Starting phenix.real_space_refine on Thu Sep 26 23:33:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d1w_7786/09_2024/6d1w_7786.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d1w_7786/09_2024/6d1w_7786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d1w_7786/09_2024/6d1w_7786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d1w_7786/09_2024/6d1w_7786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d1w_7786/09_2024/6d1w_7786.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d1w_7786/09_2024/6d1w_7786.cif" } resolution = 3.54 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= 0.001 sd= 0.008 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 72 5.16 5 C 9620 2.51 5 N 2312 2.21 5 O 2488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14492 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3581 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 10} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: C, B, D Time building chain proxies: 7.11, per 1000 atoms: 0.49 Number of scatterers: 14492 At special positions: 0 Unit cell: (110.62, 110.62, 92.3856, 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 72 16.00 O 2488 8.00 N 2312 7.00 C 9620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.02 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 328 " " NAG A 802 " - " ASN A 362 " " NAG A 803 " - " ASN A 375 " " NAG B 801 " - " ASN B 328 " " NAG B 802 " - " ASN B 362 " " NAG B 803 " - " ASN B 375 " " NAG C 801 " - " ASN C 328 " " NAG C 802 " - " ASN C 362 " " NAG C 803 " - " ASN C 375 " " NAG D 801 " - " ASN D 328 " " NAG D 802 " - " ASN D 362 " " NAG D 803 " - " ASN D 375 " Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 1.6 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 60.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 216 through 242 removed outlier: 3.518A pdb=" N ILE A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.825A pdb=" N TYR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.577A pdb=" N ASP A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.614A pdb=" N SER A 330 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N CYS A 331 " --> pdb=" O ASN A 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 331' Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 491 removed outlier: 3.505A pdb=" N ILE A 484 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 528 removed outlier: 3.793A pdb=" N VAL A 513 " --> pdb=" O CYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 532 through 541 removed outlier: 3.691A pdb=" N ASP A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 572 Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.769A pdb=" N ILE A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A 579 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 619 removed outlier: 3.901A pdb=" N THR A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N THR A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG A 592 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY A 599 " --> pdb=" O LYS A 595 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Proline residue: A 604 - end of helix Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 645 through 653 removed outlier: 4.009A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 681 removed outlier: 3.653A pdb=" N PHE A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 242 removed outlier: 3.518A pdb=" N ILE B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 258 removed outlier: 3.824A pdb=" N TYR B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 285 through 291 removed outlier: 3.578A pdb=" N ASP B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.615A pdb=" N SER B 330 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N CYS B 331 " --> pdb=" O ASN B 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 331' Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 491 removed outlier: 3.505A pdb=" N ILE B 484 " --> pdb=" O PHE B 480 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 490 " --> pdb=" O TYR B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 528 removed outlier: 3.793A pdb=" N VAL B 513 " --> pdb=" O CYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 532 through 541 removed outlier: 3.691A pdb=" N ASP B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 572 Processing helix chain 'B' and resid 573 through 581 removed outlier: 3.768A pdb=" N ILE B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE B 579 " --> pdb=" O LYS B 575 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG B 581 " --> pdb=" O ILE B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 619 removed outlier: 3.902A pdb=" N THR B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N THR B 589 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Proline residue: B 604 - end of helix Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 645 through 653 removed outlier: 4.009A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 