hydrogen bonds : angle 5.05530 ( 2688) covalent geometry : bond 0.00271 (17420) covalent geometry : angle 0.60931 (23915) *********************** 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 308 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8472 (m-30) cc_final: 0.7917 (m-30) REVERT: A 351 MET cc_start: 0.5134 (ptp) cc_final: 0.4896 (ptp) REVERT: A 449 PHE cc_start: 0.7626 (t80) cc_final: 0.7326 (t80) REVERT: A 562 MET cc_start: 0.6914 (ppp) cc_final: 0.6583 (ppp) REVERT: A 594 TYR cc_start: 0.7962 (m-80) cc_final: 0.7563 (m-80) REVERT: A 710 TRP cc_start: 0.6618 (t60) cc_final: 0.6369 (t60) REVERT: B 166 ASP cc_start: 0.8522 (m-30) cc_final: 0.8051 (m-30) REVERT: B 712 ARG cc_start: 0.5860 (tpt90) cc_final: 0.4974 (tpt90) REVERT: C 166 ASP cc_start: 0.8398 (m-30) cc_final: 0.7943 (m-30) REVERT: C 240 ASP cc_start: 0.7061 (m-30) cc_final: 0.6748 (m-30) REVERT: C 562 MET cc_start: 0.7014 (ppp) cc_final: 0.6676 (ppp) REVERT: D 166 ASP cc_start: 0.8530 (m-30) cc_final: 0.7991 (m-30) REVERT: D 240 ASP cc_start: 0.7458 (m-30) cc_final: 0.7244 (m-30) REVERT: D 712 ARG cc_start: 0.6154 (tpt90) cc_final: 0.4829 (tpt90) REVERT: E 166 ASP cc_start: 0.8422 (m-30) cc_final: 0.7923 (m-30) REVERT: E 240 ASP cc_start: 0.7375 (m-30) cc_final: 0.7143 (m-30) REVERT: E 488 MET cc_start: 0.7040 (mtt) cc_final: 0.6289 (mtt) REVERT: E 562 MET cc_start: 0.7131 (ppp) cc_final: 0.6868 (ppp) REVERT: E 565 TYR cc_start: 0.7152 (m-80) cc_final: 0.6929 (m-80) REVERT: E 712 ARG cc_start: 0.5871 (tpt90) cc_final: 0.5271 (tpt90) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2739 time to fit residues: 127.7152 Evaluate side-chains 269 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 6 optimal weight: 0.0020 chunk 180 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 221 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 261 optimal weight: 0.0370 chunk 252 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.6468 ------------------------------------------------------------------------------- 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** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 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 = 0.4462 r_free = 0.4462 target = 0.216348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.174324 restraints weight = 35379.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.178815 restraints weight = 24340.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.182046 restraints weight = 18315.662| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.2961 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= 0.103 Angle : 0.578 7.644 23915 Z= 0.304 Chirality : 0.041 0.226 2905 Planarity : 0.003 0.031 3225 Dihedral : 4.181 20.438 2780 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.28 % Favored : 86.45 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2650 helix: 0.95 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -3.55 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 692 HIS 0.005 0.001 HIS B 256 PHE 0.020 0.001 PHE A 449 TYR 0.029 0.001 TYR E 594 ARG 0.005 0.000 ARG D 690 Details of bonding type rmsd hydrogen bonds : bond 0.03079 ( 921) hydrogen bonds : angle 4.68893 ( 2688) covalent geometry : bond 0.00216 (17420) covalent geometry : angle 0.57814 (23915) *********************** 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 304 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8416 (m-30) cc_final: 0.7854 (m-30) REVERT: A 351 MET cc_start: 0.5037 (ptp) cc_final: 0.4753 (ptp) REVERT: A 466 GLU cc_start: 0.4569 (mt-10) cc_final: 0.4243 (mm-30) REVERT: A 562 MET cc_start: 0.7016 (ppp) cc_final: 0.6694 (ppp) REVERT: A 594 TYR cc_start: 0.7967 (m-80) cc_final: 0.7558 (m-80) REVERT: B 166 ASP cc_start: 0.8420 (m-30) cc_final: 0.7971 (m-30) REVERT: B 565 TYR cc_start: 0.7518 (m-80) cc_final: 0.7263 (m-80) REVERT: B 712 ARG cc_start: 0.5710 (tpt90) cc_final: 0.4822 (tpt90) REVERT: C 166 ASP cc_start: 0.8196 (m-30) cc_final: 0.7748 (m-30) REVERT: C 240 ASP cc_start: 0.7141 (m-30) cc_final: 0.6904 (m-30) REVERT: C 562 MET cc_start: 0.7055 (ppp) cc_final: 0.6709 (ppp) REVERT: C 712 ARG cc_start: 0.5226 (tpt170) cc_final: 0.4410 (tpt90) REVERT: D 166 ASP cc_start: 0.8418 (m-30) cc_final: 0.7931 (m-30) REVERT: D 240 ASP cc_start: 0.7385 (m-30) cc_final: 0.7174 (m-30) REVERT: D 327 ARG cc_start: 0.7671 (mmt90) cc_final: 0.7461 (mmt90) REVERT: E 166 ASP cc_start: 0.8319 (m-30) cc_final: 0.7820 (m-30) REVERT: E 240 ASP cc_start: 0.7358 (m-30) cc_final: 0.7100 (m-30) REVERT: E 488 MET cc_start: 0.6890 (mtt) cc_final: 0.6164 (mtt) REVERT: E 594 TYR cc_start: 0.8138 (m-80) cc_final: 0.7752 (m-80) REVERT: E 706 MET cc_start: 0.6386 (mmm) cc_final: 0.6085 (tpt) REVERT: E 712 ARG cc_start: 0.5846 (tpt90) cc_final: 0.5038 (tpt90) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2604 time to fit residues: 122.3379 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 : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 95 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 91 optimal weight: 3.9990 chunk 230 optimal weight: 0.2980 chunk 107 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 267 optimal weight: 6.9990 chunk 136 optimal weight: 0.0370 chunk 15 optimal weight: 0.5980 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 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 = 0.4472 r_free = 0.4472 target = 0.217377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.183428 restraints weight = 36075.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.185032 restraints weight = 27476.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.186085 restraints weight = 22770.514| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.3056 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= 0.100 Angle : 0.581 15.867 23915 Z= 0.301 Chirality : 0.041 0.217 2905 Planarity : 0.003 0.056 3225 Dihedral : 4.036 19.882 2780 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.23 % Favored : 85.51 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2650 helix: 0.98 (0.14), residues: 1485 sheet: None (None), residues: 0 loop : -3.70 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 692 HIS 0.004 0.001 HIS B 256 PHE 0.017 0.001 PHE B 449 TYR 0.028 0.001 TYR E 594 ARG 0.005 0.000 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.03000 ( 921) hydrogen bonds : angle 4.54498 ( 2688) covalent geometry : bond 0.00215 (17420) covalent geometry : angle 0.58054 (23915) *********************** 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 298 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8455 (m-30) cc_final: 0.7881 (m-30) REVERT: A 351 MET cc_start: 0.5281 (ptp) cc_final: 0.5035 (ptp) REVERT: A 466 GLU cc_start: 0.4639 (mt-10) cc_final: 0.4156 (mm-30) REVERT: A 562 MET cc_start: 0.6728 (ppp) cc_final: 0.6390 (ppp) REVERT: A 594 TYR cc_start: 0.7964 (m-80) cc_final: 0.7567 (m-80) REVERT: B 166 ASP cc_start: 0.8483 (m-30) cc_final: 0.8035 (m-30) REVERT: B 712 ARG cc_start: 0.5915 (tpt90) cc_final: 0.4825 (tpt90) REVERT: C 166 ASP cc_start: 0.8363 (m-30) cc_final: 0.7933 (m-30) REVERT: C 240 ASP cc_start: 0.7222 (m-30) cc_final: 0.7000 (m-30) REVERT: C 562 MET cc_start: 0.6970 (ppp) cc_final: 0.6685 (ppp) REVERT: D 166 ASP cc_start: 0.8456 (m-30) cc_final: 0.7918 (m-30) REVERT: D 240 ASP cc_start: 0.7457 (m-30) cc_final: 0.7245 (m-30) REVERT: E 166 ASP cc_start: 0.8370 (m-30) cc_final: 0.7859 (m-30) REVERT: E 240 ASP cc_start: 0.7287 (m-30) cc_final: 0.7037 (m-30) REVERT: E 261 PHE cc_start: 0.8560 (m-10) cc_final: 0.8332 (m-80) REVERT: E 488 MET cc_start: 0.6973 (mtt) cc_final: 0.6458 (mtt) REVERT: E 594 TYR cc_start: 0.8007 (m-80) cc_final: 0.7628 (m-80) REVERT: E 706 MET cc_start: 0.6405 (mmm) cc_final: 0.6077 (tpt) REVERT: E 712 ARG cc_start: 0.5858 (tpt90) cc_final: 0.5169 (tpt90) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2533 time to fit residues: 115.7344 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 : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 152 optimal weight: 7.9990 chunk 182 optimal weight: 0.0060 chunk 53 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 70 optimal weight: 0.0770 chunk 106 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 overall best weight: 1.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 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 = 0.4456 r_free = 0.4456 target = 0.215665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.173750 restraints weight = 35607.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.177945 restraints weight = 24848.