Starting phenix.real_space_refine on Fri Feb 16 17:26:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2k_23131/02_2024/7l2k_23131.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2k_23131/02_2024/7l2k_23131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2k_23131/02_2024/7l2k_23131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2k_23131/02_2024/7l2k_23131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2k_23131/02_2024/7l2k_23131.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2k_23131/02_2024/7l2k_23131.pdb" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 100 5.16 5 C 10494 2.51 5 N 2588 2.21 5 O 2816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 212": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15998 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4000 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 480} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4000 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 480} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3998 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 480} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4000 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 480} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 8.59, per 1000 atoms: 0.54 Number of scatterers: 15998 At special positions: 0 Unit cell: (127.65, 127.65, 111.55, 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 100 16.00 O 2816 8.00 N 2588 7.00 C 10494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.14 Conformation dependent library (CDL) restraints added in 2.8 seconds 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 4 sheets defined 68.0% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.738A pdb=" N VAL A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 removed outlier: 3.616A pdb=" N ALA A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 267 removed outlier: 3.919A pdb=" N VAL A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.767A pdb=" N ALA A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.848A pdb=" N SER A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 362 through 366 removed outlier: 4.005A pdb=" N LEU A 365 " --> pdb=" O CYS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.797A pdb=" N ASN A 419 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.537A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 498 removed outlier: 3.600A pdb=" N TYR A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 510 through 532 removed outlier: 4.262A pdb=" N PHE A 516 " --> pdb=" O SER A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.708A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.666A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 599 removed outlier: 4.919A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 640 removed outlier: 3.941A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 673 through 689 removed outlier: 3.512A pdb=" N ASN A 687 " --> pdb=" O GLY A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 712 removed outlier: 3.662A pdb=" N SER A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 216 through 221 removed outlier: 4.003A pdb=" N VAL C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 258 removed outlier: 3.881A pdb=" N THR C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 267 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.647A pdb=" N ALA C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.780A pdb=" N PHE C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 362 through 366 removed outlier: 4.138A pdb=" N LEU C 365 " --> pdb=" O CYS C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 410 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.534A pdb=" N ASN C 419 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 498 removed outlier: 3.650A pdb=" N TYR C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 552 removed outlier: 3.592A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.563A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 599 removed outlier: 3.947A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 640 through 643 Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 673 through 712 removed outlier: 3.759A pdb=" N ASN C 687 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 Processing helix chain 'D' and resid 216 through 221 removed outlier: 3.662A pdb=" N VAL D 221 " --> pdb=" O VAL D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 258 removed outlier: 3.654A pdb=" N THR D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 268 removed outlier: 3.990A pdb=" N LEU D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.505A pdb=" N ALA D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 removed outlier: 3.811A pdb=" N SER D 307 " --> pdb=" O LYS D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 346 through 354 Processing helix chain 'D' and resid 362 through 366 removed outlier: 3.968A pdb=" N LEU D 365 " --> pdb=" O CYS D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 410 through 414 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.740A pdb=" N ASN D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 498 removed outlier: 3.623A pdb=" N TYR D 472 " --> pdb=" O THR D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.617A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.697A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 599 removed outlier: 4.874A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 640 removed outlier: 3.942A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 673 through 689 Processing helix chain 'D' and resid 691 through 712 removed outlier: 3.533A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.740A pdb=" N VAL B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 258 removed outlier: 3.759A pdb=" N THR B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 267 removed outlier: 3.896A pdb=" N VAL B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.504A pdb=" N ALA B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.880A pdb=" N SER B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 362 through 366 removed outlier: 4.032A pdb=" N LEU B 365 " --> pdb=" O CYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.787A pdb=" N ASN B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 498 removed outlier: 3.610A pdb=" N TYR B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 510 through 532 removed outlier: 3.749A pdb=" N PHE B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 552 removed outlier: 3.622A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 removed outlier: 3.660A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 599 removed outlier: 4.972A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 640 removed outlier: 3.960A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 673 through 