681 removed outlier: 3.652A pdb=" N PHE B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B 674 " --> pdb=" O PHE B 670 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 242 removed outlier: 3.519A pdb=" N ILE C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.825A pdb=" N TYR C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 285 through 291 removed outlier: 3.578A pdb=" N ASP C 289 " --> pdb=" O GLY C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 331 removed outlier: 3.615A pdb=" N SER C 330 " --> pdb=" O ARG C 327 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N CYS C 331 " --> pdb=" O ASN C 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 327 through 331' Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 491 removed outlier: 3.505A pdb=" N ILE C 484 " --> pdb=" O PHE C 480 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 490 " --> pdb=" O TYR C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 528 removed outlier: 3.793A pdb=" N VAL C 513 " --> pdb=" O CYS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 531 No H-bonds generated for 'chain 'C' and resid 529 through 531' Processing helix chain 'C' and resid 532 through 541 removed outlier: 3.692A pdb=" N ASP C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 572 Processing helix chain 'C' and resid 573 through 581 removed outlier: 3.769A pdb=" N ILE C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE C 579 " --> pdb=" O LYS C 575 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG C 581 " --> pdb=" O ILE C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 619 removed outlier: 3.901A pdb=" N THR C 588 " --> pdb=" O SER C 584 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N THR C 589 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 592 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 598 " --> pdb=" O ALA C 594 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY C 599 " --> pdb=" O LYS C 595 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Proline residue: C 604 - end of helix Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 642 Processing helix chain 'C' and resid 645 through 653 removed outlier: 4.010A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 681 removed outlier: 3.652A pdb=" N PHE C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN C 674 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 242 removed outlier: 3.519A pdb=" N ILE D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.826A pdb=" N TYR D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 285 through 291 removed outlier: 3.578A pdb=" N ASP D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.614A pdb=" N SER D 330 " --> pdb=" O ARG D 327 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N CYS D 331 " --> pdb=" O ASN D 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 331' Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 491 removed outlier: 3.505A pdb=" N ILE D 484 " --> pdb=" O PHE D 480 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 490 " --> pdb=" O TYR D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 528 removed outlier: 3.793A pdb=" N VAL D 513 " --> pdb=" O CYS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 531 No H-bonds generated for 'chain 'D' and resid 529 through 531' Processing helix chain 'D' and resid 532 through 541 removed outlier: 3.691A pdb=" N ASP D 541 " --> pdb=" O GLN D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 572 Processing helix chain 'D' and resid 573 through 581 removed outlier: 3.769A pdb=" N ILE D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE D 579 " --> pdb=" O LYS D 575 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG D 581 " --> pdb=" O ILE D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 619 removed outlier: 3.901A pdb=" N THR D 588 " --> pdb=" O SER D 584 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N THR D 589 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 598 " --> pdb=" O ALA D 594 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY D 599 " --> pdb=" O LYS D 595 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N MET D 603 " --> pdb=" O GLY D 599 " (cutoff:3.500A) Proline residue: D 604 - end of helix Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 642 Processing helix chain 'D' and resid 645 through 653 removed outlier: 4.009A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 681 removed outlier: 3.653A pdb=" N PHE D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN D 674 " --> pdb=" O PHE D 670 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309 removed outlier: 6.310A pdb=" N LEU A 316 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A 429 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 318 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N SER A 427 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 435 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AA5, first