Starting phenix.real_space_refine on Mon Nov 18 19:03:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkg_40183/11_2024/8gkg_40183.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkg_40183/11_2024/8gkg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkg_40183/11_2024/8gkg_40183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkg_40183/11_2024/8gkg_40183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkg_40183/11_2024/8gkg_40183.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkg_40183/11_2024/8gkg_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17160 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 3432 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 269} Link IDs: {'PTRANS': 12, 'TRANS': 527} Chain breaks: 4 Unresolved non-hydrogen bonds: 985 Unresolved non-hydrogen angles: 1258 Unresolved non-hydrogen dihedrals: 798 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 12, 'PHE:plan': 16, 'GLU:plan': 25, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 500 Restraints were copied for chains: C, B, E, D Time building chain proxies: 7.53, per 1000 atoms: 0.44 Number of scatterers: 17160 At special positions: 0 Unit cell: (170.008, 172.16, 110.828, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 3260 8.00 N 3095 7.00 C 10755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.57 Conformation dependent library (CDL) restraints added in 2.7 seconds 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5160 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 0 sheets defined 61.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 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: 5.32 Time building geometry restraints manager: 5.21 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.790 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 34.980 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 43.110 ------------------------------------------------------------------------------- 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= 0.157 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 *********************** 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 : 2.029 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: 0.2722 time to fit residues: 127.6723 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 : 1.936 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17420 Z= 0.193 Angle : 0.586 5.886 23915 Z= 0.321 Chirality : 0.040 0.132 2905 Planarity : 0.004 0.032 3225 Dihedral : 4.160 18.067 2780 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.28 % Favored : 84.53 % Rotamer: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2650 helix: 0.24 (0.14), residues: 1430 sheet: None (None), residues: 0 loop : -3.58 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 692 HIS 0.002 0.001 HIS A 284 PHE 0.016 0.002 PHE E 445 TYR 0.037 0.002 TYR A 594 ARG 0.007 0.000 ARG D 690 *********************** 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 : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8565 (m-30) cc_final: 0.8029 (m-30) REVERT: A 240 ASP cc_start: 0.7019 (m-30) cc_final: 0.6784 (m-30) REVERT: A 645 GLN cc_start: 0.6272 (mp10) cc_final: 0.5307 (mp10) REVERT: A 712 ARG cc_start: 0.5099 (tpt90) cc_final: 0.4151 (tpt90) REVERT: B 166 ASP cc_start: 0.8362 (m-30) cc_final: 0.7857 (m-30) REVERT: B 240 ASP cc_start: 0.7640 (m-30) cc_final: 0.7262 (m-30) REVERT: B 282 MET cc_start: 0.7675 (tpt) cc_final: 0.7436 (tpt) REVERT: B 641 ASP cc_start: 0.7938 (m-30) cc_final: 0.7384 (m-30) REVERT: B 712 ARG cc_start: 0.5508 (tpt90) cc_final: 0.4855 (tpt90) REVERT: C 166 ASP cc_start: 0.8236 (m-30) cc_final: 0.7735 (m-30) REVERT: C 240 ASP cc_start: 0.6855 (m-30) cc_final: 