Starting phenix.real_space_refine on Fri Sep 11 21:06:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bwa_30231/09_2026/7bwa_30231.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bwa_30231/09_2026/7bwa_30231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bwa_30231/09_2026/7bwa_30231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bwa_30231/09_2026/7bwa_30231.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bwa_30231/09_2026/7bwa_30231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bwa_30231/09_2026/7bwa_30231.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 94 5.16 5 C 7420 2.51 5 N 1998 2.21 5 O 2158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11670 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5459 Classifications: {'peptide': 674} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 639} Chain breaks: 6 Chain: "C" Number of atoms: 5459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5459 Classifications: {'peptide': 674} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 639} Chain breaks: 6 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "E" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Time building chain proxies: 2.87, per 1000 atoms: 0.25 Number of scatterers: 11670 At special positions: 0 Unit cell: (91.79, 152.07, 132.89, 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 94 16.00 O 2158 8.00 N 1998 7.00 C 7420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.04 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.02 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.02 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 26 " distance=2.04 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG CYS C 208 " - pdb=" SG CYS C 216 " distance=2.02 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 241 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 284 " distance=2.04 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 312 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 435 " - pdb=" SG CYS C 468 " distance=2.02 Simple disulfide: pdb=" SG CYS C 786 " - pdb=" SG CYS C 795 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 62 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 548.4 milliseconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2740 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 22 sheets defined 17.9% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 removed outlier: 4.311A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 4.153A pdb=" N PHE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 435 through 445 Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'A' and resid 695 through 714 removed outlier: 4.182A pdb=" N SER A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 712 " --> pdb=" O TYR A 708 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'C' and resid 16 through 23 removed outlier: 4.311A pdb=" N ARG C 19 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS C 21 " --> pdb=" O THR C 18 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 22 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 removed outlier: 4.154A pdb=" N PHE C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 435 through 445 Processing helix chain 'C' and resid 458 through 462 Processing helix chain 'C' and resid 638 through 642 Processing helix chain 'C' and resid 695 through 714 removed outlier: 4.182A pdb=" N SER C 699 " --> pdb=" O GLU C 695 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER C 700 " --> pdb=" O LEU C 696 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C 707 " --> pdb=" O LYS C 703 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 712 " --> pdb=" O TYR C 708 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE C 714 " --> pdb=" O HIS C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 813 Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 67 through 73 Processing helix chain 'E' and resid 7 through 19 Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 67 through 73 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.538A pdb=" N MET A 11 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU A 36 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE A 13 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.944A pdb=" N ILE A 29 " --> pdb=" O MET A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 252 through 255 removed outlier: 7.719A pdb=" N CYS A 284 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N HIS A 247 " --> pdb=" O CYS A 284 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA6, first strand: chain 'A' and resid 363 through 364 removed outlier: 3.798A pdb=" N ILE A 364 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 368 through 371 removed outlier: 5.331A pdb=" N TYR A 398 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N PHE A 427 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE A 400 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N HIS A 429 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 474 through 479 removed outlier: 5.475A pdb=" N PHE A 475 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLU A 490 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 532 through 533 removed outlier: 3.602A pdb=" N VAL A 532 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 569 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN A 561 " --> pdb=" O ALA A 510 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL A 566 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP A 584 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR A 568 " --> pdb=" O LYS A 582 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LYS A 582 " --> pdb=" O THR A 568 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 599 through 604 removed outlier: 5.977A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 759 through 762 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.537A pdb=" N MET C 11 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU C 36 " --> pdb=" O MET C 11 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE