Starting phenix.real_space_refine on Fri Sep 27 02:36:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t4d_8354/09_2024/5t4d_8354.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t4d_8354/09_2024/5t4d_8354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t4d_8354/09_2024/5t4d_8354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t4d_8354/09_2024/5t4d_8354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t4d_8354/09_2024/5t4d_8354.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t4d_8354/09_2024/5t4d_8354.cif" } resolution = 3.0 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= 0.013 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 9860 2.51 5 N 2360 2.21 5 O 2584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14876 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3677 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 449} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 98 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: 7.59, per 1000 atoms: 0.51 Number of scatterers: 14876 At special positions: 0 Unit cell: (110.62, 110.62, 102.11, 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 2584 8.00 N 2360 7.00 C 9860 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=2.03 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: 3.65 Conformation dependent library (CDL) restraints added in 1.7 seconds 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 60.7% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 216 through 242 removed outlier: 3.541A pdb=" N THR A 226 " --> pdb=" O ARG A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.770A pdb=" N TYR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.709A pdb=" N SER A 330 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 4.204A 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 334 through 338 Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 492 removed outlier: 3.569A pdb=" N CYS A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 484 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 528 Processing helix chain 'A' and resid 532 through 541 removed outlier: 3.811A pdb=" N LEU A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.665A 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 579 removed outlier: 4.521A pdb=" N ASN A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 579 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 619 removed outlier: 3.746A pdb=" N THR A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 646 through 653 Processing helix chain 'A' and resid 655 through 670 Processing helix chain 'A' and resid 672 through 693 removed outlier: 3.661A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 242 removed outlier: 3.542A pdb=" N THR B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 258 removed outlier: 3.770A pdb=" N TYR B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.708A pdb=" N SER B 330 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 4.205A 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 334 through 338 Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 492 removed outlier: 3.569A pdb=" N CYS B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 484 " --> pdb=" O PHE B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 528 Processing helix chain 'B' and resid 532 through 541 removed outlier: 3.811A pdb=" N LEU B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.665A 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 579 removed outlier: 4.522A pdb=" N ASN B 578 " --> pdb=" O LYS B 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE B 579 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 619 removed outlier: 3.747A pdb=" N THR B 589 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 646 through 653 Processing helix chain 'B' and resid 655 through 670 Processing helix chain 'B' and resid 672 through 693 removed outlier: 3.661A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 242 removed outlier: 3.541A pdb=" N THR C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.769A pdb=" N TYR C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 327 through 331 removed outlier: 3.709A pdb=" N SER C 330 " --> pdb=" O ARG C 327 " (cutoff:3.500A) removed outlier: 4.205A 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 334 through 338 Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 492 removed outlier: 3.570A pdb=" N CYS C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 484 " --> pdb=" O PHE C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 528 Processing helix chain 'C' and resid 532 through 541 removed outlier: 3.811A pdb=" N LEU