712 removed outlier: 6.053A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.728A pdb=" N SER A 379 " --> pdb=" O TRP A 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 368 through 373 removed outlier: 5.369A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.516A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 368 through 373 removed outlier: 4.086A pdb=" N GLU B 371 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2712 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: 4.79 Time building geometry restraints manager: 6.66 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: 4854 1.34 - 1.46: 3547 1.46 - 1.58: 7797 1.58 - 1.70: 0 1.70 - 1.81: 164 Bond restraints: 16362 Sorted by residual: bond pdb=" C ASN B 652 " pdb=" N TYR B 653 " ideal model delta sigma weight residual 1.332 1.221 0.111 1.40e-02 5.10e+03 6.28e+01 bond pdb=" C ASN C 652 " pdb=" N TYR C 653 " ideal model delta sigma weight residual 1.332 1.258 0.075 1.40e-02 5.10e+03 2.85e+01 bond pdb=" CA TYR C 555 " pdb=" C TYR C 555 " ideal model delta sigma weight residual 1.523 1.468 0.054 1.41e-02 5.03e+03 1.49e+01 bond pdb=" C THR C 650 " pdb=" N GLU C 651 " ideal model delta sigma weight residual 1.332 1.368 -0.035 1.29e-02 6.01e+03 7.41e+00 bond pdb=" C ASN D 652 " pdb=" N TYR D 653 " ideal model delta sigma weight residual 1.332 1.295 0.037 1.40e-02 5.10e+03 6.99e+00 ... (remaining 16357 not shown) Histogram of bond angle deviations from ideal: 96.64 - 104.14: 198 104.14 - 111.63: 7432 111.63 - 119.13: 5923 119.13 - 126.62: 8423 126.62 - 134.12: 177 Bond angle restraints: 22153 Sorted by residual: angle pdb=" CA ASN C 652 " pdb=" C ASN C 652 " pdb=" N TYR C 653 " ideal model delta sigma weight residual 116.43 108.51 7.92 1.37e+00 5.33e-01 3.34e+01 angle pdb=" O ASN C 652 " pdb=" C ASN C 652 " pdb=" N TYR C 653 " ideal model delta sigma weight residual 122.96 129.66 -6.70 1.26e+00 6.30e-01 2.83e+01 angle pdb=" C THR B 650 " pdb=" N GLU B 651 " pdb=" CA GLU B 651 " ideal model delta sigma weight residual 122.60 116.94 5.66 1.56e+00 4.11e-01 1.32e+01 angle pdb=" C PHE B 712 " pdb=" N LEU B 713 " pdb=" CA LEU B 713 " ideal model delta sigma weight residual 121.54 128.43 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" C ASN D 652 " pdb=" N TYR D 653 " pdb=" CA TYR D 653 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 ... (remaining 22148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 8899 15.71 - 31.41: 657 31.41 - 47.12: 89 47.12 - 62.83: 24 62.83 - 78.54: 10 Dihedral angle restraints: 9679 sinusoidal: 3839 harmonic: 5840 Sorted by residual: dihedral pdb=" CA PRO A 732 " pdb=" C PRO A 732 " pdb=" N ASP A 733 " pdb=" CA ASP A 733 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA SER A 711 " pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA THR D 389 " pdb=" C THR D 389 " pdb=" N CYS D 390 " pdb=" CA CYS D 390 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 9676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1487 0.035 - 0.069: 773 0.069 - 0.104: 224 0.104 - 0.138: 54 0.138 - 0.173: 9 Chirality restraints: 2547 Sorted by residual: chirality pdb=" CG LEU C 637 " pdb=" CB LEU C 637 " pdb=" CD1 LEU C 637 " pdb=" CD2 LEU C 637 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CB ILE B 689 " pdb=" CA ILE B 689 " pdb=" CG1 ILE B 689 " pdb=" CG2 ILE B 689 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CG LEU A 637 " pdb=" CB LEU A 637 " pdb=" CD1 LEU A 637 " pdb=" CD2 LEU A 637 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.93e-01 ... (remaining 2544 not shown) Planarity restraints: 2724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 650 " -0.019 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C THR C 650 " 0.068 2.00e-02 2.50e+03 pdb=" O THR C 650 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU C 651 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 650 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C THR B 650 " -0.064 2.00e-02 2.50e+03 pdb=" O THR B 650 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU B 651 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 548 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C GLY C 548 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY C 548 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP C 549 " -0.015 2.00e-02 2.50e+03 ... (remaining 2721 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 114 2.59 - 3.16: 14465 3.16 - 3.74: 24044 3.74 - 4.32: 32807 4.32 - 4.90: 54071 Nonbonded interactions: 125501 Sorted by model distance: nonbonded pdb=" OG1 THR A 731 " pdb=" O ASP A 733 " model vdw 2.007 2.440 nonbonded pdb=" OG1 THR C 731 " pdb=" O ASP C 733 " model vdw 2.026 2.440 nonbonded pdb=" OG1 THR D 731 " pdb=" O ASP D 733 " model vdw 2.029 2.440 nonbonded pdb=" OE1 GLU C 651 " pdb=" NZ LYS C 656 " model vdw 2.073 2.520 nonbonded pdb=" O ILE D 672 " pdb=" ND2 ASN D 676 " model vdw 2.108 2.520 ... (remaining 125496 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 203 through 727 or (resid 728 and (name N or name CA or na \ me C or name O or name CB )) or resid 729 through 745)) selection = (chain 'B' and (resid 203 through 727 or (resid 728 and (name N or name CA or na \ me C or name O or name CB )) or resid 729 through 745)) selection = (chain 'C' and (resid 203 through 727 or (resid 728 and (name N or name CA or na \ me C or name O or name CB )) or resid 729 through 745)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.420 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 41.370 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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 : 0.008 0.111 16362 Z= 0.504 Angle : 0.819 7.921 22153 Z= 0.466 Chirality : 0.044 0.173 2547 Planarity : 0.005 0.040 2724 Dihedral : 11.267 78.535 5911 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.56 % Favored : 93.24 % Rotamer: Outliers : 0.46 % Allowed : 2.45 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1952 helix: 1.07 (0.14), residues: 1196 sheet: 0.16 (0.76), residues: 36 loop : -1.97 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 426 HIS 0.004 0.001 HIS D 206 PHE 0.023 0.003 PHE D 649 TYR 0.031 0.003 TYR C 565 ARG 0.013 0.001 ARG D 557 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 772 time to evaluate : 1.737 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7947 (mmm) cc_final: 0.7439 (mmm) REVERT: A 381 LEU cc_start: 0.7967 (mt) cc_final: 0.7594 (mm) REVERT: A 428 ARG cc_start: 0.7477 (mtp180) cc_final: 0.7275 (ptm160) REVERT: A 435 TYR cc_start: 0.8938 (m-10) cc_final: 0.8595 (m-80) REVERT: A 441 TYR cc_start: 0.9333 (t80) cc_final: 0.9126 (t80) REVERT: A 465 LEU cc_start: 0.8514 (mt) cc_final: 0.8151 (pt) REVERT: A 472 TYR cc_start: 0.8043 (m-80) cc_final: 0.7643 (m-80) REVERT: A 504 LYS cc_start: 0.8573 (mttt) cc_final: 0.8330 (ttmt) REVERT: A 515 LEU cc_start: 0.9431 (mt) cc_final: 0.9212 (mt) REVERT: A 517 PHE cc_start: 0.8850 (t80) cc_final: 0.8477 (t80) REVERT: A 536 GLU cc_start: 0.9009 (mp0) cc_final: 0.8596 (mp0) REVERT: A 557 ARG cc_start: 0.8844 (ptp-170) cc_final: 0.8513 (ptp-170) REVERT: A 572 MET cc_start: 0.7601 (tpp) cc_final: 0.7355 (tpp) REVERT: A 631 TYR cc_start: 0.7518 (t80) cc_final: 0.7262 (t80) REVERT: A 634 CYS cc_start: 0.8600 (m) cc_final: 0.8075 (m) REVERT: A 636 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8308 (mm-30) REVERT: A 684 GLU cc_start: 0.7779 (tt0) cc_final: 0.7298 (tt0) REVERT: A 740 TRP cc_start: 0.5801 (m100) cc_final: 0.5563 (m-90) REVERT: A 742 PHE cc_start: 0.7939 (t80) cc_final: 0.7588 (t80) REVERT: C 368 LYS cc_start: 0.6900 (tttt) cc_final: 0.6570 (tptm) REVERT: C 416 GLU cc_start: 0.7480 (tp30) cc_final: 0.7135 (tp30) REVERT: C 432 ARG cc_start: 0.8371 (mtt90) cc_final: 0.7152 (tpp-160) REVERT: C 435 TYR cc_start: 0.8790 (m-10) cc_final: 0.8355 (m-80) REVERT: C 442 CYS cc_start: 0.9350 (m) cc_final: 0.9052 (m) REVERT: C 498 GLN cc_start: 0.8991 (mt0) cc_final: 0.8443 (tm-30) REVERT: C 517 PHE cc_start: 0.8908 (t80) cc_final: 0.8594 (t80) REVERT: C 572 MET cc_start: 0.7698 (tpp) cc_final: 0.7238 (tpp) REVERT: C 631 TYR cc_start: 0.7688 (t80) cc_final: 0.7405 (t80) REVERT: C 636 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8361 (mm-30) REVERT: C 644 MET cc_start: 0.9073 (mmm) cc_final: 0.8396 (tpt) REVERT: C 689 ILE cc_start: 0.8755 (pt) cc_final: 0.8470 (pt) REVERT: C 693 SER cc_start: 0.9247 (m) cc_final: 0.8546 (p) REVERT: D 401 TYR cc_start: 0.7189 (m-80) cc_final: 0.6268 (m-80) REVERT: D 426 TRP cc_start: 0.8449 (t-100) cc_final: 0.8165 (t-100) REVERT: D 465 LEU cc_start: 0.8487 (mt) cc_final: 0.8214 (pt) REVERT: D 472 TYR cc_start: 0.8075 (m-80) cc_final: 0.7440 (m-80) REVERT: D 517 PHE cc_start: 0.8909 (t80) cc_final: 0.8550 (t80) REVERT: D 631 TYR cc_start: 0.7501 (t80) cc_final: 0.7105 (t80) REVERT: D 634 CYS cc_start: 0.8679 (m) cc_final: 0.8354 (m) REVERT: D 636 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8309 (mm-30) REVERT: B 363 ARG cc_start: 0.6698 (mtp180) cc_final: 0.6472 (ttm170) REVERT: B 401 TYR cc_start: 0.7204 (m-80) cc_final: 0.6559 (m-80) REVERT: B 431 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8720 (tttt) REVERT: B 435 TYR cc_start: 0.8877 (m-10) cc_final: 0.8590 (m-80) REVERT: B 460 LEU cc_start: 0.8065 (mt) cc_final: 0.7811 (mp) REVERT: B 465 LEU cc_start: 0.8478 (mt) cc_final: 0.8228 (pt) REVERT: B 494 GLN cc_start: 0.9299 (mm-40) cc_final: 0.8986 (mp10) REVERT: B 498 GLN cc_start: 0.8911 (mt0) cc_final: 0.8547 (tm-30) REVERT: B 517 PHE cc_start: 0.8854 (t80) cc_final: 0.8560 (t80) REVERT: B 535 LYS cc_start: 0.8411 (tttt) cc_final: 0.8162 (tppt) REVERT: B 581 MET cc_start: 0.8104 (mmm) cc_final: 0.7799 (mmm) REVERT: B 631 TYR cc_start: 0.7492 (t80) cc_final: 0.7200 (t80) REVERT: B 634 CYS cc_start: 0.8649 (m) cc_final: 0.8367 (m) REVERT: B 636 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8315 (mm-30) REVERT: B 689 ILE cc_start: 0.8793 (pt) cc_final: 0.8485 (pt) REVERT: B 742 PHE cc_start: 0.7974 (t80) cc_final: 0.7657 (t80) outliers start: 8 outliers final: 3 residues processed: 778 average time/residue: 0.2693 time to fit residues: 306.9978 Evaluate side-chains 508 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 505 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain D residue 512 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 8.9990 chunk 148 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 0.0980 chunk 177 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 519 GLN A 560 GLN A 561 GLN C 519 GLN D 354 GLN D 423 GLN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 GLN D 652 ASN D 727 GLN B 423 GLN B 519 GLN B 560 GLN B 561 GLN B 727 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16362 Z= 0.210 Angle : 0.634 7.964 22153 Z= 0.332 Chirality : 0.039 0.141 2547 Planarity : 0.004 0.039 2724 Dihedral : 4.870 42.380 2176 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.96 % Allowed : 13.11 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 1952 helix: 1.61 (0.14), residues: 1196 sheet: 0.45 (0.78), residues: 36 loop : -1.98 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 697 HIS 0.013 0.001 HIS A 378 PHE 0.025 0.002 PHE D 659 TYR 0.025 0.002 TYR D 435 ARG 0.005 0.000 ARG D 557 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 641 time to evaluate : 1.880 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 TYR cc_start: 0.9388 (t80) cc_final: 0.9105 (t80) REVERT: A 517 PHE cc_start: 0.8707 (t80) cc_final: 0.8175 (t80) REVERT: A 742 PHE cc_start: 0.7886 (t80) cc_final: 0.7682 (t80) REVERT: C 368 LYS cc_start: 0.6953 (tttt) cc_final: 0.6451 (tptm) REVERT: C 397 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8288 (tm-30) REVERT: C 428 ARG cc_start: 0.8140 (mtp180) cc_final: 0.7571 (mmt180) REVERT: C 474 ARG cc_start: 0.8601 (ttp-110) cc_final: 0.7986 (ttp-110) REVERT: C 498 GLN cc_start: 0.8912 (mt0) cc_final: 0.8403 (tm-30) REVERT: C 512 SER cc_start: 0.7746 (OUTLIER) cc_final: 0.7544 (p) REVERT: C 517 PHE cc_start: 0.8781 (t80) cc_final: 0.8349 (t80) REVERT: C 536 GLU cc_start: 0.9121 (mp0) cc_final: 0.8910 (mp0) REVERT: C 555 TYR cc_start: 0.9163 (m-80) cc_final: 0.8750 (m-80) REVERT: C 636 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8452 (mm-30) REVERT: C 644 MET cc_start: 0.8970 (mmm) cc_final: 0.8537 (tpt) REVERT: C 661 ILE cc_start: 0.9478 (mt) cc_final: 0.9212 (tp) REVERT: C 682 MET cc_start: 0.8184 (mtm) cc_final: 0.7520 (mtm) REVERT: C 691 GLN cc_start: 0.7568 (pm20) cc_final: 0.6851 (pp30) REVERT: C 693 SER cc_start: 0.9109 (m) cc_final: 0.8604 (p) REVERT: C 697 TRP cc_start: 0.8728 (t60) cc_final: 0.8391 (t60) REVERT: D 381 LEU cc_start: 0.7588 (mm) cc_final: 0.7117 (tt) REVERT: D 401 TYR cc_start: 0.7279 (m-80) cc_final: 0.6242 (m-80) REVERT: D 426 TRP cc_start: 0.8280 (t-100) cc_final: 0.7954 (t-100) REVERT: D 474 ARG cc_start: 0.8696 (ttp-110) cc_final: 0.8338 (ttm110) REVERT: D 517 PHE cc_start: 0.8736 (t80) cc_final: 0.8289 (t80) REVERT: D 555 TYR cc_start: 0.9147 (m-80) cc_final: 0.8600 (m-80) REVERT: D 557 ARG cc_start: 0.8899 (ptp-170) cc_final: 0.8509 (ptp-110) REVERT: D 634 CYS cc_start: 0.8338 (m) cc_final: 0.7831 (m) REVERT: D 661 ILE cc_start: 0.9486 (mt) cc_final: 0.9270 (tp) REVERT: D 741 CYS cc_start: 0.6233 (p) cc_final: 0.5460 (p) REVERT: B 267 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8228 (mt) REVERT: B 363 ARG cc_start: 0.6536 (mtp180) cc_final: 0.6264 (ttm170) REVERT: B 401 TYR cc_start: 0.7249 (m-80) cc_final: 0.6482 (m-80) REVERT: B 474 ARG cc_start: 0.8567 (ttp-110) cc_final: 0.7903 (ttp-170) REVERT: B 494 GLN cc_start: 0.9245 (mm-40) cc_final: 0.8999 (mm110) REVERT: B 517 PHE cc_start: 0.8805 (t80) cc_final: 0.8592 (t80) REVERT: B 555 TYR cc_start: 0.9162 (m-80) cc_final: 