C 13 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU C 93 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLU C 120 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 95 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN C 122 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN C 148 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.944A pdb=" N ILE C 29 " --> pdb=" O MET C 56 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 231 through 233 Processing sheet with id=AB6, first strand: chain 'C' and resid 252 through 255 removed outlier: 7.720A pdb=" N CYS C 284 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N HIS C 247 " --> pdb=" O CYS C 284 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AB8, first strand: chain 'C' and resid 363 through 364 removed outlier: 3.797A pdb=" N ILE C 364 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 368 through 371 removed outlier: 5.331A pdb=" N TYR C 398 " --> pdb=" O LYS C 425 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N PHE C 427 " --> pdb=" O TYR C 398 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE C 400 " --> pdb=" O PHE C 427 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N HIS C 429 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA C 402 " --> pdb=" O HIS C 429 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 474 through 479 removed outlier: 5.475A pdb=" N PHE C 475 " --> pdb=" O GLU C 490 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLU C 490 " --> pdb=" O PHE C 475 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 532 through 533 removed outlier: 3.602A pdb=" N VAL C 532 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY C 502 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 569 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN C 561 " --> pdb=" O ALA C 510 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL C 566 " --> pdb=" O ASP C 584 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP C 584 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C 568 " --> pdb=" O LYS C 582 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LYS C 582 " --> pdb=" O THR C 568 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 599 through 604 removed outlier: 5.976A pdb=" N ASP C 600 " --> pdb=" O LYS C 616 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS C 616 " --> pdb=" O ASP C 600 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 759 through 762 262 hydrogen bonds defined for protein. 636 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: 1.85 Time building geometry restraints manager: 1.35 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: 3799 1.34 - 1.46: 2701 1.46 - 1.58: 5330 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 11944 Sorted by residual: bond pdb=" N TYR C 579 " pdb=" CA TYR C 579 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.90e+00 bond pdb=" CA ALA A 581 " pdb=" CB ALA A 581 " ideal model delta sigma weight residual 1.538 1.506 0.032 1.22e-02 6.72e+03 6.89e+00 bond pdb=" N TYR A 579 " pdb=" CA TYR A 579 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.31e-02 5.83e+03 6.30e+00 bond pdb=" N ARG C 576 " pdb=" CA ARG C 576 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.16e-02 7.43e+03 6.17e+00 bond pdb=" N ARG A 577 " pdb=" CA ARG A 577 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 6.09e+00 ... (remaining 11939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 15121 1.46 - 2.92: 890 2.92 - 4.38: 128 4.38 - 5.83: 27 5.83 - 7.29: 8 Bond angle restraints: 16174 Sorted by residual: angle pdb=" N GLU A 575 " pdb=" CA GLU A 575 " pdb=" C GLU A 575 " ideal model delta sigma weight residual 113.28 108.49 4.79 1.22e+00 6.72e-01 1.54e+01 angle pdb=" N GLU C 575 " pdb=" CA GLU C 575 " pdb=" C GLU C 575 " ideal model delta sigma weight residual 113.20 108.64 4.56 1.21e+00 6.83e-01 1.42e+01 angle pdb=" CA GLY C 580 " pdb=" C GLY C 580 " pdb=" O GLY C 580 " ideal model delta sigma weight residual 122.24 118.32 3.92 1.08e+00 8.57e-01 1.32e+01 angle pdb=" CA ARG C 577 " pdb=" C ARG C 577 " pdb=" O ARG C 577 " ideal model delta sigma weight residual 121.87 117.95 3.92 1.10e+00 8.26e-01 1.27e+01 angle pdb=" CA ARG C 576 " pdb=" C ARG C 576 " pdb=" O ARG C 576 " ideal model delta sigma weight residual 121.38 118.19 3.19 1.06e+00 8.90e-01 9.06e+00 ... (remaining 16169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6337 17.95 - 35.89: 732 35.89 - 53.84: 153 53.84 - 71.79: 22 71.79 - 89.74: 8 Dihedral angle restraints: 7252 sinusoidal: 3024 harmonic: 4228 Sorted by residual: dihedral pdb=" CB CYS D 7 " pdb=" SG CYS D 7 " pdb=" SG CYS D 62 " pdb=" CB CYS D 62 " ideal model delta sinusoidal sigma weight residual -86.00 -152.59 66.59 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CB CYS E 7 " pdb=" SG CYS E 7 " pdb=" SG CYS E 62 " pdb=" CB CYS E 62 " ideal model delta sinusoidal sigma weight residual -86.00 -152.58 66.58 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CB CYS A 312 " pdb=" SG CYS A 312 " pdb=" SG CYS A 333 " pdb=" CB CYS A 333 " ideal model delta sinusoidal sigma weight residual 93.00 148.34 -55.34 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 7249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1038 0.036 - 0.072: 486 0.072 - 0.109: 182 0.109 - 0.145: 48 0.145 - 0.181: 16 Chirality restraints: 1770 Sorted by residual: chirality pdb=" CA ARG A 577 " pdb=" N ARG A 577 " pdb=" C ARG A 577 " pdb=" CB ARG A 577 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA ARG C 577 " pdb=" N ARG C 577 " pdb=" C ARG C 577 " pdb=" CB ARG C 577 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA ILE C 145 " pdb=" N ILE C 145 " pdb=" C ILE C 145 " pdb=" CB ILE C 145 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 1767 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 574 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.35e+00 pdb=" C ASP A 574 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP A 574 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU A 575 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 