C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 3.665A 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 579 removed outlier: 4.522A pdb=" N ASN C 578 " --> pdb=" O LYS C 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE C 579 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 619 removed outlier: 3.746A pdb=" N THR C 589 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 642 Processing helix chain 'C' and resid 646 through 653 Processing helix chain 'C' and resid 655 through 670 Processing helix chain 'C' and resid 672 through 693 removed outlier: 3.661A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 242 removed outlier: 3.542A pdb=" N THR D 226 " --> pdb=" O ARG D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.770A pdb=" N TYR D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.709A pdb=" N SER D 330 " --> pdb=" O ARG D 327 " (cutoff:3.500A) removed outlier: 4.205A 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 334 through 338 Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 492 removed outlier: 3.568A pdb=" N CYS D 476 " --> pdb=" O PHE D 472 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D 484 " --> pdb=" O PHE D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 528 Processing helix chain 'D' and resid 532 through 541 removed outlier: 3.811A pdb=" N LEU D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) removed outlier: 3.664A 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 579 removed outlier: 4.521A pdb=" N ASN D 578 " --> pdb=" O LYS D 575 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE D 579 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 619 removed outlier: 3.746A pdb=" N THR D 589 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET D 603 " --> pdb=" O GLY D 599 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 642 Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 655 through 670 Processing helix chain 'D' and resid 672 through 693 removed outlier: 3.660A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 3.603A 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: 6.694A pdb=" N LEU A 316 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR A 429 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 318 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N SER A 427 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 421 " --> pdb=" O LEU A 324 " (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: 6.693A pdb=" N LEU B 316 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR B 429 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 318 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N SER B 427 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 421 " --> pdb=" O LEU B 324 " (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: 6.694A pdb=" N LEU C 316 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR C 429 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 318 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N SER C 427 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 421 " --> pdb=" O LEU C 324 " (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: 6.694A pdb=" N LEU D 316 " --> pdb=" O TYR D 429 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR D 429 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL D 318 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N SER D 427 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 421 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 379 through 380 921 hydrogen bonds defined for protein. 2619 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: 4.35 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4454 1.34 - 1.45: 3166 1.45 - 1.57: 7536 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 15264 Sorted by residual: bond pdb=" CA ALA B 356 " pdb=" C ALA B 356 " ideal model delta sigma weight residual 1.528 1.505 0.022 1.08e-02 8.57e+03 4.21e+00 bond pdb=" CA ALA C 356 " pdb=" C ALA C 356 " ideal model delta sigma weight residual 1.528 1.506 0.022 1.08e-02 8.57e+03 4.10e+00 bond pdb=" CA ALA D 356 " pdb=" C ALA D 356 " ideal model delta sigma weight residual 1.528 1.506 0.021 1.08e-02 8.57e+03 3.93e+00 bond pdb=" CA ALA A 356 " pdb=" C ALA A 356 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.08e-02 8.57e+03 3.61e+00 bond pdb=" CA ALA A 303 " pdb=" C ALA A 303 " ideal model delta sigma weight residual 1.523 1.545 -0.021 1.30e-02 5.92e+03 2.73e+00 ... (remaining 15259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 20228 2.20 - 4.40: 484 4.40 - 6.60: 60 6.60 - 8.80: 8 8.80 - 10.99: 4 Bond angle restraints: 20784 Sorted by residual: angle pdb=" N ALA C 303 " pdb=" CA ALA C 303 " pdb=" C ALA C 303 " ideal model delta sigma weight residual 111.28 116.09 -4.81 1.09e+00 8.42e-01 1.95e+01 angle pdb=" N ALA B 303 " pdb=" CA ALA B 303 " pdb=" C ALA B 303 " ideal model delta sigma weight residual 111.28 116.07 -4.79 1.09e+00 8.42e-01 1.93e+01 angle pdb=" N ALA A 303 " pdb=" CA ALA A 303 " pdb=" C ALA A 303 " ideal model delta sigma weight residual 111.28 116.06 -4.78 1.09e+00 8.42e-01 1.92e+01 angle pdb=" N ALA D 303 " pdb=" CA ALA D 303 " pdb=" C ALA D 303 " ideal model delta sigma weight residual 111.28 116.06 -4.78 1.09e+00 8.42e-01 1.92e+01 angle pdb=" C LYS D 294 " pdb=" N MET D 295 " pdb=" CA MET D 295 " ideal model delta sigma weight residual 121.70 128.56 -6.86 1.80e+00 3.09e-01 1.45e+01 ... (remaining 20779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 8569 15.83 - 31.65: 221 31.65 - 47.48: 69 47.48 - 63.30: 16 63.30 - 79.13: 12 Dihedral angle restraints: 8887 sinusoidal: 3403 harmonic: 5484 Sorted by residual: dihedral pdb=" CA ASN B 432 " pdb=" C ASN B 432 " pdb=" N ILE B 433 " pdb=" CA ILE B 433 " ideal model delta harmonic sigma weight residual 180.00 148.04 31.96 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA ASN D 432 " pdb=" C ASN D 432 " pdb=" N ILE D 433 " pdb=" CA ILE D 433 " ideal model delta harmonic sigma weight residual 180.00 148.04 31.96 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA ASN A 432 " pdb=" C ASN A 432 " pdb=" N ILE A 433 " pdb=" CA ILE A 433 " ideal model delta harmonic sigma weight residual 180.00 148.08 31.92 0 5.00e+00 4.00e-02 4.08e+01 ... (remaining 8884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1277 0.034 - 0.068: 799 0.068 - 0.103: 235 0.103 - 0.137: 95 0.137 - 0.171: 22 Chirality restraints: 2428 Sorted by residual: chirality pdb=" CG LEU D 677 " pdb=" CB LEU D 677 " pdb=" CD1 LEU D 677 " pdb=" CD2 LEU D 677 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CG LEU B 677 " pdb=" CB LEU B 677 " pdb=" CD1 LEU B 677 " pdb=" CD2 LEU B 677 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CG LEU A 314 " pdb=" CB LEU A 314 " pdb=" CD1 LEU A 314 " pdb=" CD2 LEU A 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 2425 not shown) Planarity restraints: 2564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 380 " 0.018 2.00e-02 2.50e+03 1.50e-02 5.60e+00 pdb=" CG TRP B 380 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 380 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 380 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 380 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 380 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 380 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 380 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 380 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 380 " 0.018 2.00e-02 2.50e+03 1.50e-02 5.59e+00 pdb=" CG TRP D 380 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP D 380 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP D 380 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 380 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 380 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 380 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 380 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 380 " 0.018 2.00e-02 2.50e+03 1.49e-02 5.52e+00 pdb=" CG TRP A 380 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 380 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 380 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 380 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 380 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 380 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 380 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 380 " 0.002 2.00e-02 2.50e+03 ... (remaining 2561 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 123 2.60 - 3.18: 14507 3.18 - 3.75: 23020 3.75 - 4.33: 33386 4.33 - 4.90: 53742 Nonbonded interactions: 124778 Sorted by model distance: nonbonded pdb=" SG CYS B 331 " pdb=" SG CYS B 344 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS C 331 " pdb=" SG CYS C 344 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS D 331 " pdb=" SG CYS D 344 " model vdw 2.026 3.760 nonbonded pdb=" OH TYR B 227 " pdb=" O VAL B 569 " model vdw 2.120 3.040 nonbonded pdb=" OH TYR A 227 " pdb=" O VAL A 569 " model vdw 2.120 3.040 ... (remaining 124773 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 31.700 Find NCS groups from input model: 0.670 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.010 0.051 15264 Z= 0.675 Angle : 0.809 10.994 20784 Z= 0.446 Chirality : 0.049 