0.8767 (m-80) REVERT: B 562 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7821 (mpp) REVERT: B 634 CYS cc_start: 0.8368 (m) cc_final: 0.8015 (m) REVERT: B 636 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8490 (mm-30) outliers start: 52 outliers final: 40 residues processed: 664 average time/residue: 0.2609 time to fit residues: 257.3013 Evaluate side-chains 557 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 514 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 464 LYS Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 741 CYS Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 464 LYS Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 741 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 148 optimal weight: 0.0040 chunk 121 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 178 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN D 519 GLN D 561 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16362 Z= 0.227 Angle : 0.661 12.099 22153 Z= 0.333 Chirality : 0.041 0.261 2547 Planarity : 0.004 0.073 2724 Dihedral : 4.710 32.004 2175 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.39 % Allowed : 16.64 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1952 helix: 1.56 (0.15), residues: 1204 sheet: 0.27 (0.69), residues: 36 loop : -2.07 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 740 HIS 0.005 0.001 HIS C 410 PHE 0.024 0.002 PHE A 489 TYR 0.026 0.002 TYR A 435 ARG 0.007 0.000 ARG B 721 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 527 time to evaluate : 1.832 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8346 (mm) REVERT: A 426 TRP cc_start: 0.8152 (t-100) cc_final: 0.7875 (t-100) REVERT: A 517 PHE cc_start: 0.8696 (t80) cc_final: 0.8165 (t80) REVERT: A 555 TYR cc_start: 0.9229 (m-80) cc_final: 0.8950 (m-80) REVERT: A 661 ILE cc_start: 0.9468 (mt) cc_final: 0.9064 (tp) REVERT: A 742 PHE cc_start: 0.7781 (t80) cc_final: 0.7353 (t80) REVERT: C 216 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7649 (mp) REVERT: C 368 LYS cc_start: 0.6973 (tttt) cc_final: 0.6467 (tptm) REVERT: C 428 ARG cc_start: 0.8241 (mtp180) cc_final: 0.7566 (mmt180) REVERT: C 474 ARG cc_start: 0.8561 (ttp-110) cc_final: 0.8124 (ttm110) REVERT: C 498 GLN cc_start: 0.8988 (mt0) cc_final: 0.8415 (tm-30) REVERT: C 517 PHE cc_start: 0.8677 (t80) cc_final: 0.8251 (t80) REVERT: C 555 TYR cc_start: 0.9204 (m-80) cc_final: 0.8701 (m-80) REVERT: C 556 THR cc_start: 0.8587 (p) cc_final: 0.8200 (t) REVERT: C 636 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8440 (mm-30) REVERT: C 644 MET cc_start: 0.9053 (mmm) cc_final: 0.8600 (tpt) REVERT: C 691 GLN cc_start: 0.7671 (pm20) cc_final: 0.6888 (pp30) REVERT: C 693 SER cc_start: 0.9085 (m) cc_final: 0.8586 (p) REVERT: D 309 TYR cc_start: 0.7956 (m-10) cc_final: 0.7674 (m-80) REVERT: D 401 TYR cc_start: 0.7526 (m-80) cc_final: 0.6413 (m-80) REVERT: D 426 TRP cc_start: 0.8331 (t-100) cc_final: 0.7858 (t-100) REVERT: D 474 ARG cc_start: 0.8707 (ttp-110) cc_final: 0.8352 (ttm110) REVERT: D 517 PHE cc_start: 0.8640 (t80) cc_final: 0.8171 (t80) REVERT: D 524 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8939 (mm) REVERT: D 555 TYR cc_start: 0.9220 (m-80) cc_final: 0.8599 (m-80) REVERT: D 634 CYS cc_start: 0.8406 (m) cc_final: 0.7971 (m) REVERT: B 324 LYS cc_start: 0.5437 (mmmt) cc_final: 0.5236 (mmpt) REVERT: B 363 ARG cc_start: 0.6523 (mtp180) cc_final: 0.6250 (ttm170) REVERT: B 401 TYR cc_start: 0.7293 (m-80) cc_final: 0.6429 (m-80) REVERT: B 517 PHE cc_start: 0.8809 (t80) cc_final: 0.8574 (t80) REVERT: B 533 GLN cc_start: 0.8190 (mp10) cc_final: 0.7878 (mp10) REVERT: B 555 TYR cc_start: 0.9226 (m-80) cc_final: 0.8663 (m-80) REVERT: B 562 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7864 (mpp) REVERT: B 634 CYS cc_start: 0.8318 (m) cc_final: 0.7919 (m) REVERT: B 636 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8381 (mm-30) REVERT: B 659 PHE cc_start: 0.8503 (t80) cc_final: 0.8284 (t80) REVERT: B 661 ILE cc_start: 0.9471 (mt) cc_final: 0.9124 (tp) outliers start: 77 outliers final: 50 residues processed: 562 average time/residue: 0.2582 time to fit residues: 215.6555 Evaluate side-chains 538 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 484 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 464 LYS Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 693 SER Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 307 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 574 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 378 HIS ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16362 Z= 0.171 Angle : 0.638 11.184 22153 Z= 0.322 Chirality : 0.040 0.280 2547 Planarity : 0.004 0.051 2724 Dihedral : 4.557 22.841 2173 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.10 % Allowed : 17.44 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1952 helix: 1.55 (0.15), residues: 1220 sheet: 0.77 (0.75), residues: 36 loop : -2.21 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 740 HIS 0.007 0.001 HIS C 378 PHE 0.022 0.001 PHE A 489 TYR 0.031 0.002 TYR B 435 ARG 0.006 0.000 ARG D 557 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 549 time to evaluate : 1.809 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.7723 (ptt) cc_final: 0.6810 (ptp) REVERT: A 421 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8251 (mm) REVERT: A 426 TRP cc_start: 0.8221 (t-100) cc_final: 0.7933 (t-100) REVERT: A 517 PHE cc_start: 0.8602 (t80) cc_final: 0.8380 (t80) REVERT: A 555 TYR cc_start: 0.9211 (m-80) cc_final: 0.8794 (m-80) REVERT: A 562 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7667 (mpp) REVERT: A 716 MET cc_start: 0.5411 (tpt) cc_final: 0.4993 (ttm) REVERT: A 742 PHE cc_start: 0.7669 (t80) cc_final: 0.7326 (t80) REVERT: C 289 HIS cc_start: 0.7118 (m170) cc_final: 0.6102 (m90) REVERT: C 368 LYS cc_start: 0.6992 (tttt) cc_final: 0.6365 (tptp) REVERT: C 428 ARG cc_start: 0.8207 (mtp180) cc_final: 0.7532 (mmt180) REVERT: C 474 ARG cc_start: 0.8534 (ttp-110) cc_final: 0.8171 (ttm110) REVERT: C 498 GLN cc_start: 0.9037 (mt0) cc_final: 0.8377 (tm-30) REVERT: C 509 ASP cc_start: 0.8826 (t0) cc_final: 0.8205 (m-30) REVERT: C 517 PHE cc_start: 0.8614 (t80) cc_final: 0.8311 (t80) REVERT: C 555 TYR cc_start: 0.9057 (m-80) cc_final: 0.8484 (m-80) REVERT: C 556 THR cc_start: 0.8555 (p) cc_final: 0.8263 (t) REVERT: C 636 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8357 (mm-30) REVERT: C 644 MET cc_start: 0.9062 (mmm) cc_final: 0.8581 (tpt) REVERT: C 661 ILE cc_start: 0.9432 (mt) cc_final: 0.9212 (tp) REVERT: C 693 SER cc_start: 0.9086 (m) cc_final: 0.8545 (p) REVERT: D 412 MET cc_start: 0.7869 (ptt) cc_final: 0.7014 (ptp) REVERT: D 445 MET cc_start: 0.9274 (mmm) cc_final: 0.8845 (mmm) REVERT: D 472 TYR cc_start: 0.7669 (m-80) cc_final: 0.7149 (m-80) REVERT: D 474 ARG cc_start: 0.8659 (ttp-110) cc_final: 