Starting phenix.real_space_refine on Tue Jun 10 12:15:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bwa_30231/06_2025/7bwa_30231.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bwa_30231/06_2025/7bwa_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7bwa_30231/06_2025/7bwa_30231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bwa_30231/06_2025/7bwa_30231.map" model { file = "/net/cci-nas-00/data/ceres_data/7bwa_30231/06_2025/7bwa_30231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bwa_30231/06_2025/7bwa_30231.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.57, per 1000 atoms: 0.56 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: 3.14 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.54 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: 3.92 Time building geometry restraints manager: 3.78 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: 0.06 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.090 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.002 TRP C 632 HIS 0.007 0.002 HIS A 263 PHE 0.019 0.002 PHE C 89 TYR 0.018 0.002 TYR C 91 ARG 0.004 0.001 ARG C 702 Details of bonding type rmsd hydrogen bonds : bond 0.20182 ( 262) hydrogen bonds : angle 10.08491 ( 636) SS BOND : bond 0.00509 ( 32) SS BOND : angle 1.09026 ( 64) covalent geometry : bond 0.00425 (11944) covalent geometry : angle 0.77212 (16174) *********************** 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 13 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.047 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1396 time to fit residues: 1.9347 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 : 0.048 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 : 0.637 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: 0.5451 (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: 0.2216 time to fit residues: 32.1169 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 : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 82 optimal weight: 0.2980 chunk 128 optimal weight: 0.0770 overall best weight: 2.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 = 0.3364 r_free = 0.3364 target = 0.074953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.056740 restraints weight = 1788.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.058079 restraints weight = 1448.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.059276 restraints weight = 1224.394| |-----------------------------------------------------------------------------| r_work (final): 0.3469 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.090553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.072885 restraints weight = 35336.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.074799 restraints weight = 25952.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.076166 restraints weight = 20787.843| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11976 Z= 0.159 Angle : 0.750 6.895 16238 Z= 0.397 Chirality : 0.048 0.154 1770 Planarity : 0.005 0.060 2076 Dihedral : 6.589 21.824 1566 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.51 % Favored : 88.35 % Rotamer: Outliers : 0.15 % Allowed : 8.62 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.20), residues: 1408 helix: -2.21 (0.35), residues: 164 sheet: -3.49 (0.32), residues: 178 loop : -2.69 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 632 HIS 0.005 0.001 HIS A 263 PHE 0.060 0.003 PHE C 701 TYR 0.024 0.002 TYR A 587 ARG 0.005 0.001 ARG C 345 Details of bonding type rmsd hydrogen bonds : bond 0.05726 ( 262) hydrogen bonds : angle 8.71176 ( 636) SS BOND : bond 0.00382 ( 32) SS BOND : angle 0.98190 ( 64) covalent geometry : bond 0.00340 (11944) covalent geometry : angle 0.74902 (16174) *********************** 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 15 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.043 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1366 time to fit residues: 2.1744 Evaluate side-chains 5 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.049 Evaluate side-chains 90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.714 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: 0.7453 (mt0) cc_final: 0.7231 (tt0) REVERT: A 98 MET cc_start: 0.8025 (tpt) cc_final: 0.7818 (tpp) REVERT: A 101 LEU cc_start: 0.9248 (tp) cc_final: 0.8917 (tp) REVERT: A 263 HIS cc_start: 0.8598 (t70) cc_final: 0.8109 (t70) REVERT: A 368 LEU cc_start: 0.8310 (mm) cc_final: 0.7978 (mm) REVERT: A 419 LEU cc_start: 0.8446 (tt) cc_final: 0.8182 (mt) REVERT: A 442 MET cc_start: 0.8569 (mmt) cc_final: 0.7908 (mmt) REVERT: A 504 MET cc_start: 0.8967 (mmp) cc_final: 0.8484 (mmm) REVERT: A 579 TYR cc_start: 0.8709 (m-80) cc_final: 0.8017 (m-80) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1633 time to fit residues: 19.8859 Evaluate side-chains 60 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 50.0000 chunk 59 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 115 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN 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 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 = 0.3382 r_free = 0.3382 target = 0.077269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.066834 restraints weight = 2317.