0.171 2428 Planarity : 0.005 0.052 2552 Dihedral : 9.476 79.127 5332 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.26 % Allowed : 1.58 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.69 (0.17), residues: 1828 helix: -2.42 (0.12), residues: 1004 sheet: 0.11 (0.31), residues: 192 loop : -0.88 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.005 TRP D 380 HIS 0.005 0.003 HIS A 379 PHE 0.025 0.002 PHE C 310 TYR 0.026 0.002 TYR D 249 ARG 0.009 0.001 ARG D 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 359 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASN cc_start: 0.7875 (m-40) cc_final: 0.7657 (m-40) REVERT: A 410 LYS cc_start: 0.8414 (tttm) cc_final: 0.8109 (tttm) REVERT: A 508 ASN cc_start: 0.7052 (m110) cc_final: 0.6776 (m-40) REVERT: B 269 ASN cc_start: 0.7879 (m-40) cc_final: 0.7667 (m-40) REVERT: B 410 LYS cc_start: 0.8414 (tttm) cc_final: 0.8107 (tttm) REVERT: B 508 ASN cc_start: 0.7048 (m110) cc_final: 0.6770 (m-40) REVERT: C 410 LYS cc_start: 0.8429 (tttm) cc_final: 0.8119 (tttp) REVERT: C 508 ASN cc_start: 0.7127 (m110) cc_final: 0.6822 (m-40) REVERT: D 269 ASN cc_start: 0.7871 (m-40) cc_final: 0.7658 (m-40) REVERT: D 410 LYS cc_start: 0.8412 (tttm) cc_final: 0.8107 (tttp) REVERT: D 508 ASN cc_start: 0.7056 (m110) cc_final: 0.6778 (m-40) outliers start: 4 outliers final: 0 residues processed: 359 average time/residue: 1.0950 time to fit residues: 435.9086 Evaluate side-chains 196 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 543 ASN A 636 GLN B 458 GLN B 543 ASN B 636 GLN C 458 GLN C 537 GLN C 543 ASN C 636 GLN D 458 GLN D 543 ASN D 636 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15264 Z= 0.202 Angle : 0.595 8.076 20784 Z= 0.327 Chirality : 0.042 0.145 2428 Planarity : 0.004 0.041 2552 Dihedral : 5.576 38.686 2268 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.84 % Allowed : 9.37 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 0.47 (0.19), residues: 1828 helix: 0.89 (0.15), residues: 1032 sheet: 0.56 (0.34), residues: 184 loop : -0.63 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 293 HIS 0.002 0.001 HIS A 379 PHE 0.014 0.002 PHE D 676 TYR 0.023 0.002 TYR C 249 ARG 0.006 0.001 ARG C 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 276 time to evaluate : 1.594 Fit side-chains REVERT: A 410 LYS cc_start: 0.8348 (tttm) cc_final: 0.8134 (tttm) REVERT: A 440 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7612 (ttp-170) REVERT: A 590 MET cc_start: 0.7300 (mtp) cc_final: 0.6878 (mtp) REVERT: B 410 LYS cc_start: 0.8353 (tttm) cc_final: 0.8136 (tttm) REVERT: B 440 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7614 (ttp-170) REVERT: B 590 MET cc_start: 0.7286 (mtp) cc_final: 0.6858 (mtp) REVERT: C 410 LYS cc_start: 0.8385 (tttm) cc_final: 0.8169 (tttp) REVERT: C 440 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7597 (ttp-170) REVERT: C 590 MET cc_start: 0.7298 (mtp) cc_final: 0.6872 (mtp) REVERT: D 410 LYS cc_start: 0.8348 (tttm) cc_final: 0.8129 (tttm) REVERT: D 440 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7609 (ttp-170) REVERT: D 590 MET cc_start: 0.7282 (mtp) cc_final: 0.6854 (mtp) outliers start: 43 outliers final: 14 residues processed: 311 average time/residue: 1.0896 time to fit residues: 377.1965 Evaluate side-chains 213 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain D residue 271 LYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 602 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 167 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN ** B 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 ASN ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 578 ASN ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15264 Z= 0.416 Angle : 0.669 8.562 20784 Z= 0.360 Chirality : 0.046 0.160 2428 Planarity : 0.005 0.042 2552 Dihedral : 5.377 31.347 2268 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.16 % Allowed : 12.47 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 0.57 (0.19), residues: 1828 helix: 1.19 (0.15), residues: 1032 sheet: -0.46 (0.31), residues: 200 loop : -0.64 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 293 HIS 0.007 0.002 HIS C 379 PHE 0.019 0.002 PHE C 423 TYR 0.029 0.003 TYR A 249 ARG 0.006 0.001 ARG D 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 211 time to evaluate : 1.764 Fit side-chains REVERT: A 410 LYS cc_start: 0.8581 (tttm) cc_final: 0.8323 (tttm) REVERT: A 411 LYS cc_start: 0.8658 (tttt) cc_final: 0.8427 (tttm) REVERT: A 440 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7706 (ttp-170) REVERT: B 410 LYS cc_start: 0.8582 (tttm) cc_final: 0.8314 (tttm) REVERT: B 411 