Starting phenix.real_space_refine on Sun Jun 15 10:27:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gkg_40183/06_2025/8gkg_40183.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gkg_40183/06_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_40183/06_2025/8gkg_40183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gkg_40183/06_2025/8gkg_40183.map" model { file = "/net/cci-nas-00/data/ceres_data/8gkg_40183/06_2025/8gkg_40183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gkg_40183/06_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-5710/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: 8.10, per 1000 atoms: 0.47 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: 5.10 Conformation dependent library (CDL) restraints added in 2.8 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: 2.02 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: 5.18 Time building geometry restraints manager: 5.93 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 39.860 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.250 ------------------------------------------------------------------------------- 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 : 1.772 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: 0.2682 time to fit residues: 126.7341 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 : 1.868 ------------------------------------------------------------------------------- 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 = 0.4444 r_free = 0.4444 target = 0.214193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.179477 restraints weight = 35413.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.180082 restraints weight = 26309.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.182214 restraints weight = 21605.516| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.1548 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 5.882 23915 Z= 0.321 Chirality : 0.040 0.132 2905 Planarity : 0.004 0.032 3225 Dihedral : 4.160 18.066 2780 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.74 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 0.04756 ( 921) hydrogen bonds : angle 5.98480 ( 2688) covalent geometry : bond 0.00275 (17420) covalent geometry : angle 0.58601 (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 : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8645 (m-30) cc_final: 0.8078 (m-30) REVERT: A 240 ASP cc_start: 0.6945 (m-30) cc_final: 0.6722 (m-30) REVERT: A 645 GLN cc_start: 0.6566 (mp10) cc_final: 0.5496 (mp10) REVERT: A 712 ARG cc_start: 0.5048 (tpt90) cc_final: 0.4106 (tpt90) REVERT: B 166 ASP cc_start: 0.8441 (m-30) cc_final: 0.7920 (m-30) REVERT: B 240 ASP cc_start: 0.7513 (m-30) cc_final: 0.7170 (m-30) REVERT: B 282 MET cc_start: 0.7808 (tpt) cc_final: 0.7564 (tpt) REVERT: B 641 ASP cc_start: 0.7792 (m-30) cc_final: 0.7234 (m-30) REVERT: B 706 MET cc_start: 0.5666 (mmm) cc_final: 0.5457 (mmp) REVERT: B 712 ARG cc_start: 0.5495 (tpt90) cc_final: 0.4828 (tpt90) REVERT: C 166 ASP cc_start: 0.8275 (m-30) cc_final: 0.7766 (m-30) REVERT: C 240 ASP cc_start: 0.6797 (m-30) cc_final: 0.6421 (m-30) REVERT: C 645 GLN cc_start: 0.7042 (mp10) cc_final: 0.6363 (mp10) REVERT: D 166 ASP cc_start: 0.8316 (m-30) cc_final: 0.7763 (m-30) REVERT: D 240 ASP cc_start: 0.6956 (m-30) cc_final: 0.6614 (m-30) REVERT: D 449 PHE cc_start: 0.7380 (t80) cc_final: 0.7155 (t80) REVERT: D 706 MET cc_start: 0.6033 (mmm) cc_final: 0.5609 (tpt) REVERT: D 712 ARG cc_start: 0.5718 (tpt90) cc_final: 0.5287 (tpt90) REVERT: E 166 ASP cc_start: 0.8385 (m-30) cc_final: 0.7873 (m-30) REVERT: E 240 ASP cc_start: 0.7433 (m-30) cc_final: 0.7113 (m-30) REVERT: E 594 TYR cc_start: 0.8023 (m-80) cc_final: 0.7667 (m-80) REVERT: E 712 ARG cc_start: 0.5527 (tpt90) cc_final: 0.4858 (tpt90) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2543 time to fit