strand: chain 'B' and resid 308 through 309 removed outlier: 6.310A pdb=" N LEU B 316 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR B 429 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL B 318 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N SER B 427 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 435 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA8, first strand: chain 'C' and resid 308 through 309 removed outlier: 6.309A pdb=" N LEU C 316 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR C 429 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL C 318 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N SER C 427 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 435 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AB2, first strand: chain 'D' and resid 308 through 309 removed outlier: 6.309A pdb=" N LEU D 316 " --> pdb=" O TYR D 429 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR D 429 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL D 318 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N SER D 427 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 435 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 379 through 380 837 hydrogen bonds defined for protein. 2403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2136 1.28 - 1.41: 4296 1.41 - 1.54: 8324 1.54 - 1.68: 12 1.68 - 1.81: 108 Bond restraints: 14876 Sorted by residual: bond pdb=" C ALA C 356 " pdb=" N PRO C 357 " ideal model delta sigma weight residual 1.334 1.145 0.189 2.34e-02 1.83e+03 6.54e+01 bond pdb=" C ALA D 356 " pdb=" N PRO D 357 " ideal model delta sigma weight residual 1.334 1.145 0.189 2.34e-02 1.83e+03 6.49e+01 bond pdb=" C ALA A 356 " pdb=" N PRO A 357 " ideal model delta sigma weight residual 1.334 1.145 0.189 2.34e-02 1.83e+03 6.49e+01 bond pdb=" C ALA B 356 " pdb=" N PRO B 357 " ideal model delta sigma weight residual 1.334 1.145 0.188 2.34e-02 1.83e+03 6.49e+01 bond pdb=" CA ALA D 303 " pdb=" C ALA D 303 " ideal model delta sigma weight residual 1.524 1.550 -0.026 1.29e-02 6.01e+03 4.13e+00 ... (remaining 14871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 19579 1.85 - 3.70: 560 3.70 - 5.55: 85 5.55 - 7.40: 32 7.40 - 9.25: 4 Bond angle restraints: 20260 Sorted by residual: angle pdb=" N ALA B 303 " pdb=" CA ALA B 303 " pdb=" C ALA B 303 " ideal model delta sigma weight residual 111.36 118.10 -6.74 1.09e+00 8.42e-01 3.83e+01 angle pdb=" N ALA C 303 " pdb=" CA ALA C 303 " pdb=" C ALA C 303 " ideal model delta sigma weight residual 111.36 118.08 -6.72 1.09e+00 8.42e-01 3.80e+01 angle pdb=" N ALA A 303 " pdb=" CA ALA A 303 " pdb=" C ALA A 303 " ideal model delta sigma weight residual 111.36 118.05 -6.69 1.09e+00 8.42e-01 3.77e+01 angle pdb=" N ALA D 303 " pdb=" CA ALA D 303 " pdb=" C ALA D 303 " ideal model delta sigma weight residual 111.36 118.03 -6.67 1.09e+00 8.42e-01 3.75e+01 angle pdb=" C LYS D 294 " pdb=" N MET D 295 " pdb=" CA MET D 295 " ideal model delta sigma weight residual 121.70 128.13 -6.43 1.80e+00 3.09e-01 1.28e+01 ... (remaining 20255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 8430 16.03 - 32.07: 141 32.07 - 48.10: 76 48.10 - 64.13: 4 64.13 - 80.16: 12 Dihedral angle restraints: 8663 sinusoidal: 3327 harmonic: 5336 Sorted by residual: dihedral pdb=" CA ILE A 644 " pdb=" C ILE A 644 " pdb=" N ASN A 645 " pdb=" CA ASN A 645 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ILE D 644 " pdb=" C ILE D 644 " pdb=" N ASN D 645 " pdb=" CA ASN D 645 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ILE C 644 " pdb=" C ILE C 644 " pdb=" N ASN C 645 " pdb=" CA ASN C 645 " ideal model delta harmonic sigma weight residual 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 8660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1342 0.030 - 0.059: 636 0.059 - 0.089: 251 0.089 - 0.118: 123 0.118 - 0.148: 16 Chirality restraints: 2368 Sorted by residual: chirality pdb=" CA ILE C 644 " pdb=" N ILE C 644 " pdb=" C ILE C 644 " pdb=" CB ILE C 644 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE A 644 " pdb=" N ILE A 644 " pdb=" C ILE A 644 " pdb=" CB ILE A 644 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA ILE D 644 " pdb=" N ILE D 644 " pdb=" C ILE D 644 " pdb=" CB ILE D 644 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 2365 not shown) Planarity restraints: 2496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 458 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO A 459 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 459 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 459 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 458 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO B 459 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 459 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 459 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 458 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO D 