LYS cc_start: 0.8656 (tttt) cc_final: 0.8418 (tttm) REVERT: B 440 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7706 (ttp-170) REVERT: C 251 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8120 (ttt180) REVERT: C 410 LYS cc_start: 0.8583 (tttm) cc_final: 0.8317 (tttm) REVERT: C 411 LYS cc_start: 0.8657 (tttt) cc_final: 0.8421 (tttm) REVERT: C 440 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7701 (ttp-170) REVERT: C 590 MET cc_start: 0.7639 (mtp) cc_final: 0.7430 (mtp) REVERT: D 410 LYS cc_start: 0.8574 (tttm) cc_final: 0.8313 (tttm) REVERT: D 411 LYS cc_start: 0.8656 (tttt) cc_final: 0.8417 (tttm) REVERT: D 440 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7705 (ttp-170) outliers start: 63 outliers final: 34 residues processed: 256 average time/residue: 1.0858 time to fit residues: 310.2669 Evaluate side-chains 232 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 430 ASN A 578 ASN A 585 GLN B 323 GLN B 430 ASN B 578 ASN B 585 GLN C 323 GLN C 578 ASN D 323 GLN D 430 ASN D 578 ASN D 585 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15264 Z= 0.179 Angle : 0.532 8.332 20784 Z= 0.288 Chirality : 0.040 0.147 2428 Planarity : 0.004 0.039 2552 Dihedral : 4.663 31.666 2268 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.84 % Allowed : 13.52 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1.04 (0.19), residues: 1828 helix: 1.72 (0.16), residues: 1020 sheet: -0.35 (0.30), residues: 200 loop : -0.66 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 293 HIS 0.001 0.001 HIS B 379 PHE 0.015 0.001 PHE D 600 TYR 0.015 0.002 TYR B 527 ARG 0.003 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 222 time to evaluate : 1.703 Fit side-chains REVERT: A 410 LYS cc_start: 0.8439 (tttm) cc_final: 0.8205 (tttp) REVERT: A 440 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7640 (ttp-170) REVERT: B 410 LYS cc_start: 0.8429 (tttm) cc_final: 0.8182 (tttm) REVERT: B 411 LYS cc_start: 0.8595 (tttt) cc_final: 0.8341 (tttm) REVERT: B 440 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7636 (ttp-170) REVERT: C 410 LYS cc_start: 0.8434 (tttm) cc_final: 0.8190 (tttp) REVERT: C 440 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7634 (ttp-170) REVERT: C 590 MET cc_start: 0.7891 (mtp) cc_final: 0.7653 (mtp) REVERT: D 410 LYS cc_start: 0.8429 (tttm) cc_final: 0.8175 (tttm) REVERT: D 411 LYS cc_start: 0.8594 (tttt) cc_final: 0.8340 (tttm) REVERT: D 440 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7637 (ttp-170) outliers start: 43 outliers final: 17 residues processed: 250 average time/residue: 1.1226 time to fit residues: 311.6477 Evaluate side-chains 223 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 202 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 151 optimal weight: 0.0020 chunk 122 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15264 Z= 0.174 Angle : 0.519 7.962 20784 Z= 0.280 Chirality : 0.039 0.150 2428 Planarity : 0.004 0.040 2552 Dihedral : 4.421 29.403 2268 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.63 % Allowed : 15.37 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 1.17 (0.19), residues: 1828 helix: 1.83 (0.16), residues: 1020 sheet: -0.22 (0.31), residues: 200 loop : -0.65 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 293 HIS 0.002 0.001 HIS B 379 PHE 0.017 0.001 PHE B 600 TYR 0.016 0.001 TYR C 527 ARG 0.003 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 227 time to evaluate : 1.772 Fit side-chains REVERT: A 440 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7629 (ttp-170) REVERT: B 440 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7624 (ttp-170) REVERT: C 440 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7621 (ttp-170) REVERT: C 590 MET cc_start: 0.7898 (mtp) cc_final: 0.7644 (mtp) REVERT: D 440 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7624 (ttp-170) outliers start: 55 outliers final: 24 residues processed: 264 average time/residue: 1.0225 time to fit residues: 302.5617 Evaluate side-chains 232 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 204 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN C 313 ASN C 578 ASN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15264 Z= 0.193 Angle : 0.530 8.521 20784 Z= 0.282 Chirality : 0.040 0.152 2428 Planarity : 0.004 0.038 2552 Dihedral : 4.396 26.084 2268 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.23 % Allowed : 17.15 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 1.19 (0.19), residues: 1828 helix: 1.83 (0.16), residues: 1024 sheet: -0.38 (0.31), residues: 200 loop : -0.56 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 293 HIS 0.002 0.001 