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.068494 restraints weight = 1715.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.069804 restraints weight = 1340.842| |-----------------------------------------------------------------------------| r_work (final): 0.3244 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.092307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.073196 restraints weight = 35483.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.075376 restraints weight = 25345.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.076935 restraints weight = 19855.834| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11976 Z= 0.155 Angle : 0.810 24.919 16238 Z= 0.413 Chirality : 0.048 0.167 1770 Planarity : 0.006 0.054 2076 Dihedral : 6.427 33.232 1566 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.22 % Favored : 88.64 % Rotamer: Outliers : 0.15 % Allowed : 5.75 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.21), residues: 1408 helix: -2.07 (0.37), residues: 156 sheet: -3.22 (0.31), residues: 196 loop : -2.52 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 133 HIS 0.015 0.001 HIS D 10 PHE 0.029 0.002 PHE A 39 TYR 0.019 0.002 TYR A 587 ARG 0.008 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.05158 ( 262) hydrogen bonds : angle 8.41477 ( 636) SS BOND : bond 0.00244 ( 32) SS BOND : angle 0.95417 ( 64) covalent geometry : bond 0.00342 (11944) covalent geometry : angle 0.80921 (16174) *********************** 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 7 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.046 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.1765 time to fit residues: 1.3292 Evaluate side-chains 5 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.045 Evaluate side-chains 89 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.4767 (ppp) cc_final: 0.2667 (mmm) REVERT: A 93 LEU cc_start: 0.6938 (tp) cc_final: 0.6714 (tp) REVERT: A 98 MET cc_start: 0.8272 (tpt) cc_final: 0.7707 (tpp) REVERT: A 101 LEU cc_start: 0.9215 (tp) cc_final: 0.8702 (tp) REVERT: A 109 LEU cc_start: 0.8747 (mm) cc_final: 0.8538 (mm) REVERT: A 263 HIS cc_start: 0.8629 (t70) cc_final: 0.8173 (t70) REVERT: A 368 LEU cc_start: 0.8592 (mm) cc_final: 0.8284 (mm) REVERT: A 442 MET cc_start: 0.8598 (mmt) cc_final: 0.8126 (mmt) REVERT: A 477 TYR cc_start: 0.8517 (m-80) cc_final: 0.8298 (m-80) REVERT: A 504 MET cc_start: 0.9021 (mmp) cc_final: 0.8553 (mmm) REVERT: A 579 TYR cc_start: 0.8573 (m-80) cc_final: 0.8107 (m-80) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.1537 time to fit residues: 18.5289 Evaluate side-chains 56 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 4 optimal weight: 0.3980 chunk 2 optimal weight: 0.0000 chunk 48 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 26 optimal weight: 0.4980 chunk 34 optimal weight: 0.3980 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3356 r_free = 0.3356 target = 0.076155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.065017 restraints weight = 2318.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066329 restraints weight = 1786.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.067591 restraints weight = 1457.041| |-----------------------------------------------------------------------------| r_work (final): 0.3222 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.093810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.075439 restraints weight = 34865.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.077529 restraints weight = 25132.