0.8305 (ttm110) REVERT: D 494 GLN cc_start: 0.9143 (mm110) cc_final: 0.8858 (tm-30) REVERT: D 517 PHE cc_start: 0.8574 (t80) cc_final: 0.7995 (t80) REVERT: D 533 GLN cc_start: 0.8372 (mp10) cc_final: 0.7969 (mp10) REVERT: D 555 TYR cc_start: 0.9103 (m-80) cc_final: 0.8533 (m-80) REVERT: D 572 MET cc_start: 0.8488 (tmm) cc_final: 0.7951 (tpp) REVERT: D 634 CYS cc_start: 0.8377 (m) cc_final: 0.7962 (m) REVERT: D 682 MET cc_start: 0.8330 (ttm) cc_final: 0.7531 (ttp) REVERT: D 716 MET cc_start: 0.5929 (tpt) cc_final: 0.5655 (ttp) REVERT: B 324 LYS cc_start: 0.5462 (mmmt) cc_final: 0.5235 (mmpt) REVERT: B 363 ARG cc_start: 0.6385 (mtp180) cc_final: 0.6137 (ttm170) REVERT: B 445 MET cc_start: 0.9326 (mmm) cc_final: 0.9003 (mmm) REVERT: B 471 ASP cc_start: 0.6385 (OUTLIER) cc_final: 0.5497 (t0) REVERT: B 474 ARG cc_start: 0.8555 (ttp-110) cc_final: 0.8077 (ttp80) REVERT: B 498 GLN cc_start: 0.8726 (mt0) cc_final: 0.8268 (tm-30) REVERT: B 504 LYS cc_start: 0.8279 (tttt) cc_final: 0.8034 (tppt) REVERT: B 511 TYR cc_start: 0.7862 (m-80) cc_final: 0.7563 (m-80) REVERT: B 517 PHE cc_start: 0.8755 (t80) cc_final: 0.8280 (t80) REVERT: B 555 TYR cc_start: 0.9095 (m-80) cc_final: 0.8421 (m-80) REVERT: B 562 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7844 (mpp) REVERT: B 634 CYS cc_start: 0.8252 (m) cc_final: 0.7841 (m) REVERT: B 636 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8323 (mm-30) REVERT: B 644 MET cc_start: 0.9038 (mmm) cc_final: 0.8838 (mmm) REVERT: B 701 ARG cc_start: 0.8922 (mtp-110) cc_final: 0.8666 (mtp85) outliers start: 72 outliers final: 45 residues processed: 576 average time/residue: 0.2571 time to fit residues: 221.9589 Evaluate side-chains 548 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 499 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 575 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.2980 chunk 107 optimal weight: 0.0570 chunk 2 optimal weight: 0.0770 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.4860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN A 652 ASN ** C 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN B 561 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16362 Z= 0.200 Angle : 0.662 16.612 22153 Z= 0.329 Chirality : 0.041 0.225 2547 Planarity : 0.004 0.042 2724 Dihedral : 4.524 20.579 2172 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.84 % Allowed : 18.01 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 1952 helix: 1.54 (0.15), residues: 1220 sheet: 0.36 (0.76), residues: 36 loop : -2.25 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 426 HIS 0.004 0.001 HIS C 410 PHE 0.039 0.001 PHE D 507 TYR 0.035 0.002 TYR C 435 ARG 0.006 0.000 ARG C 557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 516 time to evaluate : 1.730 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.8042 (m-80) cc_final: 0.6542 (m-80) REVERT: A 412 MET cc_start: 0.7990 (ptt) cc_final: 0.7206 (ptp) REVERT: A 421 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8231 (mm) REVERT: A 426 TRP cc_start: 0.8184 (t-100) cc_final: 0.7877 (t-100) REVERT: A 517 PHE cc_start: 0.8684 (t80) cc_final: 0.8121 (t80) REVERT: A 555 TYR cc_start: 0.9205 (m-80) cc_final: 0.8742 (m-80) REVERT: A 562 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7776 (mpp) REVERT: A 661 ILE cc_start: 0.9449 (mt) cc_final: 0.9126 (tp) REVERT: A 716 MET cc_start: 0.5196 (tpt) cc_final: 0.4847 (ttm) REVERT: A 742 PHE cc_start: 0.7474 (t80) cc_final: 0.7135 (t80) REVERT: C 368 LYS cc_start: 0.7015 (tttt) cc_final: 0.6356 (tptp) REVERT: C 428 ARG cc_start: 0.8216 (mtp180) cc_final: 0.7543 (mmt180) REVERT: C 445 MET cc_start: 0.9282 (mmm) cc_final: 0.8956 (mmm) REVERT: C 474 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8197 (ttm110) REVERT: C 509 ASP cc_start: 0.8730 (t0) cc_final: 0.8151 (m-30) REVERT: C 517 PHE cc_start: 0.8529 (t80) cc_final: 0.8109 (t80) REVERT: C 555 TYR cc_start: 0.8936 (m-80) cc_final: 0.8531 (m-80) REVERT: C 556 THR cc_start: 0.8511 (p) cc_final: 0.8288 (t) REVERT: C 644 MET cc_start: 0.9007 (mmm) cc_final: 0.8613 (tpt) REVERT: C 661 ILE cc_start: 0.9449 (mt) cc_final: 0.9233 (tp) REVERT: D 381 LEU cc_start: 0.7698 (tp) cc_final: 0.7265 (tt) REVERT: D 445 MET cc_start: 0.9257 (mmm) cc_final: 0.8895 (mmm) REVERT: D 472 TYR cc_start: 0.7730 (m-80) cc_final: 0.7172 (m-80) REVERT: D 474 ARG cc_start: 0.8663 (ttp-110) cc_final: 0.8309 (ttm110) REVERT: D 517 PHE cc_start: 0.8514 (t80) cc_final: 0.8031 (t80) REVERT: D 524 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8866 (mm) REVERT: D 533 GLN cc_start: 0.8341 (mp10) cc_final: 0.7884 (mp10) REVERT: D 555 TYR cc_start: 0.9032 (m-80) cc_final: 0.8644 (m-80) REVERT: D 634 CYS cc_start: 0.8412 (m) cc_final: 0.7990 (m) REVERT: D 716 MET cc_start: 0.6162 (tpt) cc_final: 0.5795 (ttp) REVERT: B 324 LYS cc_start: 0.5685 (mmmt) cc_final: 0.5480 (mmpt) REVERT: B 363 ARG cc_start: 0.6407 (mtp180) cc_final: 0.6124 (ttm170) REVERT: B 366 SER cc_start: 0.6496 (m) cc_final: 0.5903 (m) REVERT: B 409 ARG cc_start: 0.6423 (ptp90) cc_final: 0.6033 (ptp90) REVERT: B 412 MET cc_start: 0.8061 (ptt) cc_final: 0.7306 (ptp) REVERT: B 445 MET cc_start: 0.9306 (mmm) cc_final: 0.9034 (mmm) REVERT: B 504 LYS cc_start: 0.8306 (tttt) cc_final: 0.8019 (tppt) REVERT: B 511 TYR cc_start: 0.7896 (m-80) cc_final: 0.7649 (m-80) REVERT: B 517 PHE cc_start: 0.8770 (t80) cc_final: 0.8304 (t80) REVERT: B 555 TYR cc_start: 0.9022 (m-80) cc_final: 0.8616 (m-80) REVERT: B 562 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7834 (mpp) REVERT: B 634 CYS cc_start: 0.8300 (m) cc_final: 0.7916 (m) REVERT: B 644 MET cc_start: 0.9012 (mmm) cc_final: 0.8811 (mmm) REVERT: B 661 ILE cc_start: 0.9459 (mt) cc_final: 0.9159 (tp) REVERT: B 701 ARG cc_start: 0.8867 (mtp-110) cc_final: 0.8062 (ttm-80) outliers start: 85 outliers final: 62 residues processed: 556 average time/residue: 0.2577 time to fit residues: 213.5134 Evaluate side-chains 540 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 474 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 741 CYS Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 575 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 20.0000 chunk 170 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 0.0270 chunk 99 optimal weight: 0.1980 overall best weight: 1.0444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 GLN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16362 Z= 0.182 Angle : 0.652 15.165 22153 Z= 0.324 Chirality : 0.041 0.311 2547 Planarity : 0.003 0.040 2724 Dihedral : 4.447 21.794 2172 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.16 % Allowed : 20.00 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 1952 helix: 1.52 (0.15), residues: 1220 sheet: 0.09 (0.78), residues: 36 loop : -2.24 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 372 HIS 0.004 0.001 HIS C 410 PHE 0.031 0.001 