Starting phenix.real_space_refine on Wed May 14 09:38:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bwa_30231/05_2025/7bwa_30231.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bwa_30231/05_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_30231/05_2025/7bwa_30231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bwa_30231/05_2025/7bwa_30231.map" model { file = "/net/cci-nas-00/data/ceres_data/7bwa_30231/05_2025/7bwa_30231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bwa_30231/05_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-5687/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: 6.37, per 1000 atoms: 0.55 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: 2.65 Conformation dependent library (CDL) restraints added in 1.4 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: 1.29 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: 3.51 Time building geometry restraints manager: 3.16 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: 0.210 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: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.260 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.800 ------------------------------------------------------------------------------- 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 : 0.042 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1406 time to fit residues: 1.9390 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 : 0.039 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 : 0.533 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: 0.2240 time to fit residues: 32.6266 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 : 0.596 ------------------------------------------------------------------------------- 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 = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.056739 restraints weight = 1788.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.058087 restraints weight = 1448.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.059293 restraints weight = 1222.112| |-----------------------------------------------------------------------------| 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 = 54)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.072895 restraints weight = 35336.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.074816 restraints weight = 25886.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.076150 restraints weight = 20771.070| |-----------------------------------------------------------------------------| 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 : 0.047 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1232 time to fit residues: 1.9664 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 : 0.048 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 : 0.587 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: 0.7454 (mt0) cc_final: 0.7236 (tt0) REVERT: A 98 MET cc_start: 0.8037 (tpt) cc_final: 0.7826 (tpp) REVERT: A 101 LEU cc_start: 0.9248 (tp) cc_final: 0.8919 (tp) REVERT: A 263 HIS cc_start: 0.8597 (t70) cc_final: 0.8109 (t70) REVERT: A 368 LEU cc_start: 0.8309 (mm) cc_final: 0.7976 (mm) REVERT: A 419 LEU cc_start: 0.8447 (tt) cc_final: 0.8184 (mt) REVERT: A 442 MET cc_start: 0.8571 (mmt) cc_final: 0.7911 (mmt) REVERT: A 504 MET cc_start: 0.8966 (mmp) cc_final: 0.8484 (mmm) REVERT: A 579 TYR cc_start: 0.8711 (m-80) cc_final: 0.8019 (m-80) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1658 time to fit residues: 19.9212 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 : 0.653 ------------------------------------------------------------------------------- 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: 0.4980 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 50.0000 chunk 59 optimal weight: 30.0000 chunk 28 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 115 optimal weight: 0.0870 chunk 92 optimal weight: 0.0970 chunk 79 optimal weight: 9.9990 chunk 125 optimal weight: 0.0000 overall best weight: 0.3160 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.073409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.057591 restraints weight = 1985.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.059350 restraints weight = 1504.