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.079020 restraints weight = 19845.077| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11976 Z= 0.144 Angle : 0.780 18.766 16238 Z= 0.396 Chirality : 0.048 0.182 1770 Planarity : 0.006 0.064 2076 Dihedral : 6.167 25.138 1566 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.21), residues: 1408 helix: -2.07 (0.37), residues: 154 sheet: -3.02 (0.32), residues: 192 loop : -2.46 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 551 HIS 0.003 0.001 HIS A 263 PHE 0.048 0.003 PHE C 701 TYR 0.016 0.001 TYR A 67 ARG 0.005 0.000 ARG A 576 Details of bonding type rmsd hydrogen bonds : bond 0.04759 ( 262) hydrogen bonds : angle 7.81930 ( 636) SS BOND : bond 0.00237 ( 32) SS BOND : angle 0.90549 ( 64) covalent geometry : bond 0.00315 (11944) covalent geometry : angle 0.77962 (16174) *********************** 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 6 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.051 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0675 time to fit residues: 0.5009 Evaluate side-chains 5 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.042 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 : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.4518 (ppp) cc_final: 0.3478 (mmm) REVERT: A 98 MET cc_start: 0.8426 (tpt) cc_final: 0.7952 (tpp) REVERT: A 368 LEU cc_start: 0.8575 (mm) cc_final: 0.8174 (mm) REVERT: A 442 MET cc_start: 0.8618 (mmt) cc_final: 0.8128 (mmt) REVERT: A 477 TYR cc_start: 0.8505 (m-80) cc_final: 0.8283 (m-80) REVERT: A 504 MET cc_start: 0.8999 (mmp) cc_final: 0.8344 (mmm) REVERT: A 579 TYR cc_start: 0.8646 (m-80) cc_final: 0.8370 (m-80) REVERT: A 706 GLU cc_start: 0.8843 (mp0) cc_final: 0.8267 (pm20) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1651 time to fit residues: 19.6116 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 : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 23 optimal weight: 0.2980 chunk 140 optimal weight: 9.9990 chunk 66 optimal weight: 0.0170 chunk 139 optimal weight: 5.9990 chunk 138 optimal weight: 0.0470 chunk 123 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 60 optimal weight: 0.0370 chunk 96 optimal weight: 10.0000 chunk 43 optimal weight: 0.2980 overall best weight: 0.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** 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 = 0.3295 r_free = 0.3295 target = 0.071250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.057581 restraints weight = 1876.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.059347 restraints weight = 1318.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.060550 restraints weight = 1001.302| |-----------------------------------------------------------------------------| r_work (final): 0.3458 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.094251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.075643 restraints weight = 34779.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.077844 restraints weight = 24608.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.079335 restraints weight = 19240.291| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11976 Z= 0.127 Angle : 0.704 12.594 16238 Z= 0.363 Chirality : 0.047 0.196 1770 Planarity : 0.005 0.046 2076 Dihedral : 5.756 22.820 1566 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.21), residues: 1408 helix: -1.75 (0.38), residues: 160 sheet: -2.66 (0.30), residues: 234 loop : -2.25 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 551 HIS 0.004 0.001 HIS E 10 PHE 0.048 0.002 PHE C 701 TYR 0.028 0.002 TYR A 562 ARG 0.004 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 262) hydrogen bonds : angle 7.42001 ( 636) SS BOND : bond 0.00174 ( 32) SS BOND : angle 0.64600 ( 64) covalent geometry : bond 0.00269 (11944) covalent geometry : angle 0.70431 (16174) *********************** 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 7 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.042 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0711 time to fit residues: 0.5881 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 : 0.042 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 : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.9307 (tp) cc_final: 0.8928 (tp) REVERT: A 109 LEU cc_start: 0.8525 (mm) cc_final: 0.7841 (mm) REVERT: A 110 MET cc_start: 0.7471 (mmp) cc_final: 0.6808 (ttt) REVERT: A 125 LEU cc_start: 0.8811 (tp) cc_final: 0.8587 (tp) REVERT: A 368 LEU cc_start: 0.8548 (mm) cc_final: 0.8105 (mm) REVERT: A 442 MET cc_start: 0.8439 (mmt) cc_final: 0.7920 (mmt) REVERT: A 504 MET cc_start: 0.8993 (mmp) cc_final: 0.8310 (mmm) REVERT: A 552 LEU cc_start: 0.8401 (pt) cc_final: 0.8185 (pt) REVERT: A 579 TYR cc_start: 0.8506 (m-80) cc_final: 0.8151 (m-80) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1395 time to fit residues: 17.9457 Evaluate side-chains 60 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 126 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 50.0000 chunk 138 optimal weight: 0.0370 chunk 40 optimal weight: 0.4980 chunk 84 optimal weight: 40.0000 chunk 22 optimal weight: 0.0670 chunk 23 optimal weight: 0.0000 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN A 589 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 = 0.3279 r_free = 0.3279 target = 0.071596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.056830 restraints weight = 2040.