Starting phenix.real_space_refine on Sat Jul 4 19:42:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8edg_28034/07_2026/8edg_28034.cif Found real_map, /net/cci-nas-00/data/ceres_data/8edg_28034/07_2026/8edg_28034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8edg_28034/07_2026/8edg_28034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8edg_28034/07_2026/8edg_28034.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8edg_28034/07_2026/8edg_28034.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8edg_28034/07_2026/8edg_28034.cif" model { file = "/net/cci-nas-00/data/ceres_data/8edg_28034/07_2026/8edg_28034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8edg_28034/07_2026/8edg_28034.cif" } resolution = 4.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 212 5.49 5 S 112 5.16 5 C 14194 2.51 5 N 4050 2.21 5 O 4784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23358 Number of models: 1 Model: "" Number of chains: 18 Chain: "M" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Classifications: {'DNA': 7} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 6} Chain: "N" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 941 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Chain: "O" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1126 Classifications: {'DNA': 55} Link IDs: {'rna3p': 54} Chain: "Q" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 941 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Chain: "R" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1126 Classifications: {'DNA': 55} Link IDs: {'rna3p': 54} Chain: "P" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Classifications: {'DNA': 7} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4432 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 16, 'TRANS': 533} Chain breaks: 1 Chain: "C" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4432 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 16, 'TRANS': 533} Chain breaks: 1 Chain: "I" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 601 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4432 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 16, 'TRANS': 533} Chain breaks: 1 Chain: "G" Number of atoms: 4432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4432 Classifications: {'peptide': 550} Link IDs: {'PTRANS': 16, 'TRANS': 533} Chain breaks: 1 Chain: "K" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 601 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4813 SG CYS A 51 106.456 85.404 40.489 1.00140.54 S ATOM 4839 SG CYS A 54 108.768 82.042 40.981 1.00149.72 S ATOM 4998 SG CYS A 73 107.446 84.117 43.987 1.00166.29 S ATOM 9245 SG CYS C 51 62.941 86.411 103.549 1.00176.12 S ATOM 9271 SG CYS C 54 65.615 85.962 106.173 1.00183.89 S ATOM 9430 SG CYS C 73 65.825 84.041 102.802 1.00186.21 S ATOM 13677 SG CYS I 51 88.952 61.126 53.931 1.00157.62 S ATOM 13703 SG CYS I 54 86.782 62.521 51.131 1.00166.93 S ATOM 13862 SG CYS I 73 87.778 64.809 54.062 1.00176.76 S ATOM 14278 SG CYS E 51 117.194 40.229 67.933 1.00162.32 S ATOM 14304 SG CYS E 54 116.798 40.517 64.180 1.00169.46 S ATOM 14463 SG CYS E 73 114.497 42.536 66.354 1.00153.25 S ATOM 18710 SG CYS G 51 116.746 101.585 112.993 1.00147.53 S ATOM 18736 SG CYS G 54 113.369 102.965 114.274 1.00158.46 S ATOM 18895 SG CYS G 73 113.488 100.760 111.150 1.00123.95 S ATOM 23142 SG CYS K 51 98.448 75.983 118.061 1.00176.17 S ATOM 23168 SG CYS K 54 101.615 73.919 117.493 1.00165.17 S ATOM 23327 SG CYS K 73 100.708 76.601 114.957 1.00156.70 S Time building chain proxies: 4.56, per 1000 atoms: 0.20 Number of scatterers: 23358 At special positions: 0 Unit cell: (200.68, 160.08, 155.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 112 16.00 P 212 15.00 O 4784 8.00 N 4050 7.00 C 14194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 859.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 71 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 73 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 51 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 54 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" NE2 HIS C 71 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 51 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 54 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 71 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 54 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 73 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 51 " pdb=" ZN G 701 " pdb="ZN ZN G 701 " - pdb=" NE2 HIS G 71 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 73 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 54 " pdb="ZN ZN G 701 " - pdb=" SG CYS G 51 " pdb=" ZN I 701 " pdb="ZN ZN I 701 " - pdb=" NE2 HIS I 71 " pdb="ZN ZN I 701 " - pdb=" SG CYS I 54 " pdb="ZN ZN I 701 " - pdb=" SG CYS I 51 " pdb="ZN ZN I 701 " - pdb=" SG CYS I 73 " pdb=" ZN K 701 " pdb="ZN ZN K 701 " - pdb=" NE2 HIS K 71 " pdb="ZN ZN K 701 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 701 " - pdb=" SG CYS K 73 " pdb="ZN ZN K 701 " - pdb=" SG CYS K 51 " Number of angles added : 18 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4556 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 16 sheets defined 61.7% alpha, 6.8% beta 49 base pairs and 142 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 4.396A pdb=" N GLU A 8 " --> pdb=" O MET A 4 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 32 Processing helix chain 'A' and resid 66 through 71 removed outlier: 3.557A pdb=" N HIS A 71 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.669A pdb=" N GLN A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.736A pdb=" N ASP A 105 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.677A pdb=" N VAL A 112 " --> pdb=" O PHE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 131 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 143 through 172 removed outlier: 4.203A pdb=" N ARG A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLU A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 234 Processing helix chain 'A' and resid 250 through 257 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 