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.060842 restraints weight = 1207.380| |-----------------------------------------------------------------------------| r_work (final): 0.3453 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.093024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.076194 restraints weight = 38311.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.077928 restraints weight = 28648.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.079188 restraints weight = 23267.316| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11976 Z= 0.157 Angle : 0.816 25.438 16238 Z= 0.416 Chirality : 0.048 0.185 1770 Planarity : 0.006 0.049 2076 Dihedral : 6.369 35.140 1566 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.80 % Favored : 89.06 % Rotamer: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.40 % 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: -3.63 (0.21), residues: 1408 helix: -2.07 (0.37), residues: 156 sheet: -3.17 (0.31), residues: 196 loop : -2.50 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 133 HIS 0.018 0.001 HIS E 10 PHE 0.029 0.002 PHE A 39 TYR 0.019 0.002 TYR A 67 ARG 0.009 0.001 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.05093 ( 262) hydrogen bonds : angle 8.28467 ( 636) SS BOND : bond 0.00241 ( 32) SS BOND : angle 0.90663 ( 64) covalent geometry : bond 0.00343 (11944) covalent geometry : angle 0.81551 (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 : 0.044 Fit side-chains REVERT: D 6 LEU cc_start: 0.8615 (mp) cc_final: 0.8402 (mp) outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.1741 time to fit residues: 1.3059 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 : 0.041 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 : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.7017 (tp) cc_final: 0.6756 (tp) REVERT: A 98 MET cc_start: 0.8160 (tpt) cc_final: 0.7819 (tpp) REVERT: A 101 LEU cc_start: 0.9208 (tp) cc_final: 0.8786 (tp) REVERT: A 109 LEU cc_start: 0.8599 (mm) cc_final: 0.8390 (mm) REVERT: A 263 HIS cc_start: 0.8607 (t70) cc_final: 0.8160 (t70) REVERT: A 368 LEU cc_start: 0.8611 (mm) cc_final: 0.8306 (mm) REVERT: A 442 MET cc_start: 0.8558 (mmt) cc_final: 0.8054 (mmt) REVERT: A 477 TYR cc_start: 0.8568 (m-80) cc_final: 0.8343 (m-80) REVERT: A 504 MET cc_start: 0.9038 (mmp) cc_final: 0.8537 (mmm) REVERT: A 579 TYR cc_start: 0.8583 (m-80) cc_final: 0.8141 (m-80) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1578 time to fit residues: 18.9336 Evaluate side-chains 62 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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: 68.658 > 50: distance: 0 - 1: 11.977 distance: 1 - 2: 17.327 distance: 1 - 4: 4.129 distance: 2 - 3: 26.039 distance: 2 - 9: 27.749 distance: 4 - 5: 8.610 distance: 9 - 10: 19.006 distance: 10 - 11: 20.316 distance: 10 - 13: 30.481 distance: 11 - 12: 37.957 distance: 11 - 17: 37.577 distance: 13 - 14: 41.559 distance: 14 - 15: 17.192 distance: 14 - 16: 44.232 distance: 17 - 18: 42.645 distance: 18 - 19: 11.693 distance: 18 - 21: 38.547 distance: 19 - 20: 39.871 distance: 19 - 23: 51.443 distance: 21 - 22: 40.269 distance: 23 - 24: 37.694 distance: 24 - 25: 39.144 distance: 24 - 27: 43.952 distance: 25 - 26: 52.356 distance: 25 - 29: 40.838 distance: 27 - 28: 36.963 distance: 29 - 30: 5.701 distance: 30 - 31: 45.505 distance: 30 - 33: 47.993 distance: 31 - 32: 16.759 distance: 31 - 36: 25.534 distance: 33 - 34: 24.881 distance: 33 - 35: 44.865 distance: 36 - 37: 3.967 distance: 37 - 38: 45.717 distance: 37 - 40: 52.206 distance: 38 - 39: 31.412 distance: 38 - 44: 9.107 distance: 40 - 41: 35.804 distance: 40 - 42: 47.725 distance: 41 - 43: 50.804 distance: 44 - 45: 23.120 distance: 45 - 46: 41.967 distance: 45 - 48: 6.082 distance: 46 - 47: 15.182 distance: 46 - 53: 16.449 distance: 48 - 49: 35.615 distance: 49 - 50: 33.907 distance: 50 - 51: 13.399 distance: 50 - 52: 44.080 distance: 53 - 54: 29.842 distance: 54 - 55: 13.571 distance: 55 - 56: 24.248 distance: 55 - 57: 24.045 distance: 57 - 58: 21.240 distance: 58 - 59: 16.279 distance: 58 - 61: 24.845 distance: 59 - 60: 67.830 distance: 59 - 67: 34.752 distance: 61 - 62: 16.360 distance: 62 - 63: 15.514 distance: 62 - 64: 10.152 distance: 63 - 65: 5.886 distance: 64 - 66: 4.589 distance: 65 - 66: 6.968 distance: 67 - 68: 10.748 distance: 68 - 69: 26.738 distance: 68 - 71: 19.256 distance: 69 - 70: 25.470 distance: 71 - 72: 31.261 distance: 72 - 73: 30.909 distance: 72 - 74: 17.266