residues: 117.9743 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 : 1.747 ------------------------------------------------------------------------------- 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: 3.9990 chunk 114 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 192 optimal weight: 0.0980 chunk 251 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 4 optimal weight: 0.0010 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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 ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS D 256 HIS E 256 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.216273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.181227 restraints weight = 35857.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.183099 restraints weight = 26454.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.185309 restraints weight = 20781.767| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17420 Z= 0.116 Angle : 0.562 5.699 23915 Z= 0.303 Chirality : 0.040 0.147 2905 Planarity : 0.003 0.028 3225 Dihedral : 4.023 18.269 2780 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.17 % Favored : 84.64 % 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: -1.81 (0.16), residues: 2650 helix: 0.52 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -3.59 (0.16), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 692 HIS 0.002 0.001 HIS B 585 PHE 0.017 0.001 PHE D 449 TYR 0.039 0.001 TYR A 594 ARG 0.006 0.000 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 921) hydrogen bonds : angle 5.24399 ( 2688) covalent geometry : bond 0.00236 (17420) covalent geometry : angle 0.56161 (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 290 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8589 (m-30) cc_final: 0.7993 (m-30) REVERT: A 240 ASP cc_start: 0.6711 (m-30) cc_final: 0.6439 (m-30) REVERT: A 594 TYR cc_start: 0.8063 (m-80) cc_final: 0.7649 (m-80) REVERT: A 645 GLN cc_start: 0.6577 (mp10) cc_final: 0.5484 (mp10) REVERT: A 712 ARG cc_start: 0.5290 (tpt90) cc_final: 0.4438 (tpt90) REVERT: B 166 ASP cc_start: 0.8387 (m-30) cc_final: 0.7894 (m-30) REVERT: B 240 ASP cc_start: 0.7409 (m-30) cc_final: 0.7187 (m-30) REVERT: B 282 MET cc_start: 0.7950 (tpt) cc_final: 0.7685 (tpt) REVERT: B 594 TYR cc_start: 0.7981 (m-80) cc_final: 0.7756 (m-80) REVERT: B 706 MET cc_start: 0.5782 (mmm) cc_final: 0.5555 (mmp) REVERT: B 712 ARG cc_start: 0.5685 (tpt90) cc_final: 0.5024 (tpt90) REVERT: C 166 ASP cc_start: 0.8274 (m-30) cc_final: 0.7803 (m-30) REVERT: C 240 ASP cc_start: 0.6852 (m-30) cc_final: 0.6447 (m-30) REVERT: C 645 GLN cc_start: 0.7037 (mp10) cc_final: 0.6359 (mp10) REVERT: D 166 ASP cc_start: 0.8376 (m-30) cc_final: 0.7800 (m-30) REVERT: D 240 ASP cc_start: 0.6934 (m-30) cc_final: 0.6610 (m-30) REVERT: D 712 ARG cc_start: 0.5859 (tpt90) cc_final: 0.5146 (tpt90) REVERT: E 166 ASP cc_start: 0.8421 (m-30) cc_final: 0.7898 (m-30) REVERT: E 240 ASP cc_start: 0.7563 (m-30) cc_final: 0.7293 (m-30) REVERT: E 488 MET cc_start: 0.6659 (mtt) cc_final: 0.6137 (mtt) REVERT: E 712 ARG cc_start: 0.5555 (tpt90) cc_final: 0.4871 (tpt90) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.2719 time to fit residues: 121.9112 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 : 1.774 ------------------------------------------------------------------------------- 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: 1.9990 chunk 182 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 chunk 161 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 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 297 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 = 0.4420 r_free = 0.4420 target = 0.211539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.177921 restraints weight = 35369.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.177918 restraints weight = 22915.