PHE D 507 TYR 0.045 0.002 TYR D 309 ARG 0.008 0.000 ARG D 701 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 515 time to evaluate : 1.786 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.8068 (m-80) cc_final: 0.7605 (m-80) REVERT: A 412 MET cc_start: 0.8168 (ptt) cc_final: 0.7578 (ptp) REVERT: A 421 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8195 (mm) REVERT: A 445 MET cc_start: 0.9332 (mmm) cc_final: 0.9089 (mmm) REVERT: A 498 GLN cc_start: 0.8990 (mt0) cc_final: 0.8779 (mp10) REVERT: A 517 PHE cc_start: 0.8689 (t80) cc_final: 0.8197 (t80) REVERT: A 562 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7759 (mpp) REVERT: A 656 LYS cc_start: 0.8199 (pttt) cc_final: 0.7877 (pttm) REVERT: A 661 ILE cc_start: 0.9468 (mt) cc_final: 0.9159 (tp) REVERT: A 716 MET cc_start: 0.5136 (tpt) cc_final: 0.4784 (ttm) REVERT: A 742 PHE cc_start: 0.7450 (t80) cc_final: 0.7123 (t80) REVERT: C 368 LYS cc_start: 0.7029 (tttt) cc_final: 0.6370 (tptp) REVERT: C 383 ASP cc_start: 0.8327 (t0) cc_final: 0.7835 (t0) REVERT: C 428 ARG cc_start: 0.8235 (mtp180) cc_final: 0.7542 (mmt180) REVERT: C 445 MET cc_start: 0.9249 (mmm) cc_final: 0.9005 (mmm) REVERT: C 474 ARG cc_start: 0.8531 (ttp-110) cc_final: 0.8177 (ttm110) REVERT: C 509 ASP cc_start: 0.8597 (t0) cc_final: 0.8092 (m-30) REVERT: C 517 PHE cc_start: 0.8572 (t80) cc_final: 0.8158 (t80) REVERT: C 555 TYR cc_start: 0.8831 (m-80) cc_final: 0.8602 (m-80) REVERT: D 381 LEU cc_start: 0.7768 (tp) cc_final: 0.7283 (tt) REVERT: D 445 MET cc_start: 0.9197 (mmm) cc_final: 0.8965 (mmm) REVERT: D 472 TYR cc_start: 0.7713 (m-80) cc_final: 0.7153 (m-80) REVERT: D 474 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.8287 (ttm110) REVERT: D 524 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8862 (mm) REVERT: D 533 GLN cc_start: 0.8334 (mp10) cc_final: 0.7966 (mp10) REVERT: D 634 CYS cc_start: 0.8391 (m) cc_final: 0.7960 (m) REVERT: D 656 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7665 (tttm) REVERT: D 691 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7387 (pp30) REVERT: D 716 MET cc_start: 0.6171 (tpt) cc_final: 0.5791 (ttp) REVERT: B 324 LYS cc_start: 0.5821 (mmmt) cc_final: 0.5546 (mmpt) REVERT: B 363 ARG cc_start: 0.6410 (mtp180) cc_final: 0.6113 (ttm170) REVERT: B 366 SER cc_start: 0.6477 (m) cc_final: 0.5891 (m) REVERT: B 409 ARG cc_start: 0.6376 (ptp90) cc_final: 0.6099 (ptp90) REVERT: B 412 MET cc_start: 0.7973 (ptt) cc_final: 0.7555 (ptp) REVERT: B 444 TYR cc_start: 0.8872 (t80) cc_final: 0.8643 (t80) REVERT: B 445 MET cc_start: 0.9219 (mmm) cc_final: 0.9004 (mmm) REVERT: B 504 LYS cc_start: 0.8272 (tttt) cc_final: 0.8011 (tppt) REVERT: B 511 TYR cc_start: 0.7954 (m-80) cc_final: 0.7652 (m-80) REVERT: B 517 PHE cc_start: 0.8734 (t80) cc_final: 0.8127 (t80) REVERT: B 533 GLN cc_start: 0.8141 (mp10) cc_final: 0.7819 (mp10) REVERT: B 552 MET cc_start: 0.8856 (ttm) cc_final: 0.8556 (ttp) REVERT: B 555 TYR cc_start: 0.8900 (m-80) cc_final: 0.8590 (m-80) REVERT: B 561 GLN cc_start: 0.8713 (tt0) cc_final: 0.8464 (tt0) REVERT: B 634 CYS cc_start: 0.8370 (m) cc_final: 0.7985 (m) REVERT: B 644 MET cc_start: 0.8987 (mmm) cc_final: 0.8510 (tpt) REVERT: B 661 ILE cc_start: 0.9465 (mt) cc_final: 0.9196 (tp) REVERT: B 701 ARG cc_start: 0.8889 (mtp-110) cc_final: 0.8115 (ttm-80) outliers start: 73 outliers final: 57 residues processed: 546 average time/residue: 0.2543 time to fit residues: 206.4054 Evaluate side-chains 530 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 468 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 741 CYS Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 691 GLN Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 575 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 108 optimal weight: 0.0370 chunk 138 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 159 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 118 optimal weight: 0.0670 chunk 115 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 HIS ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN B 652 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16362 Z= 0.178 Angle : 0.653 16.162 22153 Z= 0.325 Chirality : 0.041 0.327 2547 Planarity : 0.003 0.041 2724 Dihedral : 4.370 21.296 2172 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 3.99 % Allowed : 20.63 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.19), residues: 1952 helix: 1.39 (0.15), residues: 1244 sheet: 0.11 (0.78), residues: 36 loop : -2.39 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 426 HIS 0.004 0.001 HIS C 410 PHE 0.031 0.001 PHE B 489 TYR 0.032 0.002 TYR D 309 ARG 0.009 0.000 ARG C 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 534 time to evaluate : 1.640 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.8019 (m-80) cc_final: 0.7791 (m-80) REVERT: A 412 MET cc_start: 0.8245 (ptt) cc_final: 0.7670 (ptp) REVERT: A 421 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8149 (mm) REVERT: A 517 PHE cc_start: 0.8726 (t80) cc_final: 0.8233 (t80) REVERT: A 557 ARG cc_start: 0.8683 (ptp-170) cc_final: 0.8173 (ptp-170) REVERT: A 562 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7692 (mpp) REVERT: A 656 LYS cc_start: 0.8170 (pttt) cc_final: 0.7823 (pttm) REVERT: A 701 ARG cc_start: 0.8652 (mtp85) cc_final: 0.7686 (ttm-80) REVERT: A 716 MET cc_start: 0.5406 (tpt) cc_final: 0.5014 (ttm) REVERT: A 742 PHE cc_start: 0.7447 (t80) cc_final: 0.7150 (t80) REVERT: C 368 LYS cc_start: 0.7083 (tttt) cc_final: 0.6336 (tptp) REVERT: C 383 ASP cc_start: 0.8336 (t0) cc_final: 0.7839 (t0) REVERT: C 412 MET cc_start: 0.7602 (ptt) cc_final: 0.6863 (ptp) REVERT: C 428 ARG cc_start: 0.8231 (mtp180) cc_final: 0.7559 (mmt180) REVERT: C 474 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8219 (ttm110) REVERT: C 509 ASP cc_start: 0.8407 (t0) cc_final: 0.8007 (m-30) REVERT: C 517 PHE cc_start: 0.8574 (t80) cc_final: 0.8148 (t80) REVERT: C 572 MET cc_start: 0.8686 (tmm) cc_final: 0.7650 (tpp) REVERT: C 682 MET cc_start: 0.8367 (ttm) cc_final: 0.7155 (ttm) REVERT: D 311 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8324 (mp0) REVERT: D 381 LEU cc_start: 0.7648 (tp) cc_final: 0.7129 (tt) REVERT: D 472 TYR cc_start: 0.7700 (m-80) cc_final: 0.7132 (m-80) REVERT: D 474 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8283 (ttm110) REVERT: D 524 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8838 (mm) REVERT: D 634 CYS cc_start: 0.8364 (m) cc_final: 0.7923 (m) REVERT: D 656 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7569 (tttm) REVERT: D 716 MET cc_start: 0.6184 (tpt) cc_final: 0.5976 (ttt) REVERT: B 363 ARG cc_start: 0.6399 (mtp180) cc_final: 0.6108 (ttm170) REVERT: B 366 SER cc_start: 0.6438 (m) cc_final: 0.5876 (m) REVERT: B 409 ARG cc_start: 0.6244 (ptp90) cc_final: 0.5784 (ptp90) REVERT: B 504 LYS cc_start: 0.8287 (tttt) cc_final: 0.8020 (tppt) REVERT: B 