459 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 459 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 459 " -0.025 5.00e-02 4.00e+02 ... (remaining 2493 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 179 2.59 - 3.17: 14654 3.17 - 3.75: 23764 3.75 - 4.32: 33329 4.32 - 4.90: 51154 Nonbonded interactions: 123080 Sorted by model distance: nonbonded pdb=" SG CYS D 331 " pdb=" SG CYS D 344 " model vdw 2.014 3.760 nonbonded pdb=" SG CYS C 331 " pdb=" SG CYS C 344 " model vdw 2.014 3.760 nonbonded pdb=" SG CYS B 331 " pdb=" SG CYS B 344 " model vdw 2.015 3.760 nonbonded pdb=" O ALA B 562 " pdb=" OG1 THR B 565 " model vdw 2.154 3.040 nonbonded pdb=" O ALA C 562 " pdb=" OG1 THR C 565 " model vdw 2.154 3.040 ... (remaining 123075 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' } 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: 0.010 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 30.450 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 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 : 0.007 0.189 14876 Z= 0.504 Angle : 0.772 9.254 20260 Z= 0.442 Chirality : 0.043 0.148 2368 Planarity : 0.004 0.046 2484 Dihedral : 9.069 80.164 5204 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.52 % Favored : 93.26 % Rotamer: Outliers : 0.27 % Allowed : 0.82 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -3.21 (0.16), residues: 1780 helix: -3.02 (0.11), residues: 884 sheet: 0.77 (0.34), residues: 184 loop : -1.48 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 380 HIS 0.002 0.001 HIS A 550 PHE 0.014 0.002 PHE B 436 TYR 0.014 0.002 TYR C 527 ARG 0.011 0.001 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 425 time to evaluate : 1.652 Fit side-chains REVERT: A 249 TYR cc_start: 0.8485 (t80) cc_final: 0.7821 (t80) REVERT: A 590 MET cc_start: 0.5614 (mmm) cc_final: 0.5023 (mmt) REVERT: A 616 TYR cc_start: 0.8617 (t80) cc_final: 0.8320 (t80) REVERT: B 249 TYR cc_start: 0.8492 (t80) cc_final: 0.7809 (t80) REVERT: B 590 MET cc_start: 0.5647 (mmm) cc_final: 0.4923 (mmt) REVERT: B 616 TYR cc_start: 0.8644 (t80) cc_final: 0.8399 (t80) REVERT: B 654 ARG cc_start: 0.8421 (mtp180) cc_final: 0.8158 (mtm-85) REVERT: C 249 TYR cc_start: 0.8504 (t80) cc_final: 0.7840 (t80) REVERT: C 616 TYR cc_start: 0.8658 (t80) cc_final: 0.8377 (t80) REVERT: D 249 TYR cc_start: 0.8504 (t80) cc_final: 0.7829 (t80) REVERT: D 570 TRP cc_start: 0.8350 (m100) cc_final: 0.8143 (m100) REVERT: D 616 TYR cc_start: 0.8616 (t80) cc_final: 0.8355 (t80) outliers start: 4 outliers final: 4 residues processed: 425 average time/residue: 0.2448 time to fit residues: 153.7195 Evaluate side-chains 218 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain D residue 510 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 141 optimal weight: 0.0020 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 105 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 458 GLN A 543 ASN A 636 GLN A 645 ASN B 323 GLN B 458 GLN B 543 ASN B 636 GLN C 323 GLN C 458 GLN C 543 ASN C 636 GLN C 645 ASN D 323 GLN D 458 GLN D 543 ASN D 636 GLN D 645 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14876 Z= 0.202 Angle : 0.640 7.364 20260 Z= 0.357 Chirality : 0.043 0.154 2368 Planarity : 0.005 0.047 2484 Dihedral : 6.016 58.071 2228 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.36 % Favored : 97.42 % Rotamer: Outliers : 2.17 % Allowed : 9.71 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -0.30 (0.18), residues: 1780 helix: 0.37 (0.15), residues: 992 sheet: 0.52 (0.34), residues: 176 loop : -1.25 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 380 HIS 0.001 0.001 HIS C 550 PHE 0.028 0.002 PHE D 472 TYR 0.023 0.002 TYR C 247 ARG 0.006 0.001 ARG D 654 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 282 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 TYR cc_start: 0.8456 (t80) cc_final: 0.7702 (t80) REVERT: B 249 TYR cc_start: 0.8424 (t80) cc_final: 0.7637 (t80) REVERT: B 487 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6919 (t80) REVERT: C 249 TYR cc_start: 0.8433 (t80) cc_final: 0.7749 (t80) REVERT: D 249 TYR cc_start: 0.8459 (t80) cc_final: 0.7724 (t80) REVERT: D 570 TRP cc_start: 0.8438 (m100) cc_final: 0.8169 (m100) outliers start: 32 outliers final: 19 residues processed: 303 average time/residue: 0.2582 time to fit residues: 114.7777 Evaluate side-chains 235 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 215 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 631 GLU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain B residue 547 ASN Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 631 GLU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 547 ASN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 631 GLU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 547 ASN Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 631 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 0.0970 chunk 136 