HIS B 379 PHE 0.017 0.001 PHE B 600 TYR 0.016 0.002 TYR A 527 ARG 0.002 0.000 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 213 time to evaluate : 1.695 Fit side-chains REVERT: A 321 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8910 (tp) REVERT: A 440 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7633 (ttp-170) REVERT: A 636 GLN cc_start: 0.8837 (mt0) cc_final: 0.8491 (mt0) REVERT: B 321 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8904 (tp) REVERT: B 440 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7631 (ttp-170) REVERT: B 636 GLN cc_start: 0.8837 (mt0) cc_final: 0.8486 (mt0) REVERT: C 321 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8903 (tp) REVERT: C 440 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7629 (ttp-170) REVERT: D 321 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8908 (tp) REVERT: D 440 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7631 (ttp-170) REVERT: D 636 GLN cc_start: 0.8837 (mt0) cc_final: 0.8491 (mt0) outliers start: 49 outliers final: 28 residues processed: 250 average time/residue: 0.9730 time to fit residues: 275.5835 Evaluate side-chains 239 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 203 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 100 optimal weight: 0.0060 chunk 149 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN C 585 GLN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 537 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15264 Z= 0.164 Angle : 0.529 8.854 20784 Z= 0.284 Chirality : 0.040 0.144 2428 Planarity : 0.004 0.034 2552 Dihedral : 4.236 24.619 2268 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.03 % Allowed : 18.14 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 1.31 (0.19), residues: 1828 helix: 1.95 (0.16), residues: 1020 sheet: -0.17 (0.33), residues: 192 loop : -0.59 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 293 HIS 0.001 0.001 HIS D 379 PHE 0.017 0.001 PHE A 600 TYR 0.016 0.001 TYR B 527 ARG 0.007 0.000 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 211 time to evaluate : 1.764 Fit side-chains revert: symmetry clash REVERT: A 440 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7617 (ttp-170) REVERT: B 440 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7614 (ttp-170) REVERT: C 440 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7613 (ttp-170) REVERT: C 636 GLN cc_start: 0.8805 (mt0) cc_final: 0.8452 (mt0) REVERT: D 440 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7609 (ttp-170) outliers start: 46 outliers final: 31 residues processed: 240 average time/residue: 0.9789 time to fit residues: 264.5575 Evaluate side-chains 237 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 16 optimal weight: 0.0570 chunk 139 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN A 636 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN B 636 GLN C 537 GLN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 537 GLN D 636 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15264 Z= 0.191 Angle : 0.536 9.076 20784 Z= 0.288 Chirality : 0.040 0.159 2428 Planarity : 0.004 0.034 2552 Dihedral : 4.216 23.522 2268 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.03 % Allowed : 17.81 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 1.28 (0.19), residues: 1828 helix: 1.90 (0.16), residues: 1024 sheet: -0.35 (0.32), residues: 200 loop : -0.50 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 414 HIS 0.002 0.001 HIS B 379 PHE 0.018 0.001 PHE C 423 TYR 0.016 0.002 TYR A 527 ARG 0.007 0.000 ARG D 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 206 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7637 (ttp-170) REVERT: B 440 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7632 (ttp-170) REVERT: B 590 MET cc_start: 0.8586 (mmm) cc_final: 0.8135 (mtp) REVERT: C 440 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7629 (ttp-170) REVERT: D 321 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8893 (tp) REVERT: D 338 ARG cc_start: 0.7391 (tpp80) cc_final: 0.7031 (tpp-160) REVERT: D 440 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7635 (ttp-170) outliers start: 46 outliers final: 33 residues processed: 235 average time/residue: 1.0513 time to fit residues: 276.9185 Evaluate side-chains 234 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 196 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.8980 chunk 155 optimal weight: 0.4980 chunk 165 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 129 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN A 645 ASN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN C 537 GLN C 636 