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.058605 restraints weight = 1368.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.059871 restraints weight = 1027.231| |-----------------------------------------------------------------------------| r_work (final): 0.3447 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.095418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.078005 restraints weight = 33931.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.079927 restraints weight = 24732.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.081290 restraints weight = 19777.829| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11976 Z= 0.127 Angle : 0.698 8.253 16238 Z= 0.361 Chirality : 0.047 0.196 1770 Planarity : 0.005 0.047 2076 Dihedral : 5.647 21.874 1566 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.21), residues: 1408 helix: -1.79 (0.38), residues: 160 sheet: -2.55 (0.32), residues: 192 loop : -2.17 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 133 HIS 0.003 0.001 HIS A 313 PHE 0.022 0.002 PHE A 39 TYR 0.016 0.001 TYR A 562 ARG 0.003 0.000 ARG C 702 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 262) hydrogen bonds : angle 7.23108 ( 636) SS BOND : bond 0.00247 ( 32) SS BOND : angle 0.75616 ( 64) covalent geometry : bond 0.00279 (11944) covalent geometry : angle 0.69775 (16174) *********************** 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 7 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.050 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0727 time to fit residues: 0.6109 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 : 0.046 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 : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7836 (tpt) cc_final: 0.7606 (tpp) REVERT: A 101 LEU cc_start: 0.9360 (tp) cc_final: 0.8930 (tp) REVERT: A 109 LEU cc_start: 0.8526 (mm) cc_final: 0.7805 (mm) REVERT: A 110 MET cc_start: 0.7648 (mmp) cc_final: 0.6974 (ttt) REVERT: A 125 LEU cc_start: 0.8824 (tp) cc_final: 0.8528 (tp) REVERT: A 368 LEU cc_start: 0.8460 (mm) cc_final: 0.7997 (mm) REVERT: A 442 MET cc_start: 0.8542 (mmt) cc_final: 0.8035 (mmt) REVERT: A 504 MET cc_start: 0.9136 (mmp) cc_final: 0.8618 (mmm) REVERT: A 579 TYR cc_start: 0.8580 (m-80) cc_final: 0.8303 (m-80) REVERT: A 706 GLU cc_start: 0.8852 (mp0) cc_final: 0.8221 (pm20) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1395 time to fit residues: 17.1657 Evaluate side-chains 60 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 66 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 133 optimal weight: 0.0370 chunk 119 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 124 optimal weight: 0.0060 chunk 5 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 30.0000 overall best weight: 1.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS 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 = 0.3284 r_free = 0.3284 target = 0.071434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.058387 restraints weight = 1983.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.059688 restraints weight = 1564.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.060607 restraints weight = 1307.047| |-----------------------------------------------------------------------------| r_work (final): 0.3087 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.095028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.077090 restraints weight = 34550.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.079189 restraints weight = 24785.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.080640 restraints weight = 19502.092| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.5269 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= 0.114 Angle : 0.642 6.147 16238 Z= 0.335 Chirality : 0.046 0.164 1770 Planarity : 0.005 0.048 2076 Dihedral : 5.488 20.865 1566 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.21), residues: 1408 helix: -1.81 (0.37), residues: 160 sheet: -2.42 (0.33), residues: 192 loop : -2.07 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 133 HIS 0.008 0.001 HIS A 263 PHE 0.021 0.002 PHE A 701 TYR 0.011 0.001 TYR A 67 ARG 0.011 0.001 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 262) hydrogen bonds : angle 7.01460 ( 636) SS BOND : bond 0.00211 ( 32) SS BOND : angle 0.61571 ( 64) covalent geometry : bond 0.00249 (11944) covalent geometry : angle 0.64179 (16174) *********************** 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 7 