0.6468 (m-30) REVERT: C 645 GLN cc_start: 0.6942 (mp10) cc_final: 0.6299 (mp10) REVERT: D 166 ASP cc_start: 0.8240 (m-30) cc_final: 0.7715 (m-30) REVERT: D 240 ASP cc_start: 0.7043 (m-30) cc_final: 0.6679 (m-30) REVERT: D 449 PHE cc_start: 0.7533 (t80) cc_final: 0.7326 (t80) REVERT: D 706 MET cc_start: 0.6043 (mmm) cc_final: 0.5659 (tpt) REVERT: D 712 ARG cc_start: 0.5703 (tpt90) cc_final: 0.5268 (tpt90) REVERT: E 166 ASP cc_start: 0.8314 (m-30) cc_final: 0.7814 (m-30) REVERT: E 240 ASP cc_start: 0.7533 (m-30) cc_final: 0.7180 (m-30) REVERT: E 594 TYR cc_start: 0.8098 (m-80) cc_final: 0.7757 (m-80) REVERT: E 712 ARG cc_start: 0.5474 (tpt90) cc_final: 0.4822 (tpt90) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2634 time to fit residues: 122.4207 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 : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 204 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 67 optimal weight: 0.3980 chunk 245 optimal weight: 0.4980 chunk 265 optimal weight: 0.3980 chunk 218 optimal weight: 30.0000 chunk 243 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS D 256 HIS ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.1997 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= 0.161 Angle : 0.550 5.757 23915 Z= 0.295 Chirality : 0.040 0.153 2905 Planarity : 0.003 0.025 3225 Dihedral : 3.883 18.587 2780 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.00 % Favored : 85.81 % Rotamer: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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: -1.74 (0.17), residues: 2650 helix: 0.58 (0.14), residues: 1460 sheet: None (None), residues: 0 loop : -3.59 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 692 HIS 0.004 0.001 HIS B 439 PHE 0.016 0.001 PHE A 597 TYR 0.039 0.001 TYR A 594 ARG 0.006 0.000 ARG C 690 *********************** 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 296 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8480 (m-30) cc_final: 0.7914 (m-30) REVERT: A 240 ASP cc_start: 0.6994 (m-30) cc_final: 0.6696 (m-30) REVERT: A 562 MET cc_start: 0.7111 (ppp) cc_final: 0.6899 (ppp) REVERT: A 594 TYR cc_start: 0.8106 (m-80) cc_final: 0.7703 (m-80) REVERT: A 645 GLN cc_start: 0.6318 (mp10) cc_final: 0.5293 (mp10) REVERT: B 166 ASP cc_start: 0.8315 (m-30) cc_final: 0.7824 (m-30) REVERT: B 240 ASP cc_start: 0.7606 (m-30) cc_final: 0.7365 (m-30) REVERT: B 282 MET cc_start: 0.7767 (tpt) cc_final: 0.7507 (tpt) REVERT: B 712 ARG cc_start: 0.5475 (tpt90) cc_final: 0.4817 (tpt90) REVERT: C 166 ASP cc_start: 0.8215 (m-30) cc_final: 0.7761 (m-30) REVERT: C 240 ASP cc_start: 0.7160 (m-30) cc_final: 0.6720 (m-30) REVERT: C 645 GLN cc_start: 0.6883 (mp10) cc_final: 0.6220 (mp10) REVERT: D 166 ASP cc_start: 0.8314 (m-30) cc_final: 0.7802 (m-30) REVERT: D 240 ASP cc_start: 0.7044 (m-30) cc_final: 0.6706 (m-30) REVERT: D 665 THR cc_start: 0.8972 (m) cc_final: 0.8746 (m) REVERT: D 706 MET cc_start: 0.6111 (mmm) cc_final: 0.5758 (tpt) REVERT: D 712 ARG cc_start: 0.5821 (tpt90) cc_final: 0.5181 (tpt90) REVERT: E 166 ASP cc_start: 0.8307 (m-30) cc_final: 0.7838 (m-30) REVERT: E 240 ASP cc_start: 0.7583 (m-30) cc_final: 0.7288 (m-30) REVERT: E 488 MET cc_start: 0.6660 (mtt) cc_final: 0.6136 (mtt) REVERT: E 712 ARG cc_start: 0.5386 (tpt90) cc_final: 0.4612 (tpt90) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.2936 time to fit residues: 134.3692 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 : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 2.9990 chunk 184 optimal weight: 0.0060 chunk 127 optimal weight: 0.2980 chunk 27 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 246 optimal weight: 7.9990 chunk 260 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 233 optimal weight: 0.0050 chunk 70 optimal weight: 6.9990 overall best weight: 1.