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.178509 restraints weight = 20628.188| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.2286 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= 0.143 Angle : 0.588 6.779 23915 Z= 0.320 Chirality : 0.041 0.140 2905 Planarity : 0.004 0.034 3225 Dihedral : 4.296 19.226 2780 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.40 % Favored : 84.42 % Rotamer: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % 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: -1.79 (0.16), residues: 2650 helix: 0.65 (0.14), residues: 1415 sheet: None (None), residues: 0 loop : -3.64 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 692 HIS 0.005 0.001 HIS B 256 PHE 0.018 0.002 PHE D 445 TYR 0.027 0.002 TYR E 594 ARG 0.004 0.000 ARG A 690 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 921) hydrogen bonds : angle 5.21247 ( 2688) covalent geometry : bond 0.00278 (17420) covalent geometry : angle 0.58813 (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 : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8518 (m-30) cc_final: 0.7968 (m-30) REVERT: A 562 MET cc_start: 0.7117 (ppp) cc_final: 0.6804 (ppp) REVERT: A 645 GLN cc_start: 0.6620 (mp10) cc_final: 0.5480 (mp10) REVERT: A 712 ARG cc_start: 0.5467 (tpt90) cc_final: 0.4376 (tpt90) REVERT: B 166 ASP cc_start: 0.8398 (m-30) cc_final: 0.7922 (m-30) REVERT: B 282 MET cc_start: 0.8044 (tpt) cc_final: 0.7828 (tpt) REVERT: B 562 MET cc_start: 0.7019 (ppp) cc_final: 0.6790 (ppp) REVERT: B 706 MET cc_start: 0.5849 (mmm) cc_final: 0.5561 (mmp) REVERT: B 712 ARG cc_start: 0.6084 (tpt90) cc_final: 0.5274 (tpt90) REVERT: C 166 ASP cc_start: 0.8319 (m-30) cc_final: 0.7844 (m-30) REVERT: C 240 ASP cc_start: 0.7161 (m-30) cc_final: 0.6738 (m-30) REVERT: C 562 MET cc_start: 0.7001 (ppp) cc_final: 0.6752 (ppp) REVERT: C 712 ARG cc_start: 0.5663 (tpt170) cc_final: 0.5191 (tpt90) REVERT: D 166 ASP cc_start: 0.8328 (m-30) cc_final: 0.7760 (m-30) REVERT: D 240 ASP cc_start: 0.7224 (m-30) cc_final: 0.6979 (m-30) REVERT: D 712 ARG cc_start: 0.6043 (tpt90) cc_final: 0.4997 (tpt90) REVERT: E 166 ASP cc_start: 0.8421 (m-30) cc_final: 0.7916 (m-30) REVERT: E 240 ASP cc_start: 0.7479 (m-30) cc_final: 0.7202 (m-30) REVERT: E 488 MET cc_start: 0.6637 (mtt) cc_final: 0.6063 (mtt) REVERT: E 562 MET cc_start: 0.7152 (ppp) cc_final: 0.6909 (ppp) REVERT: E 594 TYR cc_start: 0.8117 (m-80) cc_final: 0.7730 (m-80) REVERT: E 712 ARG cc_start: 0.5748 (tpt90) cc_final: 0.5091 (tpt90) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2566 time to fit residues: 118.3882 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 : 1.920 ------------------------------------------------------------------------------- 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: 1.9990 chunk 228 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.206610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.165715 restraints weight = 36240.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.169689 restraints weight = 25159.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.172571 restraints weight = 19132.664| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17420 Z= 0.202 Angle : 0.671 7.989 23915 Z= 0.369 Chirality : 0.043 0.212 2905 Planarity : 0.004 0.047 3225 Dihedral : 4.872 23.352 2780 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.30 % Favored : 83.51 % Rotamer: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % 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: -2.33 (0.16), residues: 2650 helix: 0.14 (0.14), residues: 1415 sheet: None (None), residues: 0 loop : -3.79 (0.15), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 692 HIS 0.006 0.001 HIS C 256 PHE 0.021 0.002 PHE D 449 TYR 0.026 0.003 TYR D 594 ARG 0.008 0.001 ARG B 690 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 