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.081 Fit side-chains REVERT: D 6 LEU cc_start: 0.8132 (mp) cc_final: 0.7899 (mp) outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0711 time to fit residues: 0.6258 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 : 0.041 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 : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 VAL cc_start: 0.8778 (t) cc_final: 0.8387 (p) REVERT: A 98 MET cc_start: 0.7788 (tpt) cc_final: 0.7406 (tpp) REVERT: A 101 LEU cc_start: 0.9327 (tp) cc_final: 0.8858 (tp) REVERT: A 109 LEU cc_start: 0.8529 (mm) cc_final: 0.7667 (mm) REVERT: A 110 MET cc_start: 0.7634 (mmp) cc_final: 0.6899 (ttt) REVERT: A 125 LEU cc_start: 0.8877 (tp) cc_final: 0.8622 (tp) REVERT: A 368 LEU cc_start: 0.8503 (mm) cc_final: 0.8080 (mm) REVERT: A 442 MET cc_start: 0.8621 (mmt) cc_final: 0.8082 (mmt) REVERT: A 504 MET cc_start: 0.9129 (mmp) cc_final: 0.8678 (mmm) REVERT: A 579 TYR cc_start: 0.8547 (m-80) cc_final: 0.8200 (m-80) REVERT: A 706 GLU cc_start: 0.8887 (mp0) cc_final: 0.8390 (pm20) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1387 time to fit residues: 16.6090 Evaluate side-chains 59 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 112 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 81 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3288 r_free = 0.3288 target = 0.071774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.058602 restraints weight = 2069.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.059950 restraints weight = 1668.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.060964 restraints weight = 1380.059| |-----------------------------------------------------------------------------| r_work (final): 0.3123 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.094040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.075869 restraints weight = 34494.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.078023 restraints weight = 24663.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.079421 restraints weight = 19339.480| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.5268 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= 0.127 Angle : 0.650 5.734 16238 Z= 0.341 Chirality : 0.046 0.271 1770 Planarity : 0.005 0.046 2076 Dihedral : 5.482 19.878 1566 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.21), residues: 1408 helix: -2.06 (0.34), residues: 174 sheet: -2.39 (0.33), residues: 192 loop : -2.07 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 133 HIS 0.004 0.001 HIS E 10 PHE 0.059 0.002 PHE A 701 TYR 0.012 0.001 TYR A 67 ARG 0.007 0.001 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.03897 ( 262) hydrogen bonds : angle 7.05653 ( 636) SS BOND : bond 0.00215 ( 32) SS BOND : angle 0.72431 ( 64) covalent geometry : bond 0.00281 (11944) covalent geometry : angle 0.64925 (16174) *********************** 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 7 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.041 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0675 time to fit residues: 0.5644 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 : 0.046 Evaluate side-chains 80 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7889 (tpt) cc_final: 0.7477 (tpp) REVERT: A 101 LEU cc_start: 0.9343 (tp) cc_final: 0.8878 (tp) REVERT: A 109 LEU cc_start: 0.8651 (mm) cc_final: 0.7937 (mm) REVERT: A 110 MET cc_start: 0.7091 (mmp) cc_final: 0.6664 (ttt) REVERT: A 368 LEU cc_start: 0.8483 (mm) cc_final: 0.8024 (mm) REVERT: A 442 MET cc_start: 0.8654 (mmt) cc_final: 0.8229 (mmt) REVERT: A 504 MET cc_start: 0.9082 (mmp) cc_final: 0.8654 (mmm) REVERT: A 579 TYR cc_start: 0.8419 (m-80) cc_final: 0.8062 (m-80) REVERT: A 706 GLU cc_start: 0.8838 (mp0) cc_final: 0.8165 (pp20) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1459 time to fit residues: 16.1244 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 : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 79 optimal weight: 0.0980 chunk 124 optimal weight: 0.0270 chunk 54 optimal weight: 0.2980 chunk 127 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 31 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 overall best weight: 0.8854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 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 = 0.3258 r_free = 0.3258 target = 0.070355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.058280 restraints weight = 2051.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.059708 restraints weight = 1605.