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 163 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN A 542 GLN A 550 HIS A 578 ASN B 434 ASN B 550 HIS B 578 ASN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 GLN C 550 HIS C 578 ASN D 434 ASN D 550 HIS D 578 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14876 Z= 0.240 Angle : 0.606 7.303 20260 Z= 0.328 Chirality : 0.042 0.131 2368 Planarity : 0.004 0.054 2484 Dihedral : 4.630 29.733 2220 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.92 % Favored : 96.85 % Rotamer: Outliers : 2.24 % Allowed : 11.96 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.28 (0.19), residues: 1780 helix: 0.94 (0.16), residues: 992 sheet: 0.21 (0.33), residues: 176 loop : -0.99 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 380 HIS 0.001 0.000 HIS D 550 PHE 0.015 0.002 PHE D 436 TYR 0.020 0.002 TYR D 249 ARG 0.005 0.000 ARG D 464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 240 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 TYR cc_start: 0.8506 (t80) cc_final: 0.7547 (t80) REVERT: A 272 THR cc_start: 0.8206 (m) cc_final: 0.7994 (p) REVERT: B 249 TYR cc_start: 0.8507 (t80) cc_final: 0.7626 (t80) REVERT: B 675 MET cc_start: 0.7183 (mmm) cc_final: 0.6781 (mmp) REVERT: C 249 TYR cc_start: 0.8544 (t80) cc_final: 0.7748 (t80) REVERT: C 272 THR cc_start: 0.8232 (m) cc_final: 0.7957 (p) REVERT: C 278 ASP cc_start: 0.6555 (m-30) cc_final: 0.6319 (m-30) REVERT: D 249 TYR cc_start: 0.8502 (t80) cc_final: 0.7748 (t80) REVERT: D 272 THR cc_start: 0.8197 (m) cc_final: 0.7969 (p) outliers start: 33 outliers final: 22 residues processed: 269 average time/residue: 0.2200 time to fit residues: 91.7029 Evaluate side-chains 228 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 206 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 434 ASN Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 164 optimal weight: 0.0980 chunk 173 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 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 434 ASN A 542 GLN B 434 ASN B 537 GLN C 434 ASN C 542 GLN D 434 ASN D 537 GLN ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14876 Z= 0.157 Angle : 0.546 7.288 20260 Z= 0.296 Chirality : 0.040 0.129 2368 Planarity : 0.004 0.050 2484 Dihedral : 4.259 25.824 2220 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.42 % Favored : 97.36 % Rotamer: Outliers : 2.04 % Allowed : 14.47 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.50 (0.19), residues: 1780 helix: 1.26 (0.16), residues: 996 sheet: -0.18 (0.33), residues: 176 loop : -1.01 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 570 HIS 0.001 0.000 HIS D 550 PHE 0.018 0.001 PHE C 670 TYR 0.018 0.001 TYR C 247 ARG 0.004 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 250 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 675 MET cc_start: 0.7361 (mmm) cc_final: 0.7003 (mmp) REVERT: C 249 TYR cc_start: 0.8454 (t80) cc_final: 0.7729 (t80) REVERT: D 570 TRP cc_start: 0.8450 (m100) cc_final: 0.8226 (m100) REVERT: D 675 MET cc_start: 0.7336 (mmm) cc_final: 0.6954 (mmp) outliers start: 30 outliers final: 26 residues processed: 273 average time/residue: 0.2202 time to fit residues: 93.8060 Evaluate side-chains 236 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 210 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 547 ASN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 676 PHE Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 547 ASN Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 676 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN A 550 HIS B 434 ASN B 550 HIS C 434 ASN C 550 HIS D 434 ASN D 550 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14876 Z= 0.193 Angle : 0.541 7.284 20260 Z= 0.293 Chirality : 0.040 0.181 2368 Planarity : 0.004 0.050 2484 Dihedral : 4.212 27.674 2220 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.20 % Favored : 96.57 % Rotamer: Outliers : 2.65 % Allowed : 15.15 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.48 (0.19), residues: 1780 helix: 1.17 (0.16), residues: 1000 sheet: -0.14 (0.35), residues: 176 loop : -0.91 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 507 HIS 0.001 0.001 HIS B 550 PHE 0.023 0.001 PHE C 670 TYR 0.019 0.001 TYR C 247 ARG 0.003 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 226 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 675 MET cc_start: 0.7407 (mmm) cc_final: 0.7026 (mmp) REVERT: C 272 THR cc_start: 0.8219 (m) cc_final: 0.7942 (p) REVERT: C 583 MET cc_start: 0.3173 (tmm) cc_final: 0.2757 (ttt) REVERT: D 668 MET cc_start: 0.8031 (mmp) cc_final: 0.7818 (mmp) outliers start: 39 outliers final: 25 residues processed: 255 average time/residue: 0.2260 time to fit residues: 89.6886 Evaluate side-chains 229 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 ASN Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 640 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 6.9990 chunk 156 