574 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C ASP C 574 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP C 574 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU C 575 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 42 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO C 43 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " 0.019 5.00e-02 4.00e+02 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 258 2.56 - 3.14: 10632 3.14 - 3.73: 20249 3.73 - 4.31: 27501 4.31 - 4.90: 40931 Nonbonded interactions: 99571 Sorted by model distance: nonbonded pdb=" O GLU C 469 " pdb=" NH2 ARG C 577 " model vdw 1.970 3.120 nonbonded pdb=" OD1 ASP C 221 " pdb=" OG1 THR C 223 " model vdw 2.122 3.040 nonbonded pdb=" OD1 ASP A 221 " pdb=" OG1 THR A 223 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR C 628 " pdb=" OE2 GLU C 766 " model vdw 2.138 3.040 nonbonded pdb=" OH TYR A 628 " pdb=" OE2 GLU A 766 " model vdw 2.139 3.040 ... (remaining 99566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'E' } Set refine NCS operators NCS operators will be refined. 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.890 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 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 : 0.004 0.034 11976 Z= 0.221 Angle : 0.774 7.294 16238 Z= 0.439 Chirality : 0.049 0.181 1770 Planarity : 0.004 0.034 2076 Dihedral : 15.314 89.735 4416 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 41.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.15 (0.20), residues: 1408 helix: -2.50 (0.34), residues: 166 sheet: -3.54 (0.32), residues: 178 loop : -2.89 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 702 TYR 0.018 0.002 TYR C 91 PHE 0.019 0.002 PHE C 89 TRP 0.014 0.002 TRP C 632 HIS 0.007 0.002 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.22 (11944) covalent geometry : angle 0.77212 / 0.44 (16174) SS BOND : bond 0.00509 / 0.36 ( 32) SS BOND : angle 1.09026 / 0.78 ( 64) hydrogen bonds : bond 0.20182 / 14.18 ( 262) hydrogen bonds : angle 10.08491 / 6.62 ( 636) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.211 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: A 109 LEU cc_start: 0.8593 (mm) cc_final: 0.8379 (mm) REVERT: A 250 ASP cc_start: 0.7958 (m-30) cc_final: 0.7721 (t70) REVERT: A 368 LEU cc_start: 0.8239 (mm) cc_final: 0.7935 (mm) REVERT: A 442 MET cc_start: 0.8113 (mmt) cc_final: 0.7504 (mmt) REVERT: A 477 TYR cc_start: 0.8328 (m-10) cc_final: 0.7880 (m-80) REVERT: A 575 GLU cc_start: 0.5698 (pp20) cc_final: 0.5450 (pp20) REVERT: A 706 GLU cc_start: 0.8874 (mp0) cc_final: 0.8410 (mp0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0997 time to fit residues: 14.4828 Evaluate side-chains 65 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.188 Evaluate side-chains 11 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.009 Fit side-chains REVERT: D 22 ARG cc_start: 0.7851 (mpp80) cc_final: 0.7117 (mmm160) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0577 time to fit residues: 0.6701 Evaluate side-chains 6 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.0040 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.0050 chunk 122 optimal weight: 0.0870 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 overall best weight: 0.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 ASN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN A 431 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.091584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.073643 restraints weight = 36415.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.075711 restraints weight = 26351.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.077149 restraints weight = 20963.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.078159 restraints weight = 17714.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.078722 restraints weight = 15729.351| |-----------------------------------------------------------------------------| r_work (final): 0.3716 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.080663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.071553 restraints weight = 2226.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.073409 restraints weight = 1550.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.074826 restraints weight = 1124.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.075970 restraints weight = 839.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.076751 restraints weight = 631.507| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11976 Z= 0.161 Angle : 0.778 8.515 16238 Z= 0.405 Chirality : 0.049 0.181 1770 Planarity : 0.005 0.060 2076 Dihedral : 6.543 21.575 1566 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.36 % Favored : 88.49 % Rotamer: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.21), residues: 1408 helix: -2.24 (0.36), residues: 154 sheet: -3.19 (0.33), residues: 178 loop : -2.50 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 345 TYR 0.025 0.002 TYR A 587 PHE 0.070 0.002 PHE A 701 TRP 0.011 0.002 TRP C 133 HIS 0.029 0.002 HIS E 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (11944) covalent geometry : angle 0.77805 / 0.41 (16174) SS BOND : bond 0.00474 / 0.34 ( 32) SS BOND : angle 0.78715 / 0.54 ( 64) hydrogen bonds : bond 0.05846 / 4.06 ( 262) hydrogen bonds : angle 8.70098 / 5.51 ( 636) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.6889 (tp) cc_final: 0.6684 (tp) REVERT: A 101 LEU cc_start: 0.9235 (tp) cc_final: 0.8909 (tp) REVERT: A 263 HIS cc_start: 0.8597 (t70) cc_final: 0.8110 (t70) REVERT: A 368 LEU cc_start: 0.8063 (mm) cc_final: 0.7736 (mm) REVERT: A 419 LEU cc_start: 0.8341 (tt) cc_final: 0.8064 (mt) REVERT: A 442 MET cc_start: 0.8549 (mmt) cc_final: 0.7906 (mmt) REVERT: A 504 MET cc_start: 0.9044 (mmp) cc_final: 0.8615 (mmm) REVERT: A 579 TYR cc_start: 0.8645 (m-80) cc_final: 0.8293 (m-80) REVERT: A 706 GLU cc_start: 0.8847 (mp0) cc_final: 0.8217 (pm20) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0657 time to fit residues: 7.8377 Evaluate side-chains 67 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.210 Evaluate side-chains 9 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0541 time to fit residues: 0.5258 Evaluate side-chains 6 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 39 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 140 optimal weight: 0.0060 chunk 47 optimal weight: 3.9990 chunk 104 optimal weight: 0.2980 chunk 99 optimal weight: 0.1980 chunk 4 optimal weight: 8.9990 chunk 94 optimal weight: 0.0970 chunk 73 optimal weight: 0.0170 overall best weight: 0.1232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN A 417 HIS ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.093264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.076736 restraints weight = 37824.