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17420 Z= 0.165 Angle : 0.543 5.660 23915 Z= 0.292 Chirality : 0.040 0.132 2905 Planarity : 0.003 0.027 3225 Dihedral : 3.923 18.318 2780 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.75 % Favored : 85.06 % 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: -1.59 (0.17), residues: 2650 helix: 0.82 (0.14), residues: 1455 sheet: None (None), residues: 0 loop : -3.69 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 692 HIS 0.004 0.001 HIS D 256 PHE 0.014 0.001 PHE A 449 TYR 0.028 0.001 TYR E 594 ARG 0.003 0.000 ARG A 690 *********************** 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 293 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8481 (m-30) cc_final: 0.7906 (m-30) REVERT: A 240 ASP cc_start: 0.6951 (m-30) cc_final: 0.6700 (m-30) REVERT: A 562 MET cc_start: 0.7105 (ppp) cc_final: 0.6856 (ppp) REVERT: A 645 GLN cc_start: 0.6221 (mp10) cc_final: 0.5200 (mp10) REVERT: B 166 ASP cc_start: 0.8331 (m-30) cc_final: 0.7852 (m-30) REVERT: B 240 ASP cc_start: 0.7543 (m-30) cc_final: 0.7313 (m-30) REVERT: B 712 ARG cc_start: 0.5803 (tpt90) cc_final: 0.5073 (tpt90) REVERT: C 166 ASP cc_start: 0.8259 (m-30) cc_final: 0.7783 (m-30) REVERT: C 240 ASP cc_start: 0.7038 (m-30) cc_final: 0.6635 (m-30) REVERT: C 562 MET cc_start: 0.7142 (ppp) cc_final: 0.6933 (ppp) REVERT: C 665 THR cc_start: 0.9069 (m) cc_final: 0.8844 (m) REVERT: C 712 ARG cc_start: 0.5616 (tpt170) cc_final: 0.5149 (tpt90) REVERT: D 166 ASP cc_start: 0.8330 (m-30) cc_final: 0.7825 (m-30) REVERT: D 240 ASP cc_start: 0.7141 (m-30) cc_final: 0.6807 (m-30) REVERT: D 712 ARG cc_start: 0.5870 (tpt90) cc_final: 0.5083 (tpt90) REVERT: E 166 ASP cc_start: 0.8299 (m-30) cc_final: 0.7797 (m-30) REVERT: E 240 ASP cc_start: 0.7618 (m-30) cc_final: 0.7341 (m-30) REVERT: E 488 MET cc_start: 0.6644 (mtt) cc_final: 0.6145 (mtt) REVERT: E 712 ARG cc_start: 0.5551 (tpt90) cc_final: 0.4792 (tpt90) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2703 time to fit residues: 121.6869 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 : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 9.9990 chunk 148 optimal weight: 0.5980 chunk 3 optimal weight: 0.0040 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 180 optimal weight: 0.1980 chunk 0 optimal weight: 30.0000 chunk 133 optimal weight: 10.0000 chunk 234 optimal weight: 0.0040 chunk 65 optimal weight: 9.9990 overall best weight: 1.5606 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 17420 Z= 0.172 Angle : 0.560 6.083 23915 Z= 0.301 Chirality : 0.040 0.222 2905 Planarity : 0.003 0.029 3225 Dihedral : 4.051 18.790 2780 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.94 % Favored : 84.87 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % 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: -1.51 (0.17), residues: 2650 helix: 0.90 (0.14), residues: 1450 sheet: None (None), residues: 0 loop : -3.66 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 692 HIS 0.005 0.001 HIS B 256 PHE 0.014 0.001 PHE E 449 TYR 0.028 0.001 TYR D 594 ARG 0.008 0.000 ARG B 690 *********************** 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 293 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8477 (m-30) cc_final: 0.7912 (m-30) REVERT: A 240 ASP cc_start: 0.7047 (m-30) cc_final: 0.6828 (m-30) REVERT: A 562 MET cc_start: 0.7041 (ppp) cc_final: 0.6748 (ppp) REVERT: A 594 TYR cc_start: 0.8049 (m-80) cc_final: 0.7617 (m-80) REVERT: A 645 GLN cc_start: 0.6353 (mp10) cc_final: 0.5357 (mp10) REVERT: B 166 ASP cc_start: 0.8351 (m-30) cc_final: 0.7867 (m-30) REVERT: B 488 MET cc_start: 0.6535 (mtt) cc_final: 0.5844 (mtt) REVERT: B 562 MET cc_start: 0.7039 (ppp) cc_final: 0.6824 (ppp) REVERT: B 712 ARG cc_start: 0.6000 (tpt90) cc_final: 0.5203 (tpt90) REVERT: C 166 ASP cc_start: 0.8294 (m-30) cc_final: 0.7822 (m-30) REVERT: C 240 ASP cc_start: 0.7162 (m-30) cc_final: 0.6759 (m-30) REVERT: C 562 MET cc_start: 0.7039 (ppp) cc_final: 0.6787 (ppp) REVERT: C 712 ARG cc_start: 0.5737 (tpt170) cc_final: 0.5250 (tpt90) REVERT: D 166 ASP cc_start: 0.8362 (m-30) cc_final: 0.7830 (m-30) REVERT: D 240 ASP cc_start: 0.7204 (m-30) cc_final: 0.6860 (m-30) REVERT: D 712 ARG cc_start: 0.6078 (tpt90) cc_final: 0.5058 (tpt90) REVERT: E 166 ASP cc_start: 0.8314 (m-30) cc_final: 0.7811 (m-30) REVERT: E 240 ASP cc_start: 0.7534 (m-30) cc_final: 0.7242 (m-30) REVERT: E 488 MET cc_start: 0.6733 (mtt) cc_final: 0.6231 (mtt) REVERT: E 562 MET cc_start: 0.7121 (ppp) cc_final: 0.6919 (ppp) REVERT: E 712 ARG cc_start: 0.5670 (tpt90) cc_final: 0.4896 (tpt90) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2734 time to fit residues: 124.0901 Evaluate side-chains 261 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 0.7980 chunk 235 optimal weight: 0.0070 chunk 51 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 216 optimal weight: 30.0000 chunk 120 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 overall best weight: 3.9604 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17420 Z= 0.294 Angle : 0.702 6.936 23915 Z= 0.390 Chirality : 0.044 0.225 2905 Planarity : 0.005 0.052 3225 Dihedral : 5.057 25.551 2780 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.75 % Favored : 83.06 % 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: -2.38 (0.16), residues: 2650 helix: 0.13 (0.13), residues: 1420 sheet: None (None), residues: 0 loop : -3.88 (0.15), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 692 HIS 0.005 0.002 HIS B 256 PHE 0.030 0.003 PHE C 449 TYR 0.023 0.003 TYR E 321 ARG 0.006 0.001 ARG B 690 *********************** 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 320 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8586 (m-30) cc_final: 0.8105 (m-30) REVERT: A 282 MET cc_start: 0.7705 (tpt) cc_final: 0.7217 (tpt) REVERT: A 562 MET cc_start: 0.7084 (ppp) cc_final: 0.6736 (ppp) REVERT: A 719 GLU cc_start: 0.7228 (mm-30) cc_final: 0.7000 (mm-30) REVERT: B 166 ASP cc_start: 0.8536 (m-30) cc_final: 0.8060 (m-30) REVERT: B 282 MET cc_start: 0.8043 (tpt) cc_final: 0.7722 (tpt) REVERT: B 562 MET cc_start: 0.7053 (ppp) cc_final: 0.6824 (ppp) REVERT: B 712 ARG cc_start: 0.6059 (tpt90) cc_final: 0.5103 (tpt90) REVERT: C 166 ASP cc_start: 0.8477 (m-30) cc_final: 0.8041 (m-30) REVERT: C 240 ASP cc_start: 0.7004 (m-30) cc_final: 0.6625 (m-30) REVERT: C 522 PHE cc_start: 0.8737 (m-80) cc_final: 0.8523 (m-80) REVERT: C 562 MET cc_start: 0.7068 (ppp) cc_final: 0.6835 (ppp) REVERT: D 166 ASP cc_start: 0.8470 (m-30) cc_final: 0.7938 (m-30) REVERT: D 282 MET cc_start: 0.8020 (tpt) cc_final: 0.7802 (tpt) REVERT: D 712 ARG cc_start: 0.6144 (tpt90) cc_final: 0.4939 (tpt90) REVERT: E 166 ASP cc_start: 0.8450 (m-30) cc_final: 0.7956 (m-30) REVERT: E 240 ASP cc_start: 0.7194 (m-30) cc_final: 0.6921 (m-30) REVERT: E 562 MET cc_start: 0.7269 (ppp) cc_final: 0.6984 (ppp) REVERT: E 712 ARG cc_start: 0.5911 (tpt90) cc_final: 0.5278 (tpt90) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.2963 time to fit residues: 143.5184 Evaluate side-chains 270 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 9.9990 chunk 29 optimal weight: 0.0770 chunk 148 optimal weight: 0.3980 chunk 190 optimal weight: 10.0000 chunk 147 optimal weight: 0.0270 chunk 219 optimal weight: 0.1980 chunk 145 optimal weight: 0.5980 chunk 260 