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 0.0170 chunk 91 optimal weight: 10.0000 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 ASN B 508 ASN B 550 HIS C 434 ASN C 550 HIS D 550 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14876 Z= 0.245 Angle : 0.565 8.282 20260 Z= 0.300 Chirality : 0.041 0.202 2368 Planarity : 0.004 0.049 2484 Dihedral : 4.290 28.272 2220 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.54 % Favored : 96.24 % Rotamer: Outliers : 2.99 % Allowed : 15.56 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.46 (0.19), residues: 1780 helix: 1.17 (0.16), residues: 1000 sheet: -0.36 (0.35), residues: 176 loop : -0.88 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 570 HIS 0.001 0.001 HIS C 550 PHE 0.022 0.001 PHE A 670 TYR 0.019 0.001 TYR C 247 ARG 0.003 0.000 ARG D 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 220 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8177 (p) REVERT: A 600 PHE cc_start: 0.4870 (m-80) cc_final: 0.4561 (m-80) REVERT: A 675 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7031 (mmp) REVERT: B 272 THR cc_start: 0.8392 (m) cc_final: 0.8105 (p) REVERT: C 272 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8134 (p) REVERT: D 272 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8173 (p) REVERT: D 583 MET cc_start: 0.3116 (tmm) cc_final: 0.2763 (ttt) outliers start: 44 outliers final: 35 residues processed: 239 average time/residue: 0.2278 time to fit residues: 84.2190 Evaluate side-chains 242 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 203 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 675 MET Chi-restraints excluded: chain C residue 676 PHE Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 575 LYS Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 80 optimal weight: 0.2980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN A 550 HIS D 550 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14876 Z= 0.232 Angle : 0.554 7.503 20260 Z= 0.296 Chirality : 0.041 0.219 2368 Planarity : 0.004 0.048 2484 Dihedral : 4.246 26.026 2220 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.43 % Favored : 96.35 % Rotamer: Outliers : 3.46 % Allowed : 16.37 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.43 (0.19), residues: 1780 helix: 1.14 (0.16), residues: 1000 sheet: -0.50 (0.36), residues: 176 loop : -0.82 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 570 HIS 0.001 0.000 HIS C 550 PHE 0.022 0.001 PHE A 670 TYR 0.019 0.001 TYR C 247 ARG 0.002 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 217 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8335 (p) REVERT: A 675 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7369 (mmm) REVERT: B 272 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8204 (p) REVERT: B 675 MET cc_start: 0.6940 (mmp) cc_final: 0.6619 (mmp) REVERT: C 272 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8259 (p) REVERT: D 272 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8251 (p) outliers start: 51 outliers final: 38 residues processed: 239 average time/residue: 0.2254 time to fit residues: 83.3623 Evaluate side-chains 247 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 204 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 676 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 675 MET Chi-restraints excluded: chain C residue 676 PHE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 575 LYS Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 607 ILE Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 676 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 0.0070 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 550 HIS C 508 ASN C 550 HIS D 508 ASN D 550 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14876 Z= 0.191 Angle : 0.532 7.860 20260 Z= 0.285 Chirality : 0.040 0.193 2368 Planarity : 0.004 0.046 2484 Dihedral : 4.162 25.605 2220 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.54 % Favored : 96.24 % Rotamer: Outliers : 3.19 % Allowed : 15.96 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.50 (0.19), residues: 1780 helix: 1.20 (0.16), residues: 1000 sheet: -0.48 (0.36), residues: 176 loop : -0.80 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 570 HIS 0.001 0.000 HIS B 550 PHE 0.018 0.001 PHE B 670 TYR 0.019 0.001 TYR C 247 ARG 0.003 0.000 ARG B 464 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 217 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8313 (p) REVERT: A 675 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.6951 (mmp) REVERT: B 272 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8233 (p) REVERT: C 272 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8273 (p) REVERT: D 272 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8309 (p) outliers start: 47 outliers final: 37 residues processed: 238 average time/residue: 0.2265 time to fit residues: 83.6221 Evaluate side-chains 249 