GLN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 537 GLN D 645 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15264 Z= 0.171 Angle : 0.527 9.426 20784 Z= 0.283 Chirality : 0.040 0.155 2428 Planarity : 0.004 0.034 2552 Dihedral : 4.150 23.150 2268 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.51 % Allowed : 18.21 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 1.35 (0.20), residues: 1828 helix: 1.94 (0.16), residues: 1024 sheet: -0.15 (0.33), residues: 192 loop : -0.50 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 293 HIS 0.002 0.001 HIS C 379 PHE 0.017 0.001 PHE D 600 TYR 0.016 0.001 TYR B 527 ARG 0.008 0.000 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 202 time to evaluate : 1.414 Fit side-chains revert: symmetry clash REVERT: A 321 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8893 (tp) REVERT: A 440 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7618 (ttp-170) REVERT: B 321 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8890 (tp) REVERT: B 440 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7615 (ttp-170) REVERT: C 321 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8889 (tp) REVERT: C 440 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7616 (ttp-170) REVERT: D 321 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8885 (tp) REVERT: D 338 ARG cc_start: 0.7355 (tpp80) cc_final: 0.7008 (tpp-160) REVERT: D 440 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7615 (ttp-170) outliers start: 38 outliers final: 28 residues processed: 228 average time/residue: 0.9973 time to fit residues: 256.6918 Evaluate side-chains 233 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 197 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 440 ARG Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 0.2980 chunk 121 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 15 optimal weight: 0.0060 chunk 112 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN A 430 ASN A 537 GLN B 313 ASN B 430 ASN B 537 GLN B 645 ASN C 537 GLN D 313 ASN D 430 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15264 Z= 0.157 Angle : 0.519 9.688 20784 Z= 0.279 Chirality : 0.039 0.150 2428 Planarity : 0.004 0.033 2552 Dihedral : 4.034 22.718 2268 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.57 % Allowed : 17.81 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: 1.44 (0.20), residues: 1828 helix: 2.02 (0.16), residues: 1020 sheet: -0.11 (0.33), residues: 192 loop : -0.48 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 455 HIS 0.001 0.000 HIS B 379 PHE 0.016 0.001 PHE D 600 TYR 0.016 0.001 TYR C 527 ARG 0.007 0.000 ARG C 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 218 time to evaluate : 1.636 Fit side-chains REVERT: B 440 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7607 (ttp-170) REVERT: C 321 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8879 (tp) REVERT: D 321 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8883 (tp) REVERT: D 338 ARG cc_start: 0.7274 (tpp80) cc_final: 0.6954 (tpp-160) REVERT: D 440 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7605 (ttp-170) outliers start: 39 outliers final: 25 residues processed: 245 average time/residue: 0.9307 time to fit residues: 258.7071 Evaluate side-chains 239 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 210 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 440 ARG Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 577 ILE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 577 ILE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 644 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 134 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 GLN C 537 GLN C 681 ASN ** D 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.143400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.110574 restraints weight = 17100.523| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.62 r_work: 0.3014 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15264 Z= 0.175 Angle : 0.535 9.648 20784 Z= 0.287 Chirality : 0.040 0.158 2428 Planarity : 0.004 0.033 2552 Dihedral : 4.099 22.394 2268 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.51 % Allowed : 17.94 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.20), residues: 1828 helix: 1.95 (0.16), residues: 1020 sheet: -0.11 (0.33), residues: 192 loop : -0.41 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 455 HIS 0.002 0.001 HIS C 379 PHE 0.016 0.001 PHE D 600 TYR 0.016 0.001 TYR D 553 ARG 0.008 0.000 ARG C 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5143.49 seconds wall clock time: 90 minutes 58.04 seconds (5458.04 seconds total)