281 through 301 Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.407A pdb=" N HIS A 305 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 306 " --> pdb=" O LEU A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 306' Processing helix chain 'A' and resid 320 through 344 removed outlier: 4.425A pdb=" N THR A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLU A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N SER A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 4.145A pdb=" N ILE A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 375 removed outlier: 3.729A pdb=" N ILE A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 426 through 435 removed outlier: 4.034A pdb=" N TYR A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.766A pdb=" N GLN A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A 453 " --> pdb=" O GLN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 539 through 551 removed outlier: 4.203A pdb=" N LYS A 549 " --> pdb=" O ASN A 545 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 removed outlier: 3.579A pdb=" N LYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 583 through 587 removed outlier: 4.131A pdb=" N ASN A 587 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 607 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.929A pdb=" N TRP C 31 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 75 removed outlier: 6.294A pdb=" N LYS C 72 " --> pdb=" O CYS C 69 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N CYS C 73 " --> pdb=" O ARG C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 106 removed outlier: 3.542A pdb=" N LYS C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 114 through 132 Processing helix chain 'C' and resid 136 through 141 removed outlier: 3.987A pdb=" N LEU C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 136 through 141' Processing helix chain 'C' and resid 143 through 171 removed outlier: 4.350A pdb=" N ARG C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 235 removed outlier: 3.739A pdb=" N PHE C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 257 Processing helix chain 'C' and resid 265 through 280 Processing helix chain 'C' and resid 281 through 302 Proline residue: C 287 - end of helix Processing helix chain 'C' and resid 321 through 344 removed outlier: 5.629A pdb=" N GLU C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 Processing helix chain 'C' and resid 353 through 375 Processing helix chain 'C' and resid 385 through 396 removed outlier: 3.800A pdb=" N CYS C 396 " --> pdb=" O VAL C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 420 through 425 Processing helix chain 'C' and resid 426 through 435 removed outlier: 4.198A pdb=" N TYR C 430 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 456 removed outlier: 3.791A pdb=" N GLU C 452 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 529 Processing helix chain 'C' and resid 539 through 547 Processing helix chain 'C' and resid 553 through 563 removed outlier: 3.870A pdb=" N LEU C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 582 removed outlier: 4.135A pdb=" N GLU C 572 " --> pdb=" O SER C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 607 removed outlier: 3.523A pdb=" N VAL C 594 " --> pdb=" O GLY C 590 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 66 through 70 Processing helix chain 'I' and resid 71 through 77 removed outlier: 3.916A pdb=" N LEU I 77 " --> pdb=" O CYS I 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 16 Processing helix chain 'E' and resid 29 through 33 Processing helix chain 'E' and resid 65 through 70 removed outlier: 3.877A pdb=" N ARG E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 78 removed outlier: 3.884A pdb=" N SER E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU E 77 " --> pdb=" O CYS E 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS E 78 " --> pdb=" O CYS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 105 removed outlier: 3.633A pdb=" N LYS E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP E 105 " --> pdb=" O TRP E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 removed outlier: 3.637A pdb=" N VAL E 112 " --> pdb=" O PHE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 132 Processing helix chain 'E' and resid 136 through 141 removed outlier: 3.871A pdb=" N LEU E 140 " --> pdb=" O ASN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 172 removed outlier: 4.506A pdb=" N ARG E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 234 Processing helix chain 'E' and resid 250 through 257 Processing helix chain 'E' and resid 265 through 280 Processing helix chain 'E' and resid 281 through 301 Proline residue: E 287 - end of helix removed outlier: 3.934A pdb=" N ALA E 301 " --> pdb=" O TYR E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 331 Processing helix chain 'E' and resid 332 through 344 Processing helix chain 'E' and resid 345 through 352 removed outlier: 3.587A pdb=" N ILE E 349 " --> pdb=" O THR E 346 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL E 350 " --> pdb=" O GLN E 347 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS E 351 " --> pdb=" O ARG E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 375 Processing helix chain 'E' and resid 385 through 396 Processing helix chain 'E' and resid 403 through 421 Processing helix chain 'E' and resid 422 through 425 Processing helix chain 'E' and resid 426 through 435 removed outlier: 3.786A pdb=" N TYR E 430 " --> pdb=" O SER E 426 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE E 435 " --> pdb=" O THR E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 458 removed outlier: 3.790A pdb=" N ALA E 448 " --> pdb=" O GLN E 444 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU E 452 " --> pdb=" O ALA E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 530 Processing helix chain 'E' and resid 539 through 548 Processing helix chain 'E' and resid 553 through 563 removed outlier: 3.737A pdb=" N LEU E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 582 removed outlier: 4.037A pdb=" N GLU E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 607 Processing