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.060662 restraints weight = 1314.066| |-----------------------------------------------------------------------------| r_work (final): 0.3067 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.095486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.079546 restraints weight = 37572.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.081218 restraints weight = 28576.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.082394 restraints weight = 23392.179| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11976 Z= 0.119 Angle : 0.651 6.896 16238 Z= 0.339 Chirality : 0.047 0.254 1770 Planarity : 0.005 0.048 2076 Dihedral : 5.435 19.128 1566 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.21), residues: 1408 helix: -1.92 (0.35), residues: 174 sheet: -2.24 (0.34), residues: 192 loop : -2.05 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 632 HIS 0.003 0.001 HIS A 199 PHE 0.024 0.002 PHE C 701 TYR 0.013 0.001 TYR A 67 ARG 0.005 0.000 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 262) hydrogen bonds : angle 6.94754 ( 636) SS BOND : bond 0.00196 ( 32) SS BOND : angle 0.64329 ( 64) covalent geometry : bond 0.00267 (11944) covalent geometry : angle 0.65062 (16174) *********************** 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 7 residues out of total 43 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.044 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0669 time to fit residues: 0.5589 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 : 0.046 Evaluate side-chains 81 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.6968 (tt) cc_final: 0.6563 (mt) REVERT: A 93 LEU cc_start: 0.7863 (tp) cc_final: 0.7630 (tp) REVERT: A 98 MET cc_start: 0.8013 (tpt) cc_final: 0.7676 (tpp) REVERT: A 101 LEU cc_start: 0.9350 (tp) cc_final: 0.8863 (tp) REVERT: A 109 LEU cc_start: 0.8466 (mm) cc_final: 0.7730 (mm) REVERT: A 110 MET cc_start: 0.7279 (mmp) cc_final: 0.6685 (ttt) REVERT: A 125 LEU cc_start: 0.8787 (tp) cc_final: 0.8571 (tp) REVERT: A 345 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7450 (mmm160) REVERT: A 368 LEU cc_start: 0.8340 (mm) cc_final: 0.7867 (mm) REVERT: A 442 MET cc_start: 0.8521 (mmt) cc_final: 0.8059 (mmt) REVERT: A 504 MET cc_start: 0.9082 (mmp) cc_final: 0.8622 (mmm) REVERT: A 579 TYR cc_start: 0.8371 (m-80) cc_final: 0.7886 (m-80) REVERT: A 706 GLU cc_start: 0.8836 (mp0) cc_final: 0.8206 (pp20) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1545 time to fit residues: 17.1039 Evaluate side-chains 58 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.978 > 50: distance: 0 - 1: 30.620 distance: 1 - 2: 42.308 distance: 1 - 4: 5.503 distance: 2 - 3: 40.751 distance: 2 - 9: 68.519 distance: 4 - 5: 50.194 distance: 5 - 6: 15.877 distance: 6 - 7: 49.652 distance: 6 - 8: 35.803 distance: 9 - 10: 68.964 distance: 10 - 11: 56.469 distance: 10 - 13: 69.269 distance: 11 - 12: 69.900 distance: 11 - 17: 38.816 distance: 13 - 14: 41.664 distance: 13 - 15: 40.463 distance: 14 - 16: 47.525 distance: 17 - 18: 55.581 distance: 18 - 19: 55.180 distance: 18 - 21: 56.723 distance: 19 - 20: 56.438 distance: 19 - 25: 39.108 distance: 21 - 22: 40.129 distance: 22 - 23: 38.915 distance: 22 - 24: 41.507 distance: 25 - 26: 66.038 distance: 26 - 27: 9.281 distance: 26 - 29: 57.659 distance: 27 - 28: 44.388 distance: 27 - 33: 47.770 distance: 29 - 30: 41.314 distance: 30 - 31: 69.335 distance: 30 - 32: 55.275 distance: 33 - 34: 58.585 distance: 34 - 35: 56.249 distance: 34 - 37: 68.121 distance: 35 - 36: 56.906 distance: 35 - 41: 55.685 distance: 37 - 38: 57.130 distance: 38 - 39: 39.173 distance: 39 - 40: 48.976 distance: 41 - 42: 38.839 distance: 42 - 43: 54.868 distance: 42 - 45: 40.298 distance: 43 - 44: 56.830 distance: 43 - 52: 56.202 distance: 45 - 46: 69.369 distance: 46 - 47: 40.978 distance: 46 - 48: 40.211 distance: 47 - 49: 39.588 distance: 48 - 50: 36.552 distance: 49 - 51: 4.964 distance: 50 - 51: 35.034 distance: 52 - 53: 57.812 distance: 53 - 54: 35.103 distance: 53 - 56: 69.644 distance: 54 - 55: 39.066 distance: 54 - 61: 54.895 distance: 56 - 57: 40.656 distance: 57 - 58: 56.674 distance: 58 - 59: 57.357 distance: 59 - 60: 47.726 distance: 61 - 62: 40.025 distance: 62 - 63: 41.337 distance: 62 - 65: 59.409 distance: 63 - 64: 57.023 distance: 65 - 66: 44.997 distance: 65 - 67: 54.399 distance: 68 - 69: 55.537 distance: 69 - 70: 41.128 distance: 69 - 72: 44.915 distance: 70 - 71: 42.825 distance: 70 - 79: 39.489 distance: 72 - 73: 42.384 distance: 73 - 74: 41.123 distance: 74 - 75: 8.936 distance: 75 - 76: 51.136 distance: 76 - 77: 57.590 distance: 76 - 78: 56.492 distance: 79 - 80: 60.477 distance: 79 - 85: 67.862 distance: 80 - 81: 44.418 distance: 80 - 83: 18.018 distance: 81 - 82: 42.897 distance: 83 - 84: 60.811 distance: 84 - 85: 58.857