optimal weight: 6.9990 chunk 162 optimal weight: 30.0000 chunk 158 optimal weight: 6.9990 chunk 120 optimal weight: 0.1980 overall best weight: 0.1796 ------------------------------------------------------------------------------- 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 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 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 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17420 Z= 0.167 Angle : 0.591 11.058 23915 Z= 0.312 Chirality : 0.041 0.240 2905 Planarity : 0.003 0.036 3225 Dihedral : 4.315 19.773 2780 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.40 % Favored : 86.30 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: -1.70 (0.17), residues: 2650 helix: 0.80 (0.14), residues: 1400 sheet: None (None), residues: 0 loop : -3.65 (0.16), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 692 HIS 0.005 0.001 HIS D 256 PHE 0.011 0.001 PHE E 597 TYR 0.026 0.001 TYR D 594 ARG 0.004 0.001 ARG A 712 *********************** 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 310 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8440 (m-30) cc_final: 0.7893 (m-30) REVERT: A 351 MET cc_start: 0.5108 (ptp) cc_final: 0.4763 (ptp) REVERT: A 449 PHE cc_start: 0.7745 (t80) cc_final: 0.7523 (t80) REVERT: A 562 MET cc_start: 0.6938 (ppp) cc_final: 0.6711 (ppp) REVERT: A 594 TYR cc_start: 0.8018 (m-80) cc_final: 0.7620 (m-80) REVERT: A 645 GLN cc_start: 0.6396 (mp10) cc_final: 0.5448 (mp10) REVERT: B 166 ASP cc_start: 0.8420 (m-30) cc_final: 0.7932 (m-30) REVERT: B 712 ARG cc_start: 0.5831 (tpt90) cc_final: 0.5140 (tpt90) REVERT: C 166 ASP cc_start: 0.8396 (m-30) cc_final: 0.7949 (m-30) REVERT: C 240 ASP cc_start: 0.7187 (m-30) cc_final: 0.6935 (m-30) REVERT: C 562 MET cc_start: 0.7010 (ppp) cc_final: 0.6722 (ppp) REVERT: C 645 GLN cc_start: 0.6806 (mp10) cc_final: 0.6284 (mp10) REVERT: D 166 ASP cc_start: 0.8456 (m-30) cc_final: 0.7960 (m-30) REVERT: D 449 PHE cc_start: 0.7512 (t80) cc_final: 0.7279 (t80) REVERT: D 706 MET cc_start: 0.6252 (mmp) cc_final: 0.5938 (tpt) REVERT: E 166 ASP cc_start: 0.8418 (m-30) cc_final: 0.7889 (m-30) REVERT: E 240 ASP cc_start: 0.7315 (m-30) cc_final: 0.6989 (m-30) REVERT: E 488 MET cc_start: 0.6886 (mtt) cc_final: 0.6111 (mtt) REVERT: E 706 MET cc_start: 0.6533 (mmm) cc_final: 0.6245 (tpt) REVERT: E 712 ARG cc_start: 0.5832 (tpt90) cc_final: 0.5201 (tpt90) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2885 time to fit residues: 134.7868 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 : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.2934 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= 0.184 Angle : 0.606 7.460 23915 Z= 0.324 Chirality : 0.042 0.228 2905 Planarity : 0.004 0.051 3225 Dihedral : 4.304 18.832 2780 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.30 % Allowed : 15.06 % Favored : 84.64 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.17), residues: 2650 helix: 0.74 (0.14), residues: 1455 sheet: None (None), residues: 0 loop : -3.70 (0.16), residues: 1195 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 0.022 0.002 PHE A 449 TYR 0.027 0.002 TYR A 594 ARG 0.005 0.001 ARG C 690 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8430 (m-30) cc_final: 0.7875 (m-30) REVERT: A 351 MET cc_start: 0.5144 (ptp) cc_final: 0.4922 (ptp) REVERT: A 562 MET cc_start: 0.7000 (ppp) cc_final: 0.6747 (ppp) REVERT: A 594 TYR cc_start: 0.8003 (m-80) cc_final: 0.7612 (m-80) REVERT: B 166 ASP cc_start: 0.8463 (m-30) cc_final: 0.7987 (m-30) REVERT: B 712 ARG cc_start: 0.5997 (tpt90) cc_final: 0.5067 (tpt90) REVERT: C 166 ASP cc_start: 0.8361 (m-30) cc_final: 0.7880 (m-30) REVERT: C 240 ASP cc_start: 0.7225 (m-30) cc_final: 0.6965 (m-30) REVERT: C 562 MET cc_start: 0.7033 (ppp) cc_final: 0.6763 (ppp) REVERT: D 166 ASP cc_start: 0.8471 (m-30) cc_final: 0.7957 (m-30) REVERT: D 240 ASP cc_start: 0.7667 (m-30) cc_final: 0.7391 (m-30) REVERT: D 712 ARG cc_start: 0.6063 (tpt90) cc_final: 0.4778 (tpt90) REVERT: E 166 ASP cc_start: 0.8392 (m-30) cc_final: 0.7888 (m-30) REVERT: E 240 ASP cc_start: 0.7452 (m-30) cc_final: 0.7144 (m-30) REVERT: E 488 MET cc_start: 0.6862 (mtt) cc_final: 0.6110 (mtt) REVERT: E 562 MET cc_start: 0.7381 (ppp) cc_final: 0.7173 (ppp) REVERT: E 706 MET cc_start: 0.6414 (mmm) cc_final: 0.6109 (tpt) REVERT: E 712 ARG cc_start: 0.5803 (tpt90) cc_final: 0.5249 (tpt90) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2879 time to fit residues: 133.8283 Evaluate side-chains 257 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 0.9990 chunk 249 optimal weight: 0.5980 chunk 227 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 190 optimal weight: 0.0970 chunk 74 optimal weight: 0.8980 chunk 219 optimal weight: 50.0000 chunk 229 optimal weight: 0.7980 chunk 241 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.3055 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= 0.153 Angle : 0.576 6.607 23915 Z= 0.303 Chirality : 0.041 0.234 2905 Planarity : 0.003 0.049 3225 Dihedral : 4.098 20.839 2780 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.25 % Favored : 86.38 % 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: -1.48 (0.17), residues: 2650 helix: 0.99 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -3.64 (0.16), residues: 1225 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 0.014 0.001 PHE A 597 TYR 0.025 0.001 TYR A 594 ARG 0.006 0.001 ARG A 712 *********************** 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 316 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8404 (m-30) cc_final: 0.7856 (m-30) REVERT: A 351 MET cc_start: 0.5146 (ptp) cc_final: 0.4936 (ptp) REVERT: A 449 PHE cc_start: 0.7637 (t80) cc_final: 0.7329 (t80) REVERT: A 562 MET cc_start: 0.7005 (ppp) cc_final: 0.6767 (ppp) REVERT: A 645 GLN cc_start: 0.6440 (mp10) cc_final: 0.5420 (mp10) REVERT: B 166 ASP cc_start: 0.8352 (m-30) cc_final: 0.7861 (m-30) REVERT: B 712 ARG cc_start: 0.5849 (tpt90) cc_final: 0.5002 (tpt90) REVERT: C 166 ASP cc_start: 0.8325 (m-30) cc_final: 0.7860 (m-30) REVERT: C 240 ASP cc_start: 0.7582 (m-30) cc_final: 0.7314 (m-30) REVERT: C 562 MET cc_start: 0.7079 (ppp) cc_final: 0.6767 (ppp) REVERT: C 665 THR cc_start: 0.9045 (m) cc_final: 0.8827 (m) REVERT: C 712 ARG cc_start: 0.5264 (tpt170) cc_final: 0.4983 (tpt90) REVERT: D 166 ASP cc_start: 0.8357 (m-30) cc_final: 0.7879 (m-30) REVERT: D 240 ASP cc_start: 0.7736 (m-30) cc_final: 0.7533 (m-30) REVERT: D 665 THR cc_start: 0.8906 (m) cc_final: 0.8700 (m) REVERT: E 166 ASP cc_start: 0.8347 (m-30) cc_final: 0.7848 (m-30) REVERT: E 240 ASP cc_start: 0.7377 (m-30) cc_final: 0.7061 (m-30) REVERT: E 488 MET cc_start: 0.6876 (mtt) cc_final: 0.6365 (mtt) REVERT: E 562 MET cc_start: 0.7442 (ppp) cc_final: 0.7213 (ppp) REVERT: E 706 MET cc_start: 0.6511 (mmm) cc_final: 0.6222 (tpt) REVERT: E 712 ARG cc_start: 0.5796 (tpt90) cc_final: 0.5157 (tpt90) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.2806 time to fit residues: 136.3394 Evaluate side-chains 270 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 8.9990 chunk 256 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 chunk 247 optimal weight: 0.3980 chunk 214 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 165 optimal weight: 50.0000 chunk 131 optimal weight: 6.