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.181140 restraints weight = 18968.646| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3095 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= 0.107 Angle : 0.584 14.246 23915 Z= 0.305 Chirality : 0.041 0.308 2905 Planarity : 0.003 0.052 3225 Dihedral : 4.088 19.988 2780 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.08 % Favored : 85.70 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.17), residues: 2650 helix: 1.05 (0.14), residues: 1460 sheet: None (None), residues: 0 loop : -3.63 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 692 HIS 0.005 0.001 HIS B 256 PHE 0.018 0.001 PHE A 449 TYR 0.028 0.002 TYR E 594 ARG 0.006 0.001 ARG A 712 Details of bonding type rmsd hydrogen bonds : bond 0.02963 ( 921) hydrogen bonds : angle 4.54466 ( 2688) covalent geometry : bond 0.00224 (17420) covalent geometry : angle 0.58372 (23915) ********************** 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 300 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8385 (m-30) cc_final: 0.7829 (m-30) REVERT: A 351 MET cc_start: 0.5045 (ptp) cc_final: 0.4816 (ptp) REVERT: A 464 ARG cc_start: 0.6244 (mtp-110) cc_final: 0.5894 (tmm-80) REVERT: A 466 GLU cc_start: 0.4526 (mt-10) cc_final: 0.3817 (mm-30) REVERT: A 562 MET cc_start: 0.6879 (ppp) cc_final: 0.6574 (ppp) REVERT: A 712 ARG cc_start: 0.5278 (tpt90) cc_final: 0.3976 (tpt90) REVERT: B 166 ASP cc_start: 0.8417 (m-30) cc_final: 0.7960 (m-30) REVERT: B 712 ARG cc_start: 0.5855 (tpt90) cc_final: 0.4804 (tpt90) REVERT: C 166 ASP cc_start: 0.8287 (m-30) cc_final: 0.7841 (m-30) REVERT: C 240 ASP cc_start: 0.7404 (m-30) cc_final: 0.7113 (m-30) REVERT: C 562 MET cc_start: 0.7042 (ppp) cc_final: 0.6727 (ppp) REVERT: C 665 THR cc_start: 0.9052 (m) cc_final: 0.8847 (m) REVERT: D 166 ASP cc_start: 0.8374 (m-30) cc_final: 0.7862 (m-30) REVERT: D 240 ASP cc_start: 0.7392 (m-30) cc_final: 0.7159 (m-30) REVERT: E 166 ASP cc_start: 0.8323 (m-30) cc_final: 0.7829 (m-30) REVERT: E 240 ASP cc_start: 0.7316 (m-30) cc_final: 0.7051 (m-30) REVERT: E 449 PHE cc_start: 0.7557 (t80) cc_final: 0.7197 (t80) REVERT: E 488 MET cc_start: 0.6931 (mtt) cc_final: 0.6450 (mtt) REVERT: E 562 MET cc_start: 0.7529 (ppp) cc_final: 0.7295 (ppp) REVERT: E 594 TYR cc_start: 0.8183 (m-80) cc_final: 0.7832 (m-80) REVERT: E 706 MET cc_start: 0.6422 (mmm) cc_final: 0.6101 (tpt) REVERT: E 712 ARG cc_start: 0.5779 (tpt90) cc_final: 0.5140 (tpt90) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2528 time to fit residues: 116.8634 Evaluate side-chains 260 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 115 optimal weight: 0.0070 chunk 218 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 229 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 59 optimal weight: 0.0010 chunk 108 optimal weight: 30.0000 chunk 57 optimal weight: 50.0000 chunk 58 optimal weight: 9.9990 chunk 158 optimal weight: 0.2980 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 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 = 0.4492 r_free = 0.4492 target = 0.220027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.184936 restraints weight = 35562.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.186652 restraints weight = 26080.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.188175 restraints weight = 21246.591| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.3255 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= 0.096 Angle : 0.569 13.609 23915 Z= 0.293 Chirality : 0.041 0.298 2905 Planarity : 0.003 0.051 3225 Dihedral : 3.888 20.377 2780 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.38 % Allowed : 14.19 % Favored : 85.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.17), residues: 2650 helix: 1.21 (0.14), residues: 1465 sheet: None (None), residues: 0 loop : -3.59 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 692 HIS 0.004 0.001 HIS B 256 PHE 0.015 0.001 PHE B 450 TYR 0.027 0.001 TYR E 594 ARG 0.005 0.001 ARG D 690 Details of bonding type rmsd hydrogen bonds : bond 0.02710 ( 921) hydrogen bonds : angle 4.31402 ( 2688) covalent geometry : bond 0.00208 (17420) covalent geometry : angle 0.56911 (23915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4978.91 seconds wall clock time: 87 minutes 21.73 seconds (5241.73 seconds total)