511 TYR cc_start: 0.7805 (m-80) cc_final: 0.7604 (m-80) REVERT: B 517 PHE cc_start: 0.8720 (t80) cc_final: 0.8212 (t80) REVERT: B 533 GLN cc_start: 0.8109 (mp10) cc_final: 0.7623 (mp10) REVERT: B 561 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: B 562 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7809 (mpp) REVERT: B 634 CYS cc_start: 0.8371 (m) cc_final: 0.7996 (m) REVERT: B 701 ARG cc_start: 0.8930 (mtp-110) cc_final: 0.8246 (ttm-80) outliers start: 70 outliers final: 56 residues processed: 561 average time/residue: 0.2614 time to fit residues: 218.6397 Evaluate side-chains 540 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 478 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 741 CYS Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 575 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 148 optimal weight: 0.2980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN B 561 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16362 Z= 0.298 Angle : 0.730 15.732 22153 Z= 0.364 Chirality : 0.045 0.315 2547 Planarity : 0.004 0.040 2724 Dihedral : 4.517 19.583 2172 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.62 % Allowed : 21.37 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.19), residues: 1952 helix: 1.22 (0.15), residues: 1240 sheet: 0.07 (0.78), residues: 36 loop : -2.51 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 426 HIS 0.005 0.001 HIS B 410 PHE 0.032 0.002 PHE A 489 TYR 0.030 0.002 TYR B 441 ARG 0.008 0.001 ARG D 701 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 498 time to evaluate : 1.822 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.7976 (m-80) cc_final: 0.7676 (m-80) REVERT: A 431 LYS cc_start: 0.8066 (tttt) cc_final: 0.7844 (ttpp) REVERT: A 432 ARG cc_start: 0.8369 (mtt90) cc_final: 0.7201 (tpp-160) REVERT: A 517 PHE cc_start: 0.8741 (t80) cc_final: 0.8380 (t80) REVERT: A 557 ARG cc_start: 0.8664 (ptp-170) cc_final: 0.8228 (ptp-170) REVERT: A 562 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7811 (mpp) REVERT: A 656 LYS cc_start: 0.8260 (pttt) cc_final: 0.7905 (pttm) REVERT: A 661 ILE cc_start: 0.9475 (mt) cc_final: 0.9217 (tp) REVERT: A 716 MET cc_start: 0.5627 (tpt) cc_final: 0.5257 (ttm) REVERT: A 742 PHE cc_start: 0.7519 (t80) cc_final: 0.7239 (t80) REVERT: C 368 LYS cc_start: 0.7124 (tttt) cc_final: 0.6357 (tptp) REVERT: C 428 ARG cc_start: 0.8274 (mtp180) cc_final: 0.7520 (mmt180) REVERT: C 474 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8213 (ttm110) REVERT: C 509 ASP cc_start: 0.8484 (t0) cc_final: 0.8029 (m-30) REVERT: C 517 PHE cc_start: 0.8597 (t80) cc_final: 0.8350 (t80) REVERT: C 572 MET cc_start: 0.8673 (tmm) cc_final: 0.7787 (tpp) REVERT: C 661 ILE cc_start: 0.9429 (mt) cc_final: 0.9198 (tp) REVERT: C 677 MET cc_start: 0.8628 (tpt) cc_final: 0.8327 (tpt) REVERT: C 682 MET cc_start: 0.8367 (ttm) cc_final: 0.7396 (mtm) REVERT: D 309 TYR cc_start: 0.7956 (m-80) cc_final: 0.7181 (m-80) REVERT: D 472 TYR cc_start: 0.7767 (m-80) cc_final: 0.7219 (m-80) REVERT: D 474 ARG cc_start: 0.8703 (ttp-110) cc_final: 0.8319 (ttm110) REVERT: D 524 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8835 (mm) REVERT: D 529 LEU cc_start: 0.8962 (mm) cc_final: 0.8727 (mm) REVERT: D 634 CYS cc_start: 0.8396 (m) cc_final: 0.8037 (m) REVERT: D 656 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7620 (tttm) REVERT: D 691 GLN cc_start: 0.7981 (pp30) cc_final: 0.7387 (pp30) REVERT: D 716 MET cc_start: 0.6213 (tpt) cc_final: 0.5764 (ttm) REVERT: B 324 LYS cc_start: 0.5505 (mmtt) cc_final: 0.5291 (mmpt) REVERT: B 363 ARG cc_start: 0.6543 (mtp180) cc_final: 0.6306 (ttm170) REVERT: B 366 SER cc_start: 0.6685 (m) cc_final: 0.6100 (m) REVERT: B 471 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6172 (t0) REVERT: B 474 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8387 (ttm110) REVERT: B 504 LYS cc_start: 0.8280 (tttt) cc_final: 0.7994 (tppt) REVERT: B 511 TYR cc_start: 0.7893 (m-80) cc_final: 0.7649 (m-80) REVERT: B 513 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7918 (mm-30) REVERT: B 524 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8884 (mm) REVERT: B 634 CYS cc_start: 0.8425 (m) cc_final: 0.8005 (m) REVERT: B 661 ILE cc_start: 0.9462 (mt) cc_final: 0.9199 (tp) REVERT: B 701 ARG cc_start: 0.8905 (mtp-110) cc_final: 0.8146 (ttm-80) outliers start: 81 outliers final: 65 residues processed: 536 average time/residue: 0.2638 time to fit residues: 209.4051 Evaluate side-chains 545 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 475 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 740 TRP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 709 GLU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 656 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.0470 chunk 180 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 0.0980 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 159 optimal weight: 0.3980 chunk 166 optimal weight: 7.9990 chunk 175 optimal weight: 0.7980 overall best weight: 0.4680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 ASN C 423 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16362 Z= 0.179 Angle : 0.705 16.748 22153 Z= 0.346 Chirality : 0.042 0.293 2547 Planarity : 0.003 0.042 2724 Dihedral : 4.450 22.850 2172 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.42 % Allowed : 22.39 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 1952 helix: 1.32 (0.15), residues: 1236 sheet: 0.25 (0.78), residues: 36 loop : -2.41 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 549 HIS 0.003 0.000 HIS C 410 PHE 0.029 0.001 PHE A 489 TYR 0.044 0.002 TYR C 441 ARG 0.009 0.000 ARG D 701 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 502 time to evaluate : 1.770 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.7966 (m-80) cc_final: 0.7635 (m-80) REVERT: A 412 MET cc_start: 0.7656 (ptt) cc_final: 0.7148 (ptp) REVERT: A 428 ARG cc_start: 0.8059 (mmt180) cc_final: 0.7837 (mmt90) REVERT: A 474 ARG cc_start: 0.8638 (ttp-110) cc_final: 0.8178 (ttp80) REVERT: A 557 ARG cc_start: 0.8638 (ptp-170) cc_final: 0.8148 (ptp-170) REVERT: A 562 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7742 (mpp) REVERT: A 656 LYS cc_start: 0.8138 (pttt) cc_final: 0.7797 (pttm) REVERT: A 716 MET cc_start: 0.5771 (tpt) cc_final: 0.5342 (ttm) REVERT: A 742 PHE cc_start: 0.7434 (t80) cc_final: 0.7187 (t80) REVERT: C 368 LYS cc_start: 0.7100 (tttt) cc_final: 0.6446 (tptt) REVERT: C 428 ARG cc_start: 0.8268 (mtp180) cc_final: 0.7544 (mmt180) REVERT: C 474 ARG cc_start: 0.8561 (ttp-110) cc_final: 0.8228 (ttm110) REVERT: C 509 ASP cc_start: 0.8350 (t0) cc_final: 0.7975 (m-30) REVERT: C 572 MET cc_start: 0.8677 (tmm) cc_final: 0.7690 (tpp) REVERT: C 682 MET cc_start: 0.8296 (ttm) cc_final: 0.7315 (mtm) REVERT: D 309 TYR cc_start: 0.7900 (m-80) cc_final: 0.7186 (m-80) REVERT: D 311 