helix chain 'G' and resid 5 through 16 removed outlier: 3.572A pdb=" N VAL G 9 " --> pdb=" O ASP G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 32 Processing helix chain 'G' and resid 65 through 70 removed outlier: 3.546A pdb=" N CYS G 69 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG G 70 " --> pdb=" O SER G 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 65 through 70' Processing helix chain 'G' and resid 71 through 78 Processing helix chain 'G' and resid 87 through 106 Processing helix chain 'G' and resid 108 through 113 removed outlier: 3.620A pdb=" N VAL G 112 " --> pdb=" O PHE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 132 removed outlier: 3.790A pdb=" N ASP G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 141 removed outlier: 3.607A pdb=" N LEU G 140 " --> pdb=" O ASN G 136 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU G 141 " --> pdb=" O VAL G 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 136 through 141' Processing helix chain 'G' and resid 143 through 172 removed outlier: 4.395A pdb=" N ARG G 164 " --> pdb=" O ALA G 160 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLU G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 235 Processing helix chain 'G' and resid 250 through 257 Processing helix chain 'G' and resid 265 through 280 Processing helix chain 'G' and resid 281 through 301 Proline residue: G 287 - end of helix Processing helix chain 'G' and resid 320 through 332 removed outlier: 4.174A pdb=" N THR G 324 " --> pdb=" O ASN G 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 342 removed outlier: 4.285A pdb=" N GLU G 342 " --> pdb=" O GLN G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 350 removed outlier: 4.041A pdb=" N ILE G 349 " --> pdb=" O GLU G 345 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL G 350 " --> pdb=" O THR G 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 345 through 350' Processing helix chain 'G' and resid 353 through 375 removed outlier: 4.080A pdb=" N ILE G 357 " --> pdb=" O ASN G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 396 Processing helix chain 'G' and resid 403 through 421 Processing helix chain 'G' and resid 426 through 435 removed outlier: 4.012A pdb=" N TYR G 430 " --> pdb=" O SER G 426 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE G 435 " --> pdb=" O THR G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 460 removed outlier: 3.818A pdb=" N GLN G 449 " --> pdb=" O GLU G 445 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU G 452 " --> pdb=" O ALA G 448 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE G 453 " --> pdb=" O GLN G 449 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 529 removed outlier: 3.782A pdb=" N LYS G 529 " --> pdb=" O GLU G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 548 Processing helix chain 'G' and resid 551 through 563 Processing helix chain 'G' and resid 568 through 582 Processing helix chain 'G' and resid 590 through 607 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 28 through 33 removed outlier: 3.589A pdb=" N VAL K 33 " --> pdb=" O ILE K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 77 removed outlier: 3.815A pdb=" N LEU K 77 " --> pdb=" O CYS K 73 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 12.239A pdb=" N ALA A 35 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N GLY A 47 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE A 37 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 213 removed outlier: 5.799A pdb=" N ASP A 206 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR A 198 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 208 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU A 196 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY A 210 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 194 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 180 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 195 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR A 178 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA A 177 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 21 removed outlier: 3.649A pdb=" N THR C 21 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 36 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE C 37 " --> pdb=" O TRP C 48 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N TRP C 48 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 205 through 213 removed outlier: 3.518A pdb=" N ARG C 205 " --> pdb=" O TYR C 198 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 198 " --> pdb=" O ARG C 205 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 207 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL C 194 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU C 211 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU C 192 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER C 213 " --> pdb=" O ASN C 190 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASN C 190 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP C 180 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 195 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR C 178 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA C 177 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE C 245 " --> pdb=" O ILE C 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 19 through 21 Processing sheet with id=AA6, first strand: chain 'I' and resid 48 through 50 removed outlier: 3.676A pdb=" N VAL I 49 " --> pdb=" O LEU I 58 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU I 58 " --> pdb=" O VAL I 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 19 through 21 removed outlier: 3.934A pdb=" N LYS E 19 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN E 38 " --> pdb=" O LYS E 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 48 through 50 Processing sheet with id=AA9, first strand: chain 'E' and resid 179 through 183 removed outlier: 7.893A pdb=" N ASN E 190 " --> pdb=" O SER E 213 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N SER E 213 " --> pdb=" O ASN E 190 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU E 192 