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.3134 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= 0.215 Angle : 0.638 7.448 23915 Z= 0.342 Chirality : 0.043 0.210 2905 Planarity : 0.004 0.053 3225 Dihedral : 4.438 20.234 2780 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.55 % Favored : 84.26 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: -1.74 (0.17), residues: 2650 helix: 0.62 (0.14), residues: 1485 sheet: None (None), residues: 0 loop : -3.76 (0.16), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 692 HIS 0.005 0.001 HIS C 256 PHE 0.022 0.002 PHE C 449 TYR 0.032 0.002 TYR B 594 ARG 0.005 0.001 ARG B 690 ********************** 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 308 residues out of total 2375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8453 (m-30) cc_final: 0.7910 (m-30) REVERT: A 351 MET cc_start: 0.4999 (ptp) cc_final: 0.4529 (ptp) REVERT: A 449 PHE cc_start: 0.7767 (t80) cc_final: 0.7373 (t80) REVERT: A 562 MET cc_start: 0.7136 (ppp) cc_final: 0.6867 (ppp) REVERT: A 712 ARG cc_start: 0.5712 (tpt90) cc_final: 0.4834 (tpt90) REVERT: B 166 ASP cc_start: 0.8518 (m-30) cc_final: 0.8031 (m-30) REVERT: B 594 TYR cc_start: 0.8273 (m-80) cc_final: 0.7973 (m-80) REVERT: B 712 ARG cc_start: 0.6088 (tpt90) cc_final: 0.5127 (tpt90) REVERT: C 166 ASP cc_start: 0.8427 (m-30) cc_final: 0.7960 (m-30) REVERT: C 240 ASP cc_start: 0.7262 (m-30) cc_final: 0.6950 (m-30) REVERT: C 562 MET cc_start: 0.7214 (ppp) cc_final: 0.6891 (ppp) REVERT: C 665 THR cc_start: 0.9109 (m) cc_final: 0.8899 (m) REVERT: D 166 ASP cc_start: 0.8392 (m-30) cc_final: 0.7864 (m-30) REVERT: D 240 ASP cc_start: 0.7775 (m-30) cc_final: 0.7507 (m-30) REVERT: D 449 PHE cc_start: 0.7729 (t80) cc_final: 0.7128 (t80) REVERT: D 665 THR cc_start: 0.8960 (m) cc_final: 0.8758 (m) REVERT: D 706 MET cc_start: 0.6523 (mmp) cc_final: 0.6260 (mmm) REVERT: D 712 ARG cc_start: 0.6073 (tpt90) cc_final: 0.4725 (tpt90) REVERT: E 166 ASP cc_start: 0.8439 (m-30) cc_final: 0.7916 (m-30) REVERT: E 240 ASP cc_start: 0.7509 (m-30) cc_final: 0.7232 (m-30) REVERT: E 488 MET cc_start: 0.6853 (mtt) cc_final: 0.6013 (mtt) REVERT: E 562 MET cc_start: 0.7259 (ppp) cc_final: 0.7028 (ppp) REVERT: E 706 MET cc_start: 0.6436 (mmm) cc_final: 0.6125 (tpt) REVERT: E 712 ARG cc_start: 0.5800 (tpt90) cc_final: 0.5252 (tpt90) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2807 time to fit residues: 132.3326 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 : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 0.0670 chunk 228 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 220 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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** ** 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 = 0.4468 r_free = 0.4468 target = 0.217028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.181241 restraints weight = 35766.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.182574 restraints weight = 27366.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.184244 restraints weight = 21739.383| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.3203 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= 0.154 Angle : 0.584 6.514 23915 Z= 0.308 Chirality : 0.041 0.229 2905 Planarity : 0.004 0.069 3225 Dihedral : 4.197 20.168 2780 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.25 % Favored : 86.38 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: -1.43 (0.17), residues: 2650 helix: 0.94 (0.14), residues: 1455 sheet: None (None), residues: 0 loop : -3.59 (0.17), residues: 1195 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 0.024 0.001 PHE D 445 TYR 0.030 0.001 TYR B 594 ARG 0.005 0.001 ARG C 690 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3342.80 seconds wall clock time: 61 minutes 23.40 seconds (3683.40 seconds total)