921) hydrogen bonds : angle 5.55944 ( 2688) covalent geometry : bond 0.00383 (17420) covalent geometry : angle 0.67056 (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 316 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8594 (m-30) cc_final: 0.8079 (m-30) REVERT: A 240 ASP cc_start: 0.7105 (m-30) cc_final: 0.6879 (m-30) REVERT: A 562 MET cc_start: 0.7061 (ppp) cc_final: 0.6752 (ppp) REVERT: A 594 TYR cc_start: 0.8048 (m-80) cc_final: 0.7604 (m-80) REVERT: A 712 ARG cc_start: 0.5654 (tpt90) cc_final: 0.4437 (tpt90) REVERT: B 166 ASP cc_start: 0.8529 (m-30) cc_final: 0.8052 (m-30) REVERT: B 282 MET cc_start: 0.8060 (tpt) cc_final: 0.7854 (tpt) REVERT: B 562 MET cc_start: 0.6824 (ppp) cc_final: 0.6589 (ppp) REVERT: B 712 ARG cc_start: 0.6098 (tpt90) cc_final: 0.5259 (tpt90) REVERT: C 166 ASP cc_start: 0.8380 (m-30) cc_final: 0.7939 (m-30) REVERT: C 240 ASP cc_start: 0.6909 (m-30) cc_final: 0.6541 (m-30) REVERT: C 562 MET cc_start: 0.7030 (ppp) cc_final: 0.6782 (ppp) REVERT: D 166 ASP cc_start: 0.8535 (m-30) cc_final: 0.7992 (m-30) REVERT: D 594 TYR cc_start: 0.8144 (m-80) cc_final: 0.7757 (m-80) REVERT: D 712 ARG cc_start: 0.6193 (tpt90) cc_final: 0.4949 (tpt90) REVERT: E 166 ASP cc_start: 0.8460 (m-30) cc_final: 0.7952 (m-30) REVERT: E 240 ASP cc_start: 0.7160 (m-30) cc_final: 0.6910 (m-30) REVERT: E 324 ILE cc_start: 0.7201 (mt) cc_final: 0.6997 (mt) REVERT: E 562 MET cc_start: 0.7063 (ppp) cc_final: 0.6798 (ppp) REVERT: E 712 ARG cc_start: 0.5920 (tpt90) cc_final: 0.5234 (tpt90) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.2880 time to fit residues: 138.7136 Evaluate side-chains 275 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.884 ------------------------------------------------------------------------------- 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: 9.9990 chunk 34 optimal weight: 30.0000 chunk 126 optimal weight: 1.9990 chunk 216 optimal weight: 30.0000 chunk 191 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 chunk 250 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.210613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.168679 restraints weight = 36560.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.172835 restraints weight = 25633.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.175822 restraints weight = 19563.034| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.2844 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= 0.138 Angle : 0.616 6.615 23915 Z= 0.333 Chirality : 0.042 0.202 2905 Planarity : 0.004 0.043 3225 Dihedral : 4.650 21.633 2780 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 15.13 % Favored : 84.64 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % 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: -2.12 (0.16), residues: 2650 helix: 0.42 (0.14), residues: 1390 sheet: None (None), residues: 0 loop : -3.76 (0.15), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 692 HIS 0.006 0.001 HIS D 256 PHE 0.019 0.002 PHE D 449 TYR 0.027 0.002 TYR E 594 ARG 0.005 0.001 ARG B 690 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 921) hydrogen bonds : angle 5.23194 ( 2688) covalent geometry : bond 0.00272 (17420) covalent geometry : angle 0.61553 (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 311 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 2.118 Fit side-chains revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8524 (m-30) cc_final: 0.7954 (m-30) REVERT: A 240 ASP cc_start: 0.7167 (m-30) cc_final: 0.6931 (m-30) REVERT: A 351 MET cc_start: 0.5137 (ptp) cc_final: 0.4877 (ptp) REVERT: A 449 PHE cc_start: 0.7761 (t80) cc_final: 0.7467 (t80) REVERT: A 562 MET cc_start: 0.6911 (ppp) cc_final: 0.6656 (ppp) REVERT: A 565 TYR cc_start: 0.8232 (m-10) cc_final: 0.8026 (m-80) REVERT: B 166 ASP cc_start: 0.8508 (m-30) cc_final: 0.8017 (m-30) REVERT: B 282 MET cc_start: 0.7988 (tpt) cc_final: 0.7776 (tpt) REVERT: B 712 ARG cc_start: 0.5863 (tpt90) cc_final: 0.4997 (tpt90) REVERT: C 166 ASP cc_start: 0.8380 (m-30) cc_final: 0.7940 (m-30) REVERT: C 240 ASP cc_start: 0.6970 (m-30) cc_final: 0.6699 (m-30) REVERT: C 562 MET cc_start: 0.6951 (ppp) cc_final: 0.6727 (ppp) REVERT: D 166 ASP cc_start: 0.8464 (m-30) cc_final: 0.7922 (m-30) REVERT: D 240 ASP cc_start: 0.7486 (m-30) cc_final: 0.7252 (m-30) REVERT: D 282 MET cc_start: 0.7953 (tpt) cc_final: 0.7746 (tpt) REVERT: D 712 ARG cc_start: 0.6195 (tpt90) cc_final: 0.4866 (tpt90) REVERT: E 166 ASP cc_start: 0.8448 (m-30) cc_final: 0.7931 (m-30) REVERT: E 240 ASP cc_start: 0.7191 (m-30) cc_final: 0.6953 (m-30) REVERT: E 449 PHE cc_start: 0.7829 (t80) cc_final: 0.7514 (t80) REVERT: E 488 MET cc_start: 0.6999 (mtt) cc_final: 0.6273 (mtt) REVERT: E 562 MET cc_start: 0.7121 (ppp) cc_final: 0.6870 (ppp) REVERT: E 565 TYR cc_start: 0.8013 (m-80) cc_final: 0.7741 (m-80) REVERT: E 594 TYR cc_start: 0.8102 (m-80) cc_final: 0.7673 (m-80) REVERT: E 712 ARG cc_start: 0.5835 (tpt90) cc_final: 0.5207 (tpt90) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.3049 time to fit residues: 142.1686 Evaluate side-chains 271 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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: 5.9990 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 30.0000 chunk 90 optimal weight: 4.9990 chunk 268 optimal weight: 6.9990 chunk 256 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 237 optimal weight: 0.4980 chunk 239 optimal weight: 6.9990 chunk 253 optimal weight: 0.0670 chunk 26 optimal weight: 0.3980 overall best weight: 1.5922 ------------------------------------------------------------------------------- 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 = 0.4429 r_free = 0.4429 target = 0.212028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.176888 restraints weight = 35964.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.177832 restraints weight = 25755.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.179345 restraints weight = 22066.177| |-----------------------------------------------------------------------------| r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.2959 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= 0.124 Angle : 0.602 6.354 23915 Z= 0.323 Chirality : 0.041 0.248 2905 Planarity : 0.004 0.038 3225 Dihedral : 4.482 19.723 2780 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.06 % Favored : 84.68 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.87 (0.17), residues: 2650 helix: 0.56 (0.14), residues: 1455 sheet: None (None), residues: 0 loop : -3.77 (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 D 256 PHE 0.018 0.002 PHE B 445 TYR 0.029 0.002 TYR D 594 ARG 0.005 0.001 ARG A 690 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 921) hydrogen bonds : angle 5.02244 ( 2688) covalent geometry : bond 0.00251 (17420) covalent geometry : angle 0.60172 (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 302 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8470 (m-30) cc_final: 0.7913 (m-30) REVERT: A 240 ASP cc_start: 0.7251 (m-30) cc_final: 0.7032 (m-30) REVERT: A 351 MET cc_start: 0.5049 (ptp) cc_final: 0.4834 (ptp) REVERT: A 449 PHE cc_start: 0.7645 (t80) cc_final: 0.7422 (t80) REVERT: A 562 MET cc_start: 0.6897 (ppp) cc_final: 0.6633 (ppp) REVERT: A 594 TYR cc_start: 0.8047 (m-80) cc_final: 0.7650 (m-80) REVERT: B 166 ASP cc_start: 0.8509 (m-30) cc_final: 0.8036 (m-30) REVERT: B 282 MET cc_start: 0.7984 (tpt) cc_final: 0.7765 (tpt) REVERT: B 712 ARG cc_start: 0.5990 (tpt90) cc_final: 0.5077 (tpt90) REVERT: C 166 ASP cc_start: 0.8380 (m-30) cc_final: 0.7926 (m-30) REVERT: C 240 ASP cc_start: 0.7144 (m-30) cc_final: 0.6880 (m-30) REVERT: C 562 MET cc_start: 0.6911 (ppp) cc_final: 0.6625 (ppp) REVERT: D 166 ASP cc_start: 