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU E 211 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL E 194 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR E 198 " --> pdb=" O ARG E 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 245 through 246 removed outlier: 6.148A pdb=" N PHE E 245 " --> pdb=" O ILE E 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 20 through 21 removed outlier: 3.563A pdb=" N THR G 21 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP G 36 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 11.866A pdb=" N ALA G 35 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N GLY G 47 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE G 37 " --> pdb=" O VAL G 45 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 176 through 177 removed outlier: 3.642A pdb=" N VAL G 246 " --> pdb=" O ALA G 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 179 through 183 removed outlier: 4.376A pdb=" N ASP G 180 " --> pdb=" O GLY G 193 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY G 193 " --> pdb=" O ASP G 180 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP G 182 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 197 through 199 Processing sheet with id=AB6, first strand: chain 'K' and resid 20 through 21 removed outlier: 3.579A pdb=" N ASP K 36 " --> pdb=" O THR K 21 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 48 through 50 978 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 115 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 142 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 1.77 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: 6282 1.34 - 1.46: 5092 1.46 - 1.58: 12302 1.58 - 1.70: 422 1.70 - 1.82: 146 Bond restraints: 24244 Sorted by residual: bond pdb=" C3' DG R 9 " pdb=" C2' DG R 9 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DG O 27 " pdb=" C2' DG O 27 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DC Q 13 " pdb=" C2' DC Q 13 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT Q 22 " pdb=" C2' DT Q 22 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC R 28 " pdb=" C2' DC R 28 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.97e+00 ... (remaining 24239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 32643 1.92 - 3.85: 922 3.85 - 5.77: 59 5.77 - 7.69: 13 7.69 - 9.62: 3 Bond angle restraints: 33640 Sorted by residual: angle pdb=" C ILE A 419 " pdb=" N ILE A 420 " pdb=" CA ILE A 420 " ideal model delta sigma weight residual 123.16 118.31 4.85 1.06e+00 8.90e-01 2.10e+01 angle pdb=" N3 DT M 4 " pdb=" C4 DT M 4 " pdb=" O4 DT M 4 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT N 24 " pdb=" C4 DT N 24 " pdb=" O4 DT N 24 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT R 46 " pdb=" C4 DT R 46 " pdb=" O4 DT R 46 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT O 50 " pdb=" C4 DT O 50 " pdb=" O4 DT O 50 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 33635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 13056 34.63 - 69.25: 1108 69.25 - 103.88: 41 103.88 - 138.50: 3 138.50 - 173.13: 4 Dihedral angle restraints: 14212 sinusoidal: 7262 harmonic: 6950 Sorted by residual: dihedral pdb=" C4' DG R 9 " pdb=" C3' DG R 9 " pdb=" O3' DG R 9 " pdb=" P DC R 10 " ideal model delta sinusoidal sigma weight residual 220.00 46.87 173.13 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA Q 15 " pdb=" C3' DA Q 15 " pdb=" O3' DA Q 15 " pdb=" P DG Q 16 " ideal model delta sinusoidal sigma weight residual 220.00 54.14 165.86 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DA R 52 " pdb=" C3' DA R 52 " pdb=" O3' DA R 52 " pdb=" P DC R 53 " ideal model delta sinusoidal sigma weight residual 220.00 74.87 145.13 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 14209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2822 0.045 - 0.089: 826 0.089 - 0.134: 160 0.134 - 0.179: 9 0.179 - 0.224: 1 Chirality restraints: 3818 Sorted by residual: chirality pdb=" CA MET E 286 " pdb=" N MET E 286 " pdb=" C MET E 286 " pdb=" CB MET E 286 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU G 557 " pdb=" CB LEU G 557 " pdb=" CD1 LEU G 557 " pdb=" CD2 LEU G 557 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA GLU C 394 " pdb=" N GLU C 394 " pdb=" C GLU C 394 " pdb=" CB GLU C 394 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 3815 not shown) Planarity restraints: 3470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 564 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 565 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 544 " -0.013 2.00e-02 2.50e+03 1.46e-02 5.34e+00 pdb=" CG TRP E 544 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP E 544 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP E 544 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 544 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 544 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 544 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 544 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 544 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP E 544 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO G 437 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO G 438 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO G 438 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 438 " 0.028 5.00e-02 4.00e+02 ... (remaining 3467 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 779 2.69 - 3.25: 23513 3.25 - 3.80: 39763 3.80 - 4.35: 49243 4.35 - 4.90: 74426 Nonbonded interactions: 187724 Sorted by model distance: nonbonded pdb=" O SER G 76 " pdb=" OG SER G 80 " model vdw 2.143 3.040 nonbonded pdb=" OG SER A 87 " pdb=" OD1 ASP A 89 " model vdw 2.177 3.040 nonbonded pdb=" O ASP G 173 " pdb=" NZ LYS G 244 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR E 604 " pdb=" OE1 GLN G 100 " model vdw 2.217 3.040 nonbonded pdb=" OP1 DA Q 29 " pdb=" NZ LYS C 72 " model vdw 2.218 3.120 ... (remaining 187719 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' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'O' selection = chain 'R' } Set up NCS