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 207 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 675 MET Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 575 LYS Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 676 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 0.0570 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 HIS B 550 HIS C 550 HIS D 550 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14876 Z= 0.189 Angle : 0.535 7.281 20260 Z= 0.289 Chirality : 0.040 0.208 2368 Planarity : 0.004 0.046 2484 Dihedral : 4.118 25.442 2220 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.15 % Favored : 96.63 % Rotamer: Outliers : 3.26 % Allowed : 17.19 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.62 (0.19), residues: 1780 helix: 1.34 (0.16), residues: 980 sheet: -0.47 (0.36), residues: 176 loop : -0.75 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 570 HIS 0.001 0.000 HIS A 550 PHE 0.026 0.001 PHE B 600 TYR 0.019 0.001 TYR C 247 ARG 0.002 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 227 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.7014 (t80) REVERT: A 675 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7233 (mmm) REVERT: B 679 ILE cc_start: 0.7347 (mm) cc_final: 0.6937 (mm) REVERT: C 272 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8359 (p) REVERT: C 487 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6999 (t80) outliers start: 48 outliers final: 39 residues processed: 249 average time/residue: 0.2419 time to fit residues: 94.0163 Evaluate side-chains 246 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 203 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 675 MET Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 487 TYR Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 575 LYS Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 675 MET Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 575 LYS Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 676 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 81 optimal weight: 0.1980 chunk 118 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 0.0980 chunk 113 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 HIS B 550 HIS C 550 HIS D 550 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14876 Z= 0.154 Angle : 0.531 7.303 20260 Z= 0.287 Chirality : 0.040 0.255 2368 Planarity : 0.004 0.045 2484 Dihedral : 4.041 24.951 2220 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.15 % Favored : 96.63 % Rotamer: Outliers : 2.38 % Allowed : 18.82 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.67 (0.19), residues: 1780 helix: 1.39 (0.16), residues: 976 sheet: -0.46 (0.37), residues: 176 loop : -0.71 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 570 HIS 0.001 0.000 HIS A 550 PHE 0.022 0.001 PHE A 600 TYR 0.024 0.001 TYR D 616 ARG 0.003 0.000 ARG B 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 224 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.6946 (t80) REVERT: C 487 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.6971 (t80) outliers start: 35 outliers final: 29 residues processed: 240 average time/residue: 0.2350 time to fit residues: 86.7878 Evaluate side-chains 238 residues out of total 1628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 537 GLN Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 487 TYR Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 514 ILE Chi-restraints excluded: chain C residue 537 GLN Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 675 MET Chi-restraints excluded: chain C residue 676 PHE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 514 ILE Chi-restraints excluded: chain D residue 575 LYS Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 676 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 131 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 GLN C 550 HIS D 550 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.129806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.097439 restraints weight = 24844.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101153 restraints weight = 12520.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.103605 restraints weight = 8464.109| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14876 Z= 0.261 Angle : 0.573 7.242 20260 Z= 0.306 Chirality : 0.041 0.276 2368 Planarity : 0.004 0.047 2484 Dihedral : 4.235 26.385 2220 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.75 % Favored : 97.02 % Rotamer: Outliers : 2.31 % Allowed : 19.23 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: 0.62 (0.19), residues: 1780 helix: 1.22 (0.16), residues: 1008 sheet: -0.42 (0.37), residues: 176 loop : -0.63 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 570 HIS 0.001 0.001 HIS D 550 PHE 0.026 0.002 PHE A 670 TYR 0.019 0.001 TYR C 247 ARG 0.002 0.000 ARG B 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2713.35 seconds wall clock time: 49 minutes 34.54 seconds (2974.54 seconds total)