Starting phenix.real_space_refine on Thu Sep 26 00:39:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwa_30231/09_2024/7bwa_30231.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwa_30231/09_2024/7bwa_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwa_30231/09_2024/7bwa_30231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwa_30231/09_2024/7bwa_30231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwa_30231/09_2024/7bwa_30231.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwa_30231/09_2024/7bwa_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-5461/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: 6.94, per 1000 atoms: 0.59 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: 2.67 Conformation dependent library (CDL) restraints added in 1.5 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: 1.40 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: 3.91 Time building geometry restraints manager: 3.22 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'E' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.340 Find NCS groups from input model: 0.310 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- 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 11944 Z= 0.279 Angle : 0.772 7.294 16174 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.652 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: 0.2207 time to fit residues: 31.8791 Evaluate side-chains 65 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.627 Evaluate side-chains 11 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.044 Fit side-chains REVERT: D 22 ARG cc_start: 0.7851 (mpp80) cc_final: 0.7118 (mmm160) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.1423 time to fit residues: 1.6742 Evaluate side-chains 6 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.045 ------------------------------------------------------------------------------- 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... 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 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11944 Z= 0.229 Angle : 0.765 10.072 16174 Z= 0.405 Chirality : 0.049 0.205 1770 Planarity : 0.005 0.060 2076 Dihedral : 6.710 22.446 1566 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 25.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.65 % Favored : 88.21 % Rotamer: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % 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: -3.98 (0.20), residues: 1408 helix: -2.56 (0.34), residues: 164 sheet: -3.50 (0.32), residues: 178 loop : -2.71 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 632 HIS 0.030 0.002 HIS E 10 PHE 0.063 0.002 PHE C 701 TYR 0.024 0.002 TYR C 587 ARG 0.006 0.001 ARG C 345 *********************** 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 86 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.766 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: 0.7305 (mt0) cc_final: 0.7006 (tt0) REVERT: A 101 LEU cc_start: 0.9192 (tp) cc_final: 0.8868 (tp) REVERT: A 263 HIS cc_start: 0.8555 (t70) cc_final: 0.8008 (t70) REVERT: A 368 LEU cc_start: 0.8288 (mm) cc_final: 0.7968 (mm) REVERT: A 419 LEU cc_start: 0.8264 (tt) cc_final: 0.8022 (mt) REVERT: A 442 MET cc_start: 0.8273 (mmt) cc_final: 0.7517 (mmt) REVERT: A 504 MET cc_start: 0.8812 (mmp) cc_final: 0.8385 (mmm) REVERT: A 579 TYR cc_start: 0.8460 (m-80) cc_final: 0.8229 (m-80) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1583 time to fit residues: 18.6559 Evaluate side-chains 61 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.643 Evaluate side-chains 9 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.041 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.1714 time to fit residues: 1.6502 Evaluate side-chains 6 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 107 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* 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 470 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11944 Z= 0.218 Angle : 0.710 7.030 16174 Z= 0.378 Chirality : 0.047 0.153 1770 Planarity : 0.005 0.045 2076 Dihedral : 6.396 23.110 1566 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % 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: -3.69 (0.21), residues: 1408 helix: -2.37 (0.34), residues: 158 sheet: -3.39 (0.32), residues: 186 loop : -2.47 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 133 HIS 0.008 0.001 HIS E 10 PHE 0.025 0.002 PHE A 39 TYR 0.018 0.002 TYR A 587 ARG 0.006 0.001 ARG A 702 *********************** 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 88 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7725 (mt0) cc_final: 0.7397 (mt0) REVERT: A 101 LEU cc_start: 0.9170 (tp) cc_final: 0.8808 (tp) REVERT: A 263 HIS cc_start: 0.8572 (t70) cc_final: 0.8049 (t70) REVERT: A 368 LEU cc_start: 0.8292 (mm) cc_final: 0.8012 (mm) REVERT: A 442 MET cc_start: 0.8239 (mmt) cc_final: 0.7576 (mmt) REVERT: A 504 MET cc_start: 0.8757 (mmp) cc_final: 0.8290 (mmm) REVERT: A 579 TYR cc_start: 0.8532 (m-80) cc_final: 0.7917 (m-80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1817 time to fit residues: 21.0217 Evaluate side-chains 62 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.640 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.043 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1606 time to fit residues: 1.3838 Evaluate side-chains 7 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.0970 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 14 optimal weight: 0.3980 chunk 61 optimal weight: 0.0670 chunk 86 optimal weight: 20.0000 chunk 129 optimal weight: 0.4980 chunk 137 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.0118 ------------------------------------------------------------------------------- NQH flips ********* 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 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11944 Z= 0.182 Angle : 0.705 9.269 16174 Z= 0.367 Chirality : 0.047 0.181 1770 Planarity : 0.005 0.042 2076 Dihedral : 6.177 23.157 1566 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % 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: -3.64 (0.21), residues: 1408 helix: -2.73 (0.32), residues: 172 sheet: -3.00 (0.32), residues: 196 loop : -2.41 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 551 HIS 0.004 0.001 HIS D 10 PHE 0.040 0.002 PHE C 701 TYR 0.014 0.001 TYR C 587 ARG 0.005 0.000 ARG C 345 *********************** 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 94 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7735 (pt) cc_final: 0.6214 (pt) REVERT: A 93 LEU cc_start: 0.6953 (tp) cc_final: 0.6659 (tp) REVERT: A 98 MET cc_start: 0.7054 (tpt) cc_final: 0.6840 (tpp) REVERT: A 109 LEU cc_start: 0.8455 (mm) cc_final: 0.8175 (mm) REVERT: A 368 LEU cc_start: 0.8193 (mm) cc_final: 0.7867 (mm) REVERT: A 442 MET cc_start: 0.8242 (mmt) cc_final: 0.7614 (mmt) REVERT: A 488 ARG cc_start: 0.7422 (mmm-85) cc_final: 0.7139 (mtt180) REVERT: A 504 MET cc_start: 0.8755 (mmp) cc_final: 0.8237 (mmm) REVERT: A 551 TRP cc_start: 0.7494 (t-100) cc_final: 0.7143 (t-100) REVERT: A 579 TYR cc_start: 0.8200 (m-80) cc_final: 0.7945 (m-80) REVERT: A 706 GLU cc_start: 0.8744 (mp0) cc_final: 0.8089 (pm20) REVERT: A 710 HIS cc_start: 0.9351 (m90) cc_final: 0.8637 (m170) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1736 time to fit residues: 22.2865 Evaluate side-chains 64 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.658 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.048 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1735 time to fit residues: 1.4882 Evaluate side-chains 7 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 94 optimal weight: 0.0570 chunk 0 optimal weight: 8.9990 chunk 70 optimal weight: 0.0020 chunk 123 optimal weight: 10.0000 chunk 34 optimal weight: 0.0270 chunk 46 optimal weight: 3.9990 overall best weight: 2.0168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11944 Z= 0.188 Angle : 0.707 10.483 16174 Z= 0.368 Chirality : 0.047 0.225 1770 Planarity : 0.005 0.043 2076 Dihedral : 6.010 23.117 1566 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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: -3.48 (0.21), residues: 1408 helix: -2.30 (0.34), residues: 174 sheet: -2.83 (0.33), residues: 192 loop : -2.38 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 133 HIS 0.005 0.001 HIS C 263 PHE 0.044 0.002 PHE C 701 TYR 0.034 0.002 TYR A 562 ARG 0.004 0.000 ARG A 19 *********************** 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 92 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.7383 (tp) cc_final: 0.7173 (tp) REVERT: A 109 LEU cc_start: 0.8332 (mm) cc_final: 0.7647 (mm) REVERT: A 110 MET cc_start: 0.6994 (mmp) cc_final: 0.6410 (ttt) REVERT: A 263 HIS cc_start: 0.8424 (t70) cc_final: 0.7801 (t-90) REVERT: A 368 LEU cc_start: 0.8505 (mm) cc_final: 0.8088 (mm) REVERT: A 442 MET cc_start: 0.8220 (mmt) cc_final: 0.7725 (mmt) REVERT: A 488 ARG cc_start: 0.7224 (mmm-85) cc_final: 0.6959 (mtt180) REVERT: A 504 MET cc_start: 0.8677 (mmp) cc_final: 0.8169 (mmm) REVERT: A 579 TYR cc_start: 0.8384 (m-80) cc_final: 0.8152 (m-80) REVERT: A 706 GLU cc_start: 0.8646 (mp0) cc_final: 0.8066 (pm20) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2015 time to fit residues: 24.3844 Evaluate side-chains 61 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.651 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.046 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1746 time to fit residues: 1.5024 Evaluate side-chains 7 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 8.9990 chunk 27 optimal weight: 0.0010 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 0.0470 chunk 137 optimal weight: 0.0870 chunk 114 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 72 optimal weight: 0.0040 chunk 132 optimal weight: 4.9990 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* 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 Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11944 Z= 0.169 Angle : 0.687 8.782 16174 Z= 0.355 Chirality : 0.047 0.176 1770 Planarity : 0.005 0.047 2076 Dihedral : 5.789 21.401 1566 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % 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: -3.29 (0.21), residues: 1408 helix: -2.10 (0.36), residues: 160 sheet: -2.66 (0.30), residues: 228 loop : -2.22 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 133 HIS 0.003 0.001 HIS A 263 PHE 0.028 0.002 PHE C 39 TYR 0.015 0.001 TYR C 562 ARG 0.003 0.000 ARG A 576 *********************** 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 85 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7170 (tpp) cc_final: 0.6340 (tpp) REVERT: A 101 LEU cc_start: 0.9142 (tp) cc_final: 0.8541 (pt) REVERT: A 109 LEU cc_start: 0.8306 (mm) cc_final: 0.7481 (mm) REVERT: A 110 MET cc_start: 0.6920 (mmp) cc_final: 0.6539 (ttt) REVERT: A 125 LEU cc_start: 0.8675 (tp) cc_final: 0.8326 (tp) REVERT: A 368 LEU cc_start: 0.8451 (mm) cc_final: 0.7969 (mm) REVERT: A 442 MET cc_start: 0.7998 (mmt) cc_final: 0.7744 (mmt) REVERT: A 488 ARG cc_start: 0.7177 (mmm-85) cc_final: 0.6794 (mmt180) REVERT: A 504 MET cc_start: 0.8905 (mmp) cc_final: 0.8368 (mmm) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1848 time to fit residues: 20.5560 Evaluate side-chains 63 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.680 Evaluate side-chains 9 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.047 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.1651 time to fit residues: 1.5917 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 8.9990 chunk 78 optimal weight: 0.1980 chunk 100 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 136 optimal weight: 0.0570 chunk 85 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 40.0000 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* 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 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11944 Z= 0.193 Angle : 0.731 10.262 16174 Z= 0.373 Chirality : 0.049 0.193 1770 Planarity : 0.005 0.050 2076 Dihedral : 5.766 20.928 1566 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: -3.15 (0.21), residues: 1408 helix: -1.87 (0.38), residues: 160 sheet: -2.59 (0.33), residues: 192 loop : -2.18 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 133 HIS 0.004 0.001 HIS C 263 PHE 0.079 0.003 PHE C 701 TYR 0.034 0.002 TYR A 67 ARG 0.012 0.000 ARG C 454 *********************** 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 80 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 VAL cc_start: 0.8371 (t) cc_final: 0.7947 (t) REVERT: A 93 LEU cc_start: 0.7537 (tp) cc_final: 0.7193 (tp) REVERT: A 109 LEU cc_start: 0.8300 (mm) cc_final: 0.7547 (mm) REVERT: A 110 MET cc_start: 0.6948 (mmp) cc_final: 0.6525 (ttt) REVERT: A 143 ASN cc_start: 0.8437 (m-40) cc_final: 0.8124 (t0) REVERT: A 368 LEU cc_start: 