constraints Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'K' } pdb_interpretation.ncs_group { reference = chain 'M' selection = chain 'P' } pdb_interpretation.ncs_group { reference = chain 'N' selection = chain 'Q' } pdb_interpretation.ncs_group { reference = chain 'O' selection = chain 'R' } 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.850 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 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 0.062 24268 Z= 0.317 Angle : 0.685 11.018 33658 Z= 0.503 Chirality : 0.043 0.224 3818 Planarity : 0.004 0.062 3470 Dihedral : 21.429 173.128 9656 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.05 % Allowed : 0.65 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.18), residues: 2328 helix: 0.86 (0.15), residues: 1276 sheet: -1.76 (0.33), residues: 210 loop : -1.45 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 306 TYR 0.020 0.001 TYR G 225 PHE 0.028 0.001 PHE C 524 TRP 0.039 0.002 TRP E 544 HIS 0.006 0.001 HIS E 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.32 (24244) covalent geometry : angle 0.68125 / 0.50 (33640) hydrogen bonds : bond 0.17540 / 19.88 ( 1093) hydrogen bonds : angle 6.66273 / 8.55 ( 3022) metal coordination : bond 0.00966 / 1.16 ( 24) metal coordination : angle 3.09846 / 5.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 202 ASN cc_start: 0.7754 (m110) cc_final: 0.7545 (m-40) REVERT: A 211 LEU cc_start: 0.8910 (tp) cc_final: 0.8611 (tp) REVERT: A 361 VAL cc_start: 0.8897 (t) cc_final: 0.8670 (t) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0527 time to fit residues: 5.1631 Evaluate side-chains 43 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.139 Evaluate side-chains 20 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.024 Fit side-chains REVERT: I 8 GLU cc_start: 0.7050 (tp30) cc_final: 0.5761 (tt0) REVERT: I 17 LEU cc_start: 0.6393 (mt) cc_final: 0.5558 (mp) REVERT: I 32 ASN cc_start: 0.6637 (p0) cc_final: 0.6029 (t0) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0296 time to fit residues: 0.6577 Evaluate side-chains 10 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.024 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0028 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0134 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0099 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 0.0270 chunk 194 optimal weight: 0.1980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.3980 chunk 247 optimal weight: 7.9990 chunk 130 optimal weight: 0.0370 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 GLN A 260 ASN A 302 ASN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.094759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.077981 restraints weight = 20173.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.079409 restraints weight = 13857.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.080460 restraints weight = 10683.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081134 restraints weight = 8840.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.081528 restraints weight = 7769.547| |-----------------------------------------------------------------------------| r_work (final): 0.3392 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.123571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.113270 restraints weight = 2739.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.113265 restraints weight = 2660.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.113265 restraints weight = 2681.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.113265 restraints weight = 2681.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.113265 restraints weight = 2681.379| |-----------------------------------------------------------------------------| r_work (final): 0.4006 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.101371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.096842 restraints weight = 894.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.098067 restraints weight = 448.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.098985 restraints weight = 265.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.099600 restraints weight = 171.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.099987 restraints weight = 119.717| |-----------------------------------------------------------------------------| r_work (final): 0.3670 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.063555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.058075 restraints weight = 9113.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.059257 restraints weight = 3665.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.059933 restraints weight = 2211.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.060356 restraints weight = 1603.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.060604 restraints weight = 1269.253| |-----------------------------------------------------------------------------| r_work (final): 0.3032 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.085225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076726 restraints weight = 10822.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077587 restraints weight = 5400.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.078001 restraints weight = 3430.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.078226 restraints weight = 2708.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.078226 restraints weight = 2413.358| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 1.