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8370 (mp0) REVERT: D 472 TYR cc_start: 0.7699 (m-80) cc_final: 0.7175 (m-80) REVERT: D 474 ARG cc_start: 0.8627 (ttp-110) cc_final: 0.8301 (ttm110) REVERT: D 529 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8683 (mm) REVERT: D 634 CYS cc_start: 0.8329 (m) cc_final: 0.7941 (m) REVERT: D 656 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7535 (tttm) REVERT: D 682 MET cc_start: 0.8141 (ttp) cc_final: 0.7647 (ttt) REVERT: D 691 GLN cc_start: 0.8034 (pp30) cc_final: 0.7427 (pp30) REVERT: D 701 ARG cc_start: 0.8802 (mtp-110) cc_final: 0.8570 (mtp85) REVERT: B 363 ARG cc_start: 0.6430 (mtp180) cc_final: 0.6153 (ttm170) REVERT: B 366 SER cc_start: 0.6464 (m) cc_final: 0.5910 (m) REVERT: B 504 LYS cc_start: 0.8253 (tttt) cc_final: 0.7995 (tppt) REVERT: B 511 TYR cc_start: 0.7953 (m-80) cc_final: 0.7689 (m-80) REVERT: B 634 CYS cc_start: 0.8349 (m) cc_final: 0.7952 (m) REVERT: B 661 ILE cc_start: 0.9405 (mt) cc_final: 0.9193 (tp) REVERT: B 701 ARG cc_start: 0.8900 (mtp-110) cc_final: 0.8180 (ttm-80) outliers start: 60 outliers final: 52 residues processed: 531 average time/residue: 0.2619 time to fit residues: 205.5301 Evaluate side-chains 536 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 481 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 425 LYS Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 575 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.0570 chunk 186 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 88 optimal weight: 0.0040 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 0.0870 chunk 179 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 16 optimal weight: 0.0070 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 0.0060 overall best weight: 0.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN D 408 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS B 652 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16362 Z= 0.176 Angle : 0.719 16.855 22153 Z= 0.353 Chirality : 0.043 0.332 2547 Planarity : 0.004 0.073 2724 Dihedral : 4.371 23.243 2172 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 3.25 % Allowed : 23.48 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.19), residues: 1952 helix: 1.26 (0.15), residues: 1240 sheet: 0.53 (0.81), residues: 36 loop : -2.44 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 426 HIS 0.003 0.001 HIS C 410 PHE 0.031 0.001 PHE C 659 TYR 0.041 0.002 TYR B 441 ARG 0.013 0.001 ARG B 557 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 540 time to evaluate : 1.800 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 TYR cc_start: 0.7879 (m-80) cc_final: 0.7518 (m-80) REVERT: A 412 MET cc_start: 0.7538 (ptt) cc_final: 0.6775 (ptp) REVERT: A 421 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8029 (mm) REVERT: A 557 ARG cc_start: 0.8627 (ptp-170) cc_final: 0.8213 (ptp-170) REVERT: A 561 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8481 (tt0) REVERT: A 562 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7581 (mpp) REVERT: A 572 MET cc_start: 0.8775 (tmm) cc_final: 0.7802 (tmm) REVERT: A 656 LYS cc_start: 0.8044 (pttt) cc_final: 0.7764 (pttm) REVERT: A 682 MET cc_start: 0.7777 (mmm) cc_final: 0.7461 (ttt) REVERT: A 701 ARG cc_start: 0.8703 (mtp85) cc_final: 0.8400 (ttm-80) REVERT: A 716 MET cc_start: 0.5762 (tpt) cc_final: 0.5314 (ttm) REVERT: A 742 PHE cc_start: 0.7404 (t80) cc_final: 0.7186 (t80) REVERT: C 368 LYS cc_start: 0.7063 (tttt) cc_final: 0.6389 (tptt) REVERT: C 383 ASP cc_start: 0.8290 (t0) cc_final: 0.7851 (t0) REVERT: C 428 ARG cc_start: 0.8268 (mtp180) cc_final: 0.7553 (mmt180) REVERT: C 474 ARG cc_start: 0.8514 (ttp-110) cc_final: 0.8197 (ttm110) REVERT: C 508 VAL cc_start: 0.8539 (m) cc_final: 0.7606 (m) REVERT: C 509 ASP cc_start: 0.8188 (t0) cc_final: 0.7778 (m-30) REVERT: C 572 MET cc_start: 0.8667 (tmm) cc_final: 0.7728 (tpp) REVERT: C 682 MET cc_start: 0.8202 (ttm) cc_final: 0.7278 (mtm) REVERT: D 309 TYR cc_start: 0.7903 (m-80) cc_final: 0.7473 (m-80) REVERT: D 311 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8365 (mp0) REVERT: D 381 LEU cc_start: 0.7793 (tp) cc_final: 0.7248 (tt) REVERT: D 472 TYR cc_start: 0.7584 (m-80) cc_final: 0.7030 (m-80) REVERT: D 474 ARG cc_start: 0.8569 (ttp-110) cc_final: 0.8280 (ttm110) REVERT: D 517 PHE cc_start: 0.8374 (t80) cc_final: 0.8155 (t80) REVERT: D 524 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8792 (mm) REVERT: D 634 CYS cc_start: 0.8389 (m) cc_final: 0.7993 (m) REVERT: D 682 MET cc_start: 0.8107 (ttp) cc_final: 0.7461 (ttt) REVERT: D 691 GLN cc_start: 0.8002 (pp30) cc_final: 0.7418 (pp30) REVERT: D 701 ARG cc_start: 0.8810 (mtp-110) cc_final: 0.8526 (mtp85) REVERT: B 309 TYR cc_start: 0.7795 (m-80) cc_final: 0.6689 (m-80) REVERT: B 363 ARG cc_start: 0.6357 (mtp180) cc_final: 0.6055 (ttm170) REVERT: B 366 SER cc_start: 0.6368 (m) cc_final: 0.5800 (m) REVERT: B 426 TRP cc_start: 0.8126 (t-100) cc_final: 0.7691 (t-100) REVERT: B 504 LYS cc_start: 0.8227 (tttt) cc_final: 0.8006 (tppt) REVERT: B 562 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7843 (mpp) REVERT: B 634 CYS cc_start: 0.8351 (m) cc_final: 0.7938 (m) REVERT: B 677 MET cc_start: 0.8257 (tpt) cc_final: 0.7912 (tpt) outliers start: 57 outliers final: 45 residues processed: 561 average time/residue: 0.2648 time to fit residues: 221.0416 Evaluate side-chains 566 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 516 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 425 LYS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 740 TRP Chi-restraints excluded: chain C residue 741 CYS Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 419 ASN Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 47 optimal weight: 30.0000 chunk 143 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.194612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.148904 restraints weight = 28935.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.149753 restraints weight = 16446.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.151275 restraints weight = 10554.226| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 16362 Z= 0.262 Angle : 1.025 59.197 22153 Z= 0.577 Chirality : 0.051 1.251 2547 Planarity : 0.004 0.076 2724 Dihedral : 4.407 30.442 2172 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.89 % Favored : 92.06 % Rotamer: Outliers : 2.96 % Allowed : 24.56 % Favored : 72.48 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.02 (0.19), residues: 1952 helix: 1.24 (0.15), residues: 1240 sheet: 0.55 (0.80), residues: 36 loop : -2.46 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 426 HIS 0.003 0.000 HIS C 410 PHE 0.029 0.001 PHE A 489 TYR 0.040 0.002 TYR C 555 ARG 0.018 0.000 ARG B 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4251.93 seconds wall clock time: 77 minutes 8.34 seconds (4628.34 seconds total)