0.8500 (m-30) cc_final: 0.7961 (m-30) REVERT: D 240 ASP cc_start: 0.7519 (m-30) cc_final: 0.7290 (m-30) REVERT: D 712 ARG cc_start: 0.6083 (tpt90) cc_final: 0.4775 (tpt90) REVERT: E 166 ASP cc_start: 0.8418 (m-30) cc_final: 0.7897 (m-30) REVERT: E 240 ASP cc_start: 0.7335 (m-30) cc_final: 0.7099 (m-30) REVERT: E 449 PHE cc_start: 0.7736 (t80) cc_final: 0.7447 (t80) REVERT: E 488 MET cc_start: 0.6996 (mtt) cc_final: 0.6255 (mtt) REVERT: E 562 MET cc_start: 0.7058 (ppp) cc_final: 0.6766 (ppp) REVERT: E 565 TYR cc_start: 0.8072 (m-80) cc_final: 0.7787 (m-80) REVERT: E 712 ARG cc_start: 0.5863 (tpt90) cc_final: 0.5287 (tpt90) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.3645 time to fit residues: 169.1945 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 : 2.041 ------------------------------------------------------------------------------- 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: 4.9990 chunk 180 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 chunk 26 optimal weight: 0.0030 chunk 69 optimal weight: 0.8980 chunk 261 optimal weight: 0.2980 chunk 252 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4463 r_free = 0.4463 target = 0.216084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.179743 restraints weight = 35485.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.182388 restraints weight = 26254.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.183909 restraints weight = 19580.989| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.3048 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 : 0.579 7.614 23915 Z= 0.305 Chirality : 0.041 0.252 2905 Planarity : 0.003 0.030 3225 Dihedral : 4.228 19.790 2780 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.62 % Favored : 86.04 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.48 (0.17), residues: 2650 helix: 0.92 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -3.56 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 692 HIS 0.005 0.001 HIS E 256 PHE 0.015 0.001 PHE C 449 TYR 0.026 0.001 TYR A 594 ARG 0.005 0.001 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 921) hydrogen bonds : angle 4.67332 ( 2688) covalent geometry : bond 0.00216 (17420) covalent geometry : angle 0.57900 (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 306 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8462 (m-30) cc_final: 0.7892 (m-30) REVERT: A 240 ASP cc_start: 0.7095 (m-30) cc_final: 0.6867 (m-30) REVERT: A 351 MET cc_start: 0.5136 (ptp) cc_final: 0.4883 (ptp) REVERT: A 449 PHE cc_start: 0.7570 (t80) cc_final: 0.7369 (t80) REVERT: A 464 ARG cc_start: 0.6442 (mtp-110) cc_final: 0.6072 (tmm-80) REVERT: A 466 GLU cc_start: 0.4562 (mt-10) cc_final: 0.4161 (mm-30) REVERT: A 562 MET cc_start: 0.7085 (ppp) cc_final: 0.6800 (ppp) REVERT: B 166 ASP cc_start: 0.8568 (m-30) cc_final: 0.8114 (m-30) REVERT: B 712 ARG cc_start: 0.5876 (tpt90) cc_final: 0.4982 (tpt90) REVERT: C 166 ASP cc_start: 0.8314 (m-30) cc_final: 0.7850 (m-30) REVERT: C 240 ASP cc_start: 0.7243 (m-30) cc_final: 0.7018 (m-30) REVERT: C 562 MET cc_start: 0.6914 (ppp) cc_final: 0.6645 (ppp) REVERT: D 166 ASP cc_start: 0.8533 (m-30) cc_final: 0.8003 (m-30) REVERT: D 240 ASP cc_start: 0.7549 (m-30) cc_final: 0.7330 (m-30) REVERT: E 166 ASP cc_start: 0.8396 (m-30) cc_final: 0.7891 (m-30) REVERT: E 240 ASP cc_start: 0.7307 (m-30) cc_final: 0.7061 (m-30) REVERT: E 261 PHE cc_start: 0.7957 (m-10) cc_final: 0.7708 (m-80) REVERT: E 488 MET cc_start: 0.6965 (mtt) cc_final: 0.6189 (mtt) REVERT: E 562 MET cc_start: 0.7014 (ppp) cc_final: 0.6692 (ppp) REVERT: E 706 MET cc_start: 0.6400 (mmm) cc_final: 0.6075 (tpt) REVERT: E 712 ARG cc_start: 0.5880 (tpt90) cc_final: 0.5181 (tpt90) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2646 time to fit residues: 124.6059 Evaluate side-chains 264 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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: 6.9990 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 chunk 230 optimal weight: 0.0020 chunk 107 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 267 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 15 optimal weight: 0.4980 overall best weight: 1.