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 24268 Z= 0.232 Angle : 0.861 14.690 33658 Z= 0.482 Chirality : 0.049 0.331 3818 Planarity : 0.006 0.056 3470 Dihedral : 25.140 144.566 4884 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.86 % Allowed : 4.30 % Favored : 94.85 % Rotamer: Outliers : 1.67 % Allowed : 5.20 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.17), residues: 2328 helix: 0.48 (0.14), residues: 1366 sheet: -0.82 (0.31), residues: 240 loop : -1.63 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 70 TYR 0.021 0.002 TYR G 131 PHE 0.023 0.002 PHE E 124 TRP 0.025 0.002 TRP G 319 HIS 0.007 0.001 HIS I 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.23 (24244) covalent geometry : angle 0.82428 / 0.48 (33640) hydrogen bonds : bond 0.13020 / 14.75 ( 1093) hydrogen bonds : angle 5.37707 / 7.21 ( 3022) metal coordination : bond 0.02676 / 3.28 ( 24) metal coordination : angle 10.83484 / 19.55 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8666 (tt0) cc_final: 0.8303 (tp30) REVERT: A 360 MET cc_start: 0.8712 (mtm) cc_final: 0.8290 (mtm) REVERT: A 392 VAL cc_start: 0.8388 (t) cc_final: 0.8185 (p) REVERT: A 422 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7951 (pp20) REVERT: A 425 LEU cc_start: 0.8539 (mt) cc_final: 0.8092 (mt) outliers start: 9 outliers final: 2 residues processed: 80 average time/residue: 0.0616 time to fit residues: 6.3774 Evaluate side-chains 42 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.169 Evaluate side-chains 30 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.025 Fit side-chains REVERT: K 34 LEU cc_start: 0.7609 (tp) cc_final: 0.7100 (tp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0834 time to fit residues: 2.6149 Evaluate side-chains 12 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.027 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0136 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0167 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 136 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 242 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 49 optimal weight: 0.0040 chunk 177 optimal weight: 1.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN A 260 ASN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 ASN K 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.094554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.077946 restraints weight = 21567.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079448 restraints weight = 14676.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.080427 restraints weight = 11139.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081140 restraints weight = 9225.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081490 restraints weight = 8065.134| |-----------------------------------------------------------------------------| r_work (final): 0.3390 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.126446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.112619 restraints weight = 3027.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.113983 restraints weight = 2501.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.114360 restraints weight = 2207.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.115599 restraints weight = 2062.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.116281 restraints weight = 1921.485| |-----------------------------------------------------------------------------| r_work (final): 0.4076 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.096670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.094638 restraints weight = 799.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.095526 restraints weight = 322.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.095950 restraints weight = 154.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.096260 restraints weight = 84.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.096427 restraints weight = 45.946| |-----------------------------------------------------------------------------| r_work (final): 0.3639 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.064165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.058699 restraints weight = 9544.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.059888 restraints weight = 3888.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.060614 restraints weight = 2307.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.061030 restraints weight = 1630.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.061212 restraints weight = 1295.082| |-----------------------------------------------------------------------------| r_work (final): 0.3051 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.086213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.077509 restraints weight = 10648.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.078299 restraints weight = 5436.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.078699 restraints weight = 3542.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.079069 restraints weight = 2816.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.079069 restraints weight = 2366.514| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 1.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24268 Z= 0.173 Angle : 0.772 17.830 33658 Z= 0.430 Chirality : 0.045 0.203 3818 Planarity : 0.006 0.197 3470 Dihedral : 25.159 141.672 4884 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.19 % Allowed : 4.74 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.17), residues: 2328 helix: 0.53 (0.14), residues: 1352 sheet: -0.76 (0.32), residues: 240 loop : -1.60 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 63 TYR 0.019 0.001 TYR C 604 PHE 0.029 0.002 PHE A 575 TRP 0.020 0.002 TRP K 48 HIS 0.003 0.000 HIS I 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (24244) covalent geometry : angle 0.72876 / 0.43 (33640) hydrogen bonds : bond 0.10136 / 11.48 ( 1093) hydrogen bonds : angle 5.00431 / 6.72 ( 3022) metal coordination : bond 0.02582 / 3.21 ( 24) metal coordination : angle 11.01281 / 20.