0.8367 (mm) cc_final: 0.7900 (mm) REVERT: A 442 MET cc_start: 0.8050 (mmt) cc_final: 0.7753 (mmt) REVERT: A 488 ARG cc_start: 0.7152 (mmm-85) cc_final: 0.6812 (mmt180) REVERT: A 504 MET cc_start: 0.8835 (mmp) cc_final: 0.8408 (mmm) REVERT: A 706 GLU cc_start: 0.8741 (mp0) cc_final: 0.7999 (pp20) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1570 time to fit residues: 17.1385 Evaluate side-chains 63 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.648 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.044 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1637 time to fit residues: 1.4074 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 26 optimal weight: 0.0670 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 67 optimal weight: 20.0000 chunk 12 optimal weight: 0.0060 chunk 107 optimal weight: 0.0060 chunk 124 optimal weight: 0.9990 chunk 131 optimal weight: 0.0040 overall best weight: 0.1762 ------------------------------------------------------------------------------- NQH flips ********* 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 Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11944 Z= 0.180 Angle : 0.711 12.682 16174 Z= 0.360 Chirality : 0.048 0.312 1770 Planarity : 0.005 0.049 2076 Dihedral : 5.685 20.624 1566 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.10 (0.21), residues: 1408 helix: -1.83 (0.37), residues: 160 sheet: -2.37 (0.31), residues: 228 loop : -2.16 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 133 HIS 0.004 0.001 HIS C 263 PHE 0.048 0.002 PHE C 39 TYR 0.017 0.001 TYR C 67 ARG 0.007 0.000 ARG A 454 *********************** 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 83 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.6657 (mmp) cc_final: 0.6202 (mmp) REVERT: A 81 VAL cc_start: 0.7957 (t) cc_final: 0.7241 (p) REVERT: A 93 LEU cc_start: 0.7613 (tp) cc_final: 0.7335 (tp) REVERT: A 98 MET cc_start: 0.6949 (tpp) cc_final: 0.6153 (tpp) REVERT: A 101 LEU cc_start: 0.9148 (tp) cc_final: 0.8609 (pt) REVERT: A 109 LEU cc_start: 0.8383 (mm) cc_final: 0.7784 (mm) REVERT: A 125 LEU cc_start: 0.8563 (tp) cc_final: 0.8185 (tp) REVERT: A 263 HIS cc_start: 0.8439 (t70) cc_final: 0.7769 (t-90) REVERT: A 368 LEU cc_start: 0.8434 (mm) cc_final: 0.7930 (mm) REVERT: A 442 MET cc_start: 0.8003 (mmt) cc_final: 0.7767 (mmm) REVERT: A 488 ARG cc_start: 0.7152 (mmm-85) cc_final: 0.6801 (mmt180) REVERT: A 504 MET cc_start: 0.8826 (mmp) cc_final: 0.8441 (mmm) REVERT: A 575 GLU cc_start: 0.6491 (mp0) cc_final: 0.6177 (pm20) REVERT: A 706 GLU cc_start: 0.8697 (mp0) cc_final: 0.8006 (pp20) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1839 time to fit residues: 20.5308 Evaluate side-chains 62 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.687 Evaluate side-chains 9 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.046 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.1611 time to fit residues: 1.5509 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 131 optimal weight: 0.2980 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* 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 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11944 Z= 0.218 Angle : 0.684 7.599 16174 Z= 0.357 Chirality : 0.047 0.251 1770 Planarity : 0.005 0.049 2076 Dihedral : 5.737 20.182 1566 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -2.13 (0.35), residues: 160 sheet: -2.59 (0.32), residues: 196 loop : -2.09 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 133 HIS 0.018 0.001 HIS C 199 PHE 0.036 0.002 PHE A 39 TYR 0.010 0.001 TYR C 91 ARG 0.005 0.001 ARG A 83 *********************** 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 79 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.6747 (tt) cc_final: 0.6538 (mp) REVERT: A 81 VAL cc_start: 0.7982 (t) cc_final: 0.7441 (t) REVERT: A 93 LEU cc_start: 0.7775 (tp) cc_final: 0.7465 (tp) REVERT: A 98 MET cc_start: 0.6872 (tpp) cc_final: 0.5934 (tpp) REVERT: A 101 LEU cc_start: 0.9160 (tp) cc_final: 0.8541 (pt) REVERT: A 109 LEU cc_start: 0.8203 (mm) cc_final: 0.7913 (mm) REVERT: A 125 LEU cc_start: 0.8514 (tp) cc_final: 0.8246 (tp) REVERT: A 345 ARG cc_start: 0.7865 (mtp85) cc_final: 0.7455 (mmm160) REVERT: A 368 LEU cc_start: 0.8351 (mm) cc_final: 0.7895 (mm) REVERT: A 442 MET cc_start: 0.8072 (mmt) cc_final: 0.7694 (mmt) REVERT: A 488 ARG cc_start: 0.7214 (mmm-85) cc_final: 0.6864 (mmt180) REVERT: A 504 MET cc_start: 0.8661 (mmp) cc_final: 0.8298 (mmm) REVERT: A 575 GLU cc_start: 0.6574 (mp0) cc_final: 0.6204 (pm20) REVERT: A 706 GLU cc_start: 0.8788 (mp0) cc_final: 0.8080 (pp20) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1684 time to fit residues: 17.9624 Evaluate side-chains 61 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.668 Evaluate side-chains 9 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.048 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.1514 time to fit residues: 1.4686 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 141 optimal weight: 0.0030 chunk 130 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 69 optimal weight: 0.0040 chunk 89 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 199 HIS A 282 ASN A 410 GLN Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11944 Z= 0.179 Angle : 0.714 8.959 16174 Z= 0.366 Chirality : 0.048 0.233 1770 Planarity : 0.005 0.051 2076 Dihedral : 5.670 21.624 1566 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 0.15 % Allowed : 0.30 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.27 (0.32), residues: 170 sheet: -2.22 (0.31), residues: 228 loop : -2.13 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP C 133 HIS 0.005 0.001 HIS A 313 PHE 0.040 0.002 PHE A 39 TYR 0.013 0.001 TYR A 60 ARG 0.004 0.000 ARG A 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.6825 (tt) cc_final: 0.6600 (mt) REVERT: A 28 VAL cc_start: 0.8586 (m) cc_final: 0.8294 (m) REVERT: A 93 LEU cc_start: 0.7718 (tp) cc_final: 0.7394 (tp) REVERT: A 98 MET cc_start: 0.7130 (tpp) cc_final: 0.6375 (tpp) REVERT: A 100 HIS cc_start: 0.5183 (OUTLIER) cc_final: 0.4333 (t-170) REVERT: A 101 LEU cc_start: 0.9227 (tp) cc_final: 0.8692 (pt) REVERT: A 125 LEU cc_start: 0.8469 (tp) cc_final: 0.8208 (tp) REVERT: A 345 ARG cc_start: 0.7745 (mtp85) cc_final: 0.7468 (mmm160) REVERT: A 368 LEU cc_start: 0.8419 (mm) cc_final: 0.7990 (mm) REVERT: A 442 MET cc_start: 0.8048 (mmt) cc_final: 0.7761 (mmm) REVERT: A 488 ARG cc_start: 0.7093 (mmm-85) cc_final: 0.6765 (mmt180) REVERT: A 504 MET cc_start: 0.8813 (mmp) cc_final: 0.8439 (mmm) REVERT: A 706 GLU cc_start: 0.8694 (mp0) cc_final: 0.8040 (pp20) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.2144 time to fit residues: 23.3834 Evaluate side-chains 62 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.696 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.044 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1541 time to fit residues: 1.3299 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.0470 chunk 103 optimal weight: 0.8980 chunk 16 optimal weight: 30.0000 chunk 31 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 115 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 99 optimal weight: 6.9990 chunk 6 optimal weight: 0.0470 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.095370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.079009 restraints weight = 37112.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.080860 restraints weight = 27250.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.082153 restraints weight = 21867.775| |-----------------------------------------------------------------------------| r_work (final): 0.3769 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.068738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.058387 restraints weight = 2047.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.060735 restraints weight = 1257.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.062619 restraints weight = 850.946| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 11944 Z= 0.257 Angle : 0.722 8.904 16174 Z= 0.376 Chirality : 0.048 0.229 1770 Planarity : 0.005 0.050 2076 Dihedral : 5.656 20.089 1566 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -3.09 (0.21), residues: 1408 helix: -2.24 (0.33), residues: 170 sheet: -2.20 (0.31), residues: 228 loop : -2.11 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 133 HIS 0.040 0.002 HIS C 100 PHE 0.034 0.002 PHE A 39 TYR 0.013 0.001 TYR A 60 ARG 0.003 0.000 ARG C 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2011.42 seconds wall clock time: 38 minutes 1.23 seconds (2281.23 seconds total)