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.078202 restraints weight = 29666.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.079268 restraints weight = 24834.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.079928 restraints weight = 21540.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.080532 restraints weight = 19731.539| |-----------------------------------------------------------------------------| r_work (final): 0.3747 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.076477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.066013 restraints weight = 1867.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068580 restraints weight = 1194.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.070467 restraints weight = 810.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.071790 restraints weight = 559.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.072723 restraints weight = 403.504| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11976 Z= 0.134 Angle : 0.711 11.132 16238 Z= 0.369 Chirality : 0.047 0.167 1770 Planarity : 0.005 0.045 2076 Dihedral : 6.104 23.300 1566 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.21), residues: 1408 helix: -1.90 (0.37), residues: 154 sheet: -2.89 (0.33), residues: 188 loop : -2.45 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 702 TYR 0.019 0.002 TYR A 628 PHE 0.043 0.002 PHE C 701 TRP 0.016 0.002 TRP C 133 HIS 0.006 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (11944) covalent geometry : angle 0.70980 / 0.37 (16174) SS BOND : bond 0.00289 / 0.20 ( 32) SS BOND : angle 0.88336 / 0.59 ( 64) hydrogen bonds : bond 0.04746 / 3.29 ( 262) hydrogen bonds : angle 8.12458 / 5.15 ( 636) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7962 (mt0) cc_final: 0.7403 (mt0) REVERT: A 38 MET cc_start: 0.4015 (ttt) cc_final: 0.3429 (tpt) REVERT: A 93 LEU cc_start: 0.7160 (tp) cc_final: 0.6864 (tp) REVERT: A 368 LEU cc_start: 0.8610 (mm) cc_final: 0.8258 (mm) REVERT: A 442 MET cc_start: 0.8520 (mmt) cc_final: 0.8002 (mmt) REVERT: A 477 TYR cc_start: 0.8560 (m-80) cc_final: 0.8330 (m-80) REVERT: A 488 ARG cc_start: 0.7203 (mmm-85) cc_final: 0.6996 (mtt180) REVERT: A 504 MET cc_start: 0.9010 (mmp) cc_final: 0.8440 (mmm) REVERT: A 579 TYR cc_start: 0.8698 (m-80) cc_final: 0.8041 (m-80) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0733 time to fit residues: 9.1907 Evaluate side-chains 62 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.148 Evaluate side-chains 8 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.020 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0675 time to fit residues: 0.5811 Evaluate side-chains 7 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 134 optimal weight: 0.0000 chunk 4 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 16 optimal weight: 30.0000 chunk 136 optimal weight: 0.0010 chunk 82 optimal weight: 0.0170 chunk 58 optimal weight: 0.7980 chunk 138 optimal weight: 0.0570 chunk 18 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 overall best weight: 0.1746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 HIS ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.094097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.075356 restraints weight = 34455.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.077528 restraints weight = 24828.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.079085 restraints weight = 19502.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.080123 restraints weight = 16310.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.080808 restraints weight = 14395.697| |-----------------------------------------------------------------------------| r_work (final): 0.3775 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.081315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.072138 restraints weight = 2257.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.074095 restraints weight = 1570.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.075800 restraints weight = 1132.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.076634 restraints weight = 808.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.077665 restraints weight = 630.289| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11976 Z= 0.133 Angle : 0.682 7.769 16238 Z= 0.353 Chirality : 0.046 0.173 1770 Planarity : 0.005 0.044 2076 Dihedral : 5.839 21.488 1566 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.21), residues: 1408 helix: -2.07 (0.37), residues: 156 sheet: -2.55 (0.33), residues: 192 loop : -2.28 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 345 TYR 0.026 0.002 TYR A 562 PHE 0.030 0.002 PHE C 701 TRP 0.032 0.002 TRP A 133 HIS 0.004 0.001 HIS C 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (11944) covalent geometry : angle 0.68159 / 0.35 (16174) SS BOND : bond 0.00227 / 0.15 ( 32) SS BOND : angle 0.66741 / 0.43 ( 64) hydrogen bonds : bond 0.04639 / 3.17 ( 262) hydrogen bonds : angle 7.65819 / 4.84 ( 636) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8056 (mt0) cc_final: 0.7516 (mt0) REVERT: A 38 MET cc_start: 0.3159 (ttt) cc_final: 0.2904 (tpt) REVERT: A 98 MET cc_start: 0.7814 (tpt) cc_final: 0.6959 (tpp) REVERT: A 101 LEU cc_start: 0.9344 (tp) cc_final: 