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.211954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.176414 restraints weight = 36412.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.177936 restraints weight = 27033.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.179183 restraints weight = 22867.923| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.3121 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= 0.135 Angle : 0.619 14.475 23915 Z= 0.328 Chirality : 0.042 0.244 2905 Planarity : 0.004 0.034 3225 Dihedral : 4.408 19.465 2780 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.28 % Favored : 84.45 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -1.66 (0.17), residues: 2650 helix: 0.74 (0.14), residues: 1455 sheet: None (None), residues: 0 loop : -3.69 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 692 HIS 0.005 0.001 HIS D 256 PHE 0.023 0.002 PHE C 449 TYR 0.031 0.002 TYR A 594 ARG 0.005 0.001 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 921) hydrogen bonds : angle 4.87439 ( 2688) covalent geometry : bond 0.00269 (17420) covalent geometry : angle 0.61865 (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 : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8489 (m-30) cc_final: 0.7911 (m-30) REVERT: A 449 PHE cc_start: 0.7685 (t80) cc_final: 0.7447 (t80) REVERT: A 562 MET cc_start: 0.6871 (ppp) cc_final: 0.6547 (ppp) REVERT: A 565 TYR cc_start: 0.8210 (m-80) cc_final: 0.7982 (m-80) REVERT: A 594 TYR cc_start: 0.7987 (m-80) cc_final: 0.7658 (m-80) REVERT: A 710 TRP cc_start: 0.6535 (t60) cc_final: 0.6317 (t60) REVERT: A 712 ARG cc_start: 0.5526 (tpt90) cc_final: 0.4303 (tpt90) REVERT: B 166 ASP cc_start: 0.8495 (m-30) cc_final: 0.8028 (m-30) REVERT: B 562 MET cc_start: 0.6828 (ppp) cc_final: 0.6613 (ppp) REVERT: B 712 ARG cc_start: 0.6010 (tpt90) cc_final: 0.5006 (tpt90) REVERT: C 166 ASP cc_start: 0.8413 (m-30) cc_final: 0.7961 (m-30) REVERT: C 240 ASP cc_start: 0.7124 (m-30) cc_final: 0.6828 (m-30) REVERT: C 562 MET cc_start: 0.6909 (ppp) cc_final: 0.6603 (ppp) REVERT: D 166 ASP cc_start: 0.8539 (m-30) cc_final: 0.7990 (m-30) REVERT: D 240 ASP cc_start: 0.7600 (m-30) cc_final: 0.7360 (m-30) REVERT: D 712 ARG cc_start: 0.6198 (tpt90) cc_final: 0.4850 (tpt90) REVERT: E 166 ASP cc_start: 0.8420 (m-30) cc_final: 0.7889 (m-30) REVERT: E 240 ASP cc_start: 0.7217 (m-30) cc_final: 0.6938 (m-30) REVERT: E 488 MET cc_start: 0.7027 (mtt) cc_final: 0.6293 (mtt) REVERT: E 562 MET cc_start: 0.7064 (ppp) cc_final: 0.6717 (ppp) REVERT: E 712 ARG cc_start: 0.5854 (tpt90) cc_final: 0.5281 (tpt90) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2587 time to fit residues: 118.8937 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 : 1.750 ------------------------------------------------------------------------------- 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: 6.9990 chunk 182 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 195 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.216114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.179709 restraints weight = 36101.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.180992 restraints weight = 27223.