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6131 (mp0) cc_final: 0.5916 (mp0) REVERT: A 96 GLU cc_start: 0.8599 (tt0) cc_final: 0.8342 (tp30) REVERT: A 360 MET cc_start: 0.8689 (mtm) cc_final: 0.8236 (mtm) REVERT: A 369 ARG cc_start: 0.6280 (ttt180) cc_final: 0.5884 (tpm170) REVERT: A 418 ARG cc_start: 0.7845 (pmt-80) cc_final: 0.7394 (ptm-80) REVERT: A 421 TRP cc_start: 0.7871 (t60) cc_final: 0.7629 (t60) outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.0633 time to fit residues: 6.2121 Evaluate side-chains 45 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.104 Evaluate side-chains 20 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.015 Fit side-chains REVERT: K 34 LEU cc_start: 0.7405 (tp) cc_final: 0.6764 (tp) REVERT: K 68 LEU cc_start: 0.8192 (mm) cc_final: 0.7902 (mm) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0822 time to fit residues: 1.7172 Evaluate side-chains 13 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.024 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0028 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.024 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0217 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0156 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 73 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 175 optimal weight: 0.0170 chunk 8 optimal weight: 20.0000 chunk 199 optimal weight: 1.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.095794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079401 restraints weight = 20889.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.080873 restraints weight = 14321.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.081849 restraints weight = 10958.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.082503 restraints weight = 9098.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.082917 restraints weight = 8026.084| |-----------------------------------------------------------------------------| r_work (final): 0.3420 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.123922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.112719 restraints weight = 3226.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.113741 restraints weight = 2568.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.114969 restraints weight = 2190.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.115234 restraints weight = 1882.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.116487 restraints weight = 1764.060| |-----------------------------------------------------------------------------| r_work (final): 0.4067 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.126753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.122096 restraints weight = 776.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.122876 restraints weight = 565.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.123408 restraints weight = 423.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.124067 restraints weight = 334.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.124418 restraints weight = 250.669| |-----------------------------------------------------------------------------| r_work (final): 0.4155 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.064830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.059498 restraints weight = 9682.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.060666 restraints weight = 3911.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.061299 restraints weight = 2342.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.061673 restraints weight = 1689.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.061929 restraints weight = 1376.105| |-----------------------------------------------------------------------------| r_work (final): 0.3062 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.086205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077732 restraints weight = 10852.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.078597 restraints weight = 5071.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.079124 restraints weight = 3246.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.079293 restraints weight = 2453.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.079383 restraints weight = 2176.192| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 1.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24268 Z= 0.162 Angle : 0.718 12.323 33658 Z= 0.408 Chirality : 0.043 0.175 3818 Planarity : 0.005 0.084 3470 Dihedral : 25.205 141.940 4884 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.46 % Allowed : 3.16 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.17), residues: 2328 helix: 0.54 (0.14), residues: 1388 sheet: -0.61 (0.34), residues: 220 loop : -1.64 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 63 TYR 0.015 0.002 TYR C 604 PHE 0.041 0.002 PHE G 526 TRP 0.025 0.001 TRP G 421 HIS 0.002 0.000 HIS G 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (24244) covalent geometry : angle 0.69420 / 0.41 (33640) hydrogen bonds : bond 0.09053 / 10.24 ( 1093) hydrogen bonds : angle 4.83294 / 6.52 ( 3022) metal coordination : bond 0.02095 / 2.51 ( 24) metal coordination : angle 8.00658 / 14.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6266 (mp0) cc_final: 0.5985 (mp0) REVERT: A 96 GLU cc_start: 0.8496 (tt0) cc_final: 0.8289 (tp30) REVERT: A 360 MET cc_start: 0.8665 (mtm) cc_final: 0.8231 (mtm) REVERT: A 418 ARG cc_start: 0.8023 (pmt-80) cc_final: 0.7685 (ptm-80) outliers start: 2 outliers final: 0 residues processed: 71 average time/residue: 0.0586 time to fit residues: 5.3172 Evaluate side-chains 42 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.155 Evaluate side-chains 18 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.021 Fit side-chains REVERT: K 68 LEU cc_start: 0.8069 (mm) cc_final: 0.7852 (mm) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.0794 time to fit residues: 1.4992 Evaluate side-chains 12 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0124 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0167 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 251 optimal weight: 0.5980 chunk 188 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 chunk 181 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 135 optimal weight: 0.0570 chunk 198 optimal weight: 0.0060 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.096319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.079707 restraints weight = 21063.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081240 restraints weight = 14478.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.082281 restraints weight = 10989.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082964 restraints weight = 9079.