0.8748 (pt) REVERT: A 263 HIS cc_start: 0.8540 (t70) cc_final: 0.7945 (t70) REVERT: A 368 LEU cc_start: 0.8522 (mm) cc_final: 0.8179 (mm) REVERT: A 442 MET cc_start: 0.8522 (mmt) cc_final: 0.8023 (mmt) REVERT: A 504 MET cc_start: 0.9071 (mmp) cc_final: 0.8478 (mmm) REVERT: A 579 TYR cc_start: 0.8653 (m-80) cc_final: 0.8206 (m-80) REVERT: A 706 GLU cc_start: 0.8897 (mp0) cc_final: 0.8028 (pm20) REVERT: A 710 HIS cc_start: 0.9350 (m90) cc_final: 0.8474 (m170) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0743 time to fit residues: 9.0480 Evaluate side-chains 64 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.208 Evaluate side-chains 8 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.016 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0662 time to fit residues: 0.5685 Evaluate side-chains 7 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 92 optimal weight: 0.0370 chunk 55 optimal weight: 30.0000 chunk 13 optimal weight: 0.0980 chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 62 optimal weight: 0.3980 chunk 65 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 0.0030 chunk 77 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 overall best weight: 0.2668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.094043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.074561 restraints weight = 35869.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.076910 restraints weight = 24997.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.078452 restraints weight = 19337.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.079558 restraints weight = 16229.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.080306 restraints weight = 14292.373| |-----------------------------------------------------------------------------| r_work (final): 0.3765 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.081615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.073526 restraints weight = 2173.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.075524 restraints weight = 1335.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.077090 restraints weight = 901.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.078068 restraints weight = 620.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.078921 restraints weight = 448.556| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11976 Z= 0.118 Angle : 0.639 7.494 16238 Z= 0.331 Chirality : 0.046 0.208 1770 Planarity : 0.004 0.043 2076 Dihedral : 5.603 20.179 1566 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.21), residues: 1408 helix: -1.82 (0.38), residues: 156 sheet: -2.37 (0.33), residues: 192 loop : -2.14 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 454 TYR 0.015 0.001 TYR A 562 PHE 0.030 0.002 PHE A 714 TRP 0.011 0.001 TRP C 632 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (11944) covalent geometry : angle 0.63789 / 0.33 (16174) SS BOND : bond 0.00267 / 0.19 ( 32) SS BOND : angle 0.80591 / 0.55 ( 64) hydrogen bonds : bond 0.04497 / 3.03 ( 262) hydrogen bonds : angle 7.47928 / 4.75 ( 636) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8061 (mt0) cc_final: 0.7581 (mt0) REVERT: A 38 MET cc_start: 0.2992 (ttt) cc_final: 0.2714 (tpt) REVERT: A 109 LEU cc_start: 0.8572 (mm) cc_final: 0.7931 (mm) REVERT: A 110 MET cc_start: 0.7416 (mmp) cc_final: 0.6818 (ttt) REVERT: A 125 LEU cc_start: 0.8907 (tp) cc_final: 0.8687 (tp) REVERT: A 362 GLU cc_start: 0.5717 (mp0) cc_final: 0.5493 (mp0) REVERT: A 368 LEU cc_start: 0.8580 (mm) cc_final: 0.8170 (mm) REVERT: A 442 MET cc_start: 0.8428 (mmt) cc_final: 0.7915 (mmt) REVERT: A 504 MET cc_start: 0.9096 (mmp) cc_final: 0.8543 (mmm) REVERT: A 579 TYR cc_start: 0.8571 (m-80) cc_final: 0.8154 (m-80) REVERT: A 706 GLU cc_start: 0.8823 (mp0) cc_final: 0.8180 (pm20) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0556 time to fit residues: 7.1212 Evaluate side-chains 63 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.187 Evaluate side-chains 9 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.016 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0644 time to fit residues: 0.6198 Evaluate side-chains 8 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 50 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 128 optimal weight: 0.0030 chunk 140 optimal weight: 0.0170 chunk 91 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 27 optimal weight: 0.0040 chunk 110 optimal weight: 5.9990 overall best weight: 2.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.092520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.073337 restraints weight = 35676.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.075513 restraints weight = 25194.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.076978 restraints weight = 19794.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.077987 restraints weight = 16755.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.078705 restraints weight = 14776.575| |-----------------------------------------------------------------------------| r_work (final): 0.3733 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.079098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.070280 restraints weight = 2223.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072085 restraints weight = 1502.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.073676 restraints weight = 1087.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.074826 restraints weight = 779.