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.182757 restraints weight = 22146.366| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.3194 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 : 0.589 14.713 23915 Z= 0.307 Chirality : 0.041 0.257 2905 Planarity : 0.003 0.030 3225 Dihedral : 4.223 20.105 2780 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.40 % Favored : 86.26 % 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: -1.41 (0.17), residues: 2650 helix: 0.99 (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 0.020 0.001 TRP A 692 HIS 0.005 0.001 HIS E 256 PHE 0.031 0.001 PHE A 597 TYR 0.030 0.001 TYR A 594 ARG 0.005 0.001 ARG B 690 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 921) hydrogen bonds : angle 4.60188 ( 2688) covalent geometry : bond 0.00219 (17420) covalent geometry : angle 0.58917 (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 302 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8443 (m-30) cc_final: 0.7877 (m-30) REVERT: A 449 PHE cc_start: 0.7578 (t80) cc_final: 0.7363 (t80) REVERT: A 464 ARG cc_start: 0.6184 (mtp-110) cc_final: 0.5809 (tmm-80) REVERT: A 466 GLU cc_start: 0.4484 (mt-10) cc_final: 0.4115 (mm-30) REVERT: A 562 MET cc_start: 0.6876 (ppp) cc_final: 0.6584 (ppp) REVERT: A 565 TYR cc_start: 0.8285 (m-80) cc_final: 0.8020 (m-80) REVERT: A 594 TYR cc_start: 0.8023 (m-80) cc_final: 0.7685 (m-80) REVERT: A 712 ARG cc_start: 0.5229 (tpt90) cc_final: 0.3906 (tpt90) REVERT: B 166 ASP cc_start: 0.8500 (m-30) cc_final: 0.8052 (m-30) REVERT: B 562 MET cc_start: 0.7166 (ppp) cc_final: 0.6961 (ppp) REVERT: B 712 ARG cc_start: 0.5893 (tpt90) cc_final: 0.4802 (tpt90) REVERT: C 166 ASP cc_start: 0.8313 (m-30) cc_final: 0.7865 (m-30) REVERT: C 240 ASP cc_start: 0.7544 (m-30) cc_final: 0.7284 (m-30) REVERT: C 488 MET cc_start: 0.5031 (mtt) cc_final: 0.4553 (mtt) REVERT: C 562 MET cc_start: 0.6972 (ppp) cc_final: 0.6652 (ppp) REVERT: D 166 ASP cc_start: 0.8486 (m-30) cc_final: 0.7963 (m-30) REVERT: D 240 ASP cc_start: 0.7577 (m-30) cc_final: 0.7360 (m-30) REVERT: E 166 ASP cc_start: 0.8335 (m-30) cc_final: 0.7824 (m-30) REVERT: E 240 ASP cc_start: 0.7254 (m-30) cc_final: 0.6990 (m-30) REVERT: E 488 MET cc_start: 0.6571 (mtt) cc_final: 0.5998 (mtt) REVERT: E 562 MET cc_start: 0.6986 (ppp) cc_final: 0.6650 (ppp) REVERT: E 706 MET cc_start: 0.6375 (mmm) cc_final: 0.6084 (tpt) REVERT: E 712 ARG cc_start: 0.5870 (tpt90) cc_final: 0.5189 (tpt90) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2656 time to fit residues: 123.4216 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 : 1.949 ------------------------------------------------------------------------------- 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: 0.0670 chunk 218 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 229 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 108 optimal weight: 30.0000 chunk 57 optimal weight: 50.0000 chunk 58 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.212777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.170486 restraints weight = 36297.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.174614 restraints weight = 25465.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.177657 restraints weight = 19505.768| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.3268 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= 0.127 Angle : 0.612 13.783 23915 Z= 0.322 Chirality : 0.042 0.239 2905 Planarity : 0.003 0.033 3225 Dihedral : 4.338 19.188 2780 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.58 % Favored : 84.15 % 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: -1.60 (0.17), residues: 2650 helix: 0.77 (0.14), residues: 1485 sheet: None (None), residues: 0 loop : -3.74 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 692 HIS 0.005 0.001 HIS E 256 PHE 0.026 0.002 PHE C 449 TYR 0.029 0.002 TYR A 594 ARG 0.006 0.001 ARG C 712 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 921) hydrogen bonds : angle 4.75034 ( 2688) covalent geometry : bond 0.00258 (17420) covalent geometry : angle 0.61155 (23915) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5398.09 seconds wall clock time: 94 minutes 14.68 seconds (5654.68 seconds total)