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.083337 restraints weight = 7974.722| |-----------------------------------------------------------------------------| r_work (final): 0.3433 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.122063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.114004 restraints weight = 2539.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.114996 restraints weight = 1941.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.116027 restraints weight = 1557.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.116732 restraints weight = 1281.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.117197 restraints weight = 1085.339| |-----------------------------------------------------------------------------| r_work (final): 0.4061 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.097958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.094724 restraints weight = 914.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.095821 restraints weight = 427.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.096600 restraints weight = 230.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.097046 restraints weight = 135.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.097236 restraints weight = 83.018| |-----------------------------------------------------------------------------| r_work (final): 0.3682 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.065624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.060288 restraints weight = 9401.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.061385 restraints weight = 3907.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.062066 restraints weight = 2359.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.062320 restraints weight = 1686.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.062639 restraints weight = 1452.500| |-----------------------------------------------------------------------------| r_work (final): 0.3101 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.086844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.078505 restraints weight = 10679.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079368 restraints weight = 5136.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.079842 restraints weight = 3181.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.080144 restraints weight = 2420.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080158 restraints weight = 2042.273| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 1.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24268 Z= 0.147 Angle : 0.666 9.877 33658 Z= 0.383 Chirality : 0.042 0.182 3818 Planarity : 0.004 0.041 3470 Dihedral : 25.209 142.637 4884 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2328 helix: 0.57 (0.14), residues: 1404 sheet: -0.54 (0.35), residues: 220 loop : -1.49 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 70 TYR 0.014 0.001 TYR G 604 PHE 0.015 0.002 PHE K 50 TRP 0.020 0.001 TRP I 48 HIS 0.004 0.000 HIS E 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 (24244) covalent geometry : angle 0.65120 / 0.38 (33640) hydrogen bonds : bond 0.08230 / 9.25 ( 1093) hydrogen bonds : angle 4.65550 / 6.30 ( 3022) metal coordination : bond 0.01525 / 1.86 ( 24) metal coordination : angle 6.14275 / 11.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6354 (mp0) cc_final: 0.6095 (mp0) REVERT: A 120 MET cc_start: 0.8213 (ttm) cc_final: 0.7662 (mmt) REVERT: A 360 MET cc_start: 0.8691 (mtm) cc_final: 0.8259 (mtm) REVERT: A 418 ARG cc_start: 0.8017 (pmt-80) cc_final: 0.7410 (ptm-80) REVERT: A 425 LEU cc_start: 0.8914 (mt) cc_final: 0.8367 (mt) REVERT: A 442 MET cc_start: 0.6629 (pmm) cc_final: 0.6274 (tpp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0724 time to fit residues: 6.2202 Evaluate side-chains 38 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.174 Evaluate side-chains 14 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.025 Fit side-chains REVERT: K 68 LEU cc_start: 0.8141 (mm) cc_final: 0.7850 (mm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0483 time to fit residues: 0.7400 Evaluate side-chains 12 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0134 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0200 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 73 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 199 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 0.0970 chunk 117 optimal weight: 0.0000 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.096379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.079551 restraints weight = 21871.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081118 restraints weight = 15086.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.082169 restraints weight = 11441.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082808 restraints weight = 9402.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.083298 restraints weight = 8272.880| |-----------------------------------------------------------------------------| r_work (final): 0.3432 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.122833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.112606 restraints weight = 3012.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.113280 restraints weight = 2546.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.113872 restraints weight = 2209.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.114189 restraints weight = 1973.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.114232 restraints weight = 1835.728| |-----------------------------------------------------------------------------| r_work (final): 0.3991 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.100067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.097443 restraints weight = 719.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.098361 restraints weight = 328.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.098992 restraints weight = 166.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.099378 restraints weight = 91.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.099461 restraints weight = 54.492| |-----------------------------------------------------------