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.075609 restraints weight = 566.138| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11976 Z= 0.123 Angle : 0.617 6.974 16238 Z= 0.326 Chirality : 0.045 0.172 1770 Planarity : 0.004 0.044 2076 Dihedral : 5.491 18.754 1566 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.21), residues: 1408 helix: -2.09 (0.36), residues: 154 sheet: -2.47 (0.32), residues: 196 loop : -2.04 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 19 TYR 0.011 0.001 TYR C 562 PHE 0.020 0.002 PHE A 714 TRP 0.013 0.001 TRP A 632 HIS 0.004 0.001 HIS E 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (11944) covalent geometry : angle 0.61688 / 0.33 (16174) SS BOND : bond 0.00287 / 0.20 ( 32) SS BOND : angle 0.69652 / 0.47 ( 64) hydrogen bonds : bond 0.04322 / 2.97 ( 262) hydrogen bonds : angle 7.42789 / 4.69 ( 636) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.3218 (ttt) cc_final: 0.2672 (tpt) REVERT: A 98 MET cc_start: 0.7978 (tpp) cc_final: 0.7049 (tpp) REVERT: A 101 LEU cc_start: 0.9265 (tp) cc_final: 0.8780 (pt) REVERT: A 109 LEU cc_start: 0.8539 (mm) cc_final: 0.7932 (mm) REVERT: A 110 MET cc_start: 0.7545 (mmp) cc_final: 0.6921 (ttt) REVERT: A 125 LEU cc_start: 0.8838 (tp) cc_final: 0.8521 (tp) REVERT: A 368 LEU cc_start: 0.8557 (mm) cc_final: 0.8152 (mm) REVERT: A 442 MET cc_start: 0.8586 (mmt) cc_final: 0.8036 (mmt) REVERT: A 488 ARG cc_start: 0.7521 (mtt180) cc_final: 0.6813 (mmt180) REVERT: A 504 MET cc_start: 0.9063 (mmp) cc_final: 0.8505 (mmm) REVERT: A 579 TYR cc_start: 0.8570 (m-80) cc_final: 0.8140 (m-80) REVERT: A 706 GLU cc_start: 0.9029 (mp0) cc_final: 0.8265 (pp20) REVERT: A 710 HIS cc_start: 0.9254 (m90) cc_final: 0.8971 (m90) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0680 time to fit residues: 8.1619 Evaluate side-chains 68 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.234 Evaluate side-chains 9 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.015 Fit side-chains revert: symmetry clash REVERT: D 6 LEU cc_start: 0.8412 (mp) cc_final: 0.8202 (mp) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0637 time to fit residues: 0.6128 Evaluate side-chains 8 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 45 optimal weight: 0.9990 chunk 24 optimal weight: 0.0170 chunk 128 optimal weight: 0.2980 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 68 optimal weight: 0.0060 chunk 101 optimal weight: 3.9990 chunk 6 optimal weight: 0.0040 chunk 98 optimal weight: 0.6980 overall best weight: 0.1846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 HIS ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN A 410 GLN A 610 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.094639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.075697 restraints weight = 34923.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.077851 restraints weight = 24878.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.079352 restraints weight = 19614.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.080373 restraints weight = 16521.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.081081 restraints weight = 14649.393| |-----------------------------------------------------------------------------| r_work (final): 0.3782 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.078713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.070276 restraints weight = 2157.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.072297 restraints weight = 1443.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.073672 restraints weight = 1003.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.074792 restraints weight = 709.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.075520 restraints weight = 520.392| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11976 Z= 0.112 Angle : 0.634 10.109 16238 Z= 0.327 Chirality : 0.045 0.168 1770 Planarity : 0.005 0.049 2076 Dihedral : 5.304 18.723 1566 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.15 % Allowed : 2.27 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.21), residues: 1408 helix: -1.87 (0.37), residues: 156 sheet: -2.06 (0.30), residues: 232 loop : -1.93 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 386 TYR 0.012 0.001 TYR A 507 PHE 0.014 0.002 PHE C 76 TRP 0.012 0.001 TRP A 632 HIS 0.005 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (11944) covalent geometry : angle 0.63420 / 0.33 (16174) SS BOND : bond 0.00370 / 0.23 ( 32) SS BOND : angle 0.63310 / 0.44 ( 64) hydrogen bonds : bond 0.03975 / 2.73 ( 262) hydrogen bonds : angle 7.15511 / 4.52 ( 636) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.212 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: A 34 GLN cc_start: 0.8090 (mt0) cc_final: 0.7495 (mt0) REVERT: A 38 MET cc_start: 0.3051 (ttt) cc_final: 0.2667 (tpt) REVERT: A 98 MET cc_start: 0.7899 (tpp) cc_final: 0.7184 (tpp) REVERT: A 100 HIS cc_start: 0.5060 (OUTLIER) cc_final: 0.4206 (t-170) REVERT: A 101 LEU cc_start: 0.9300 (tp) cc_final: 0.8768 (pt) REVERT: A 109 LEU cc_start: 0.8366 (mm) cc_final: 0.7620 (mm) REVERT: A 110 MET cc_start: 0.7413 (mmp) cc_final: 0.6883 (ttt) REVERT: A 125 LEU cc_start: 0.8824 (tp) cc_final: 0.8483 (tp) REVERT: A 368 LEU cc_start: 0.8451 (mm) cc_final: 0.8024 (mm) REVERT: A 428 PHE cc_start: 0.8780 (m-10) cc_final: 0.8580 (m-10) REVERT: A 442 MET cc_start: 0.8543 (mmt) cc_final: 0.8127 (mmm) REVERT: A 504 MET cc_start: 0.9069 (mmp) cc_final: 0.8561 (mmm) REVERT: A 706 GLU cc_start: 0.8897 (mp0) cc_final: 0.8072 (pp20) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.0668 time to fit residues: 7.9889 Evaluate side-chains 67 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.212 Evaluate side-chains 10 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.015 Fit side-chains revert: symmetry clash REVERT: D 6 LEU cc_start: 0.8445 (mp) cc_final: 0.8227 (mp) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0626 time to fit residues: 0.6677 Evaluate side-chains 7 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 93 optimal weight: 0.0030 chunk 60 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 overall best weight: 1.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 HIS ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.094152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.077154 restraints weight = 38403.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.078691 restraints weight = 29538.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.079847 restraints weight = 24495.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.080597 restraints weight = 21287.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.081177 restraints weight = 19301.378| |-----------------------------------------------------------------------------| r_work (final): 0.3763 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.067757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.058863 restraints weight = 1916.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061053 restraints weight = 1201.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.062853 restraints weight = 811.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.064065 restraints weight = 555.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.064809 restraints weight = 397.891| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11976 Z= 0.118 Angle : 0.627 6.407 16238 Z= 0.325 Chirality : 0.045 0.173 1770 Planarity : 0.004 0.048 2076 Dihedral : 5.279 18.599 1566 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.21), residues: 1408 helix: -2.09 (0.34), residues: 172 sheet: -2.14 (0.33), residues: 196 loop : -1.93 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 386 TYR 0.011 0.001 TYR D 74 PHE 0.013 0.001 PHE C 714 TRP 0.012 0.001 TRP A 632 HIS 0.004 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11944) covalent geometry : angle 0.62689 / 0.32 (16174) SS BOND : bond 0.00259 / 0.17 ( 32) SS BOND : angle 0.59993 / 0.42 ( 64) hydrogen bonds : bond 0.03966 / 2.76 ( 262) hydrogen bonds : angle 7.11475 / 4.51 ( 636) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.305 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: A 34 GLN cc_start: 0.7985 (mt0) cc_final: 0.7696 (tt0) REVERT: A 38 MET cc_start: 0.3163 (ttt) cc_final: 0.2722 (tpt) REVERT: A 81 VAL cc_start: 0.8759 (t) cc_final: 0.8214 (t) REVERT: A 98 MET cc_start: 0.7847 (tpp) cc_final: 0.7207 (tpp) REVERT: A 101 LEU cc_start: 0.9337 (tp) cc_final: 0.8790 (pt) REVERT: A 109 LEU cc_start: 0.8387 (mm) cc_final: 0.7710 (mm) REVERT: A 110 MET cc_start: 0.7361 (mmp) cc_final: 0.6811 (ttt) REVERT: A 125 LEU cc_start: 0.8761 (tp) cc_final: 0.8497 (tp) REVERT: A 368 LEU cc_start: 0.8419 (mm) cc_final: 0.7996 (mm) REVERT: A 442 MET cc_start: 0.8575 (mmt) cc_final: 0.7996 (mmt) REVERT: A 504 MET cc_start: 0.8952 (mmp) cc_final: 0.8461 (mmm) REVERT: A 579 TYR cc_start: 0.8683 (m-80) cc_final: 0.7930 (m-80) REVERT: A 706 GLU cc_start: 0.9016 (mp0) cc_final: 0.8166 (pp20) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0658 time to fit residues: 7.8251 Evaluate side-chains 61 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.232 Evaluate side-chains 8 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.010 Fit side-chains revert: symmetry clash REVERT: D 65 ILE cc_start: 0.9066 (mm) cc_final: 0.8678 (tp) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0563 time to fit residues: 0.4794 Evaluate side-chains 8 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 63 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 1 optimal weight: 0.0980 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 51 optimal weight: 0.0000 chunk 91 optimal weight: 0.6980 chunk 88 optimal weight: 0.0270 chunk 27 optimal weight: 0.5980 overall best weight: 0.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.095211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.075708 restraints weight = 35801.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.077995 restraints weight = 25085.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.079513 restraints weight = 19583.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.080597 restraints weight = 16525.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.081207 restraints weight = 14551.924| |-----------------------------------------------------------------------------| r_work (final): 0.3773 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.068409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.059276 restraints weight = 1990.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.061597 restraints weight = 1194.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063365 restraints weight = 797.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.064576 restraints weight = 552.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.065330 restraints weight = 396.330| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11976 Z= 0.113 Angle : 0.645 7.059 16238 Z= 0.331 Chirality : 0.046 0.226 1770 Planarity : 0.004 0.048 2076 Dihedral : 5.160 18.456 1566 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.22), residues: 1408 helix: -1.76 (0.36), residues: 160 sheet: -1.95 (0.34), residues: 192 loop : -1.78 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 386 TYR 0.011 0.001 TYR E 74 PHE 0.013 0.001 PHE C 714 TRP 0.012 0.001 TRP A 632 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (11944) covalent geometry : angle 0.64524 / 0.33 (16174) SS BOND : bond 0.00191 / 0.12 ( 32) SS BOND : angle 0.57566 / 0.40 ( 64) hydrogen bonds : bond 0.03972 / 2.73 ( 262) hydrogen bonds : angle 6.96427 / 4.42 ( 636) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.210 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: A 28 VAL cc_start: 0.8978 (m) cc_final: 0.8641 (m) REVERT: A 38 MET cc_start: 0.2953 (ttt) cc_final: 0.2644 (tpt) REVERT: A 56 MET cc_start: 0.7521 (mmp) cc_final: 0.7284 (mtp) REVERT: A 98 MET cc_start: 0.7890 (tpp) cc_final: 0.6965 (tpp) REVERT: A 101 LEU cc_start: 0.9393 (tp) cc_final: 0.8787 (pt) REVERT: A 109 LEU cc_start: 0.8553 (mm) cc_final: 0.7893 (mm) REVERT: A 110 MET cc_start: 0.7327 (mmp) cc_final: 0.6825 (ttt) REVERT: A 125 LEU cc_start: 0.8914 (tp) cc_final: 0.8586 (tp) REVERT: A 368 LEU cc_start: 0.8482 (mm) cc_final: 0.8038 (mm) REVERT: A 442 MET cc_start: 0.8647 (mmt) cc_final: 0.8191 (mmt) REVERT: A 477 TYR cc_start: 0.8486 (m-80) cc_final: 0.8250 (m-80) REVERT: A 504 MET cc_start: 0.9085 (mmp) cc_final: 0.8649 (mmm) REVERT: A 579 TYR cc_start: 0.8463 (m-80) cc_final: 0.7999 (m-80) REVERT: A 706 GLU cc_start: 0.9002 (mp0) cc_final: 0.8343 (pp20) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0608 time to fit residues: 7.1443 Evaluate side-chains 65 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.212 Evaluate side-chains 8 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.016 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0711 time to fit residues: 0.6050 Evaluate side-chains 7 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 102 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 140 optimal weight: 0.0030 chunk 14 optimal weight: 0.5980 chunk 98 optimal weight: 0.0980 chunk 90 optimal weight: 5.9990 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.094448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.075223 restraints weight = 35496.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.077622 restraints weight = 24382.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.079210 restraints weight = 18706.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.080321 restraints weight = 15583.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.081086 restraints weight = 13689.274| |-----------------------------------------------------------------------------| r_work (final): 0.3773 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.067203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.058638 restraints weight = 1949.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.060987 restraints weight = 1147.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062472 restraints weight = 748.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.063596 restraints weight = 522.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.064338 restraints weight = 379.511| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11976 Z= 0.110 Angle : 0.614 9.151 16238 Z= 0.317 Chirality : 0.044 0.207 1770 Planarity : 0.004 0.046 2076 Dihedral : 5.089 18.395 1566 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.21), residues: 1408 helix: -1.97 (0.35), residues: 172 sheet: -1.89 (0.35), residues: 192 loop : -1.85 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 386 TYR 0.013 0.001 TYR A 60 PHE 0.016 0.001 PHE A 76 TRP 0.011 0.001 TRP A 632 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (11944) covalent geometry : angle 0.61391 / 0.32 (16174) SS BOND : bond 0.00214 / 0.14 ( 32) SS BOND : angle 0.54672 / 0.37 ( 64) hydrogen bonds : bond 0.03736 / 2.58 ( 262) hydrogen bonds : angle 6.90601 / 4.38 ( 636) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.263 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: A 28 VAL cc_start: 0.8980 (m) cc_final: 0.8692 (m) REVERT: A 38 MET cc_start: 0.3051 (ttt) cc_final: 0.2832 (tpp) REVERT: A 98 MET cc_start: 0.7861 (tpp) cc_final: 0.7228 (tpp) REVERT: A 101 LEU cc_start: 0.9356 (tp) cc_final: 0.8566 (pt) REVERT: A 109 LEU cc_start: 0.8489 (mm) cc_final: 0.7815 (mm) REVERT: A 110 MET cc_start: 0.7343 (mmp) cc_final: 0.6735 (ttt) REVERT: A 122 ASN cc_start: 0.7819 (m-40) cc_final: 0.7596 (m-40) REVERT: A 125 LEU cc_start: 0.8877 (tp) cc_final: 0.8579 (tp) REVERT: A 368 LEU cc_start: 0.8427 (mm) cc_final: 0.7985 (mm) REVERT: A 442 MET cc_start: 0.8611 (mmt) cc_final: 0.8127 (mmt) REVERT: A 477 TYR cc_start: 0.8401 (m-80) cc_final: 0.8197 (m-80) REVERT: A 504 MET cc_start: 0.9029 (mmp) cc_final: 0.8614 (mmm) REVERT: A 579 TYR cc_start: 0.8695 (m-80) cc_final: 0.7941 (m-80) REVERT: A 706 GLU cc_start: 0.8967 (mp0) cc_final: 0.8343 (pp20) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0627 time to fit residues: 7.6030 Evaluate side-chains 62 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.201 Evaluate side-chains 8 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.015 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0662 time to fit residues: 0.5657 Evaluate side-chains 7 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 129 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 126 optimal weight: 0.0050 chunk 93 optimal weight: 6.9990 chunk 130 optimal weight: 0.1980 chunk 110 optimal weight: 0.0770 chunk 127 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 84 optimal weight: 40.0000 overall best weight: 0.6556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.095244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.076283 restraints weight = 35216.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.078571 restraints weight = 24565.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.080064 restraints weight = 19144.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.081121 restraints weight = 16133.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.081631 restraints weight = 14261.292| |-----------------------------------------------------------------------------| r_work (final): 0.3789 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.067450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.059501 restraints weight = 1955.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.061621 restraints weight = 1125.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063168 restraints weight = 733.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.064190 restraints weight = 506.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.064938 restraints weight = 368.938| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11976 Z= 0.104 Angle : 0.605 6.344 16238 Z= 0.314 Chirality : 0.044 0.190 1770 Planarity : 0.004 0.046 2076 Dihedral : 4.986 18.193 1566 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.22), residues: 1408 helix: -1.82 (0.37), residues: 172 sheet: -1.77 (0.36), residues: 192 loop : -1.78 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.011 0.001 TYR A 60 PHE 0.012 0.001 PHE A 714 TRP 0.012 0.001 TRP A 632 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (11944) covalent geometry : angle 0.60553 / 0.31 (16174) SS BOND : bond 0.00192 / 0.13 ( 32) SS BOND : angle 0.53836 / 0.37 ( 64) hydrogen bonds : bond 0.03637 / 2.51 ( 262) hydrogen bonds : angle 6.76791 / 4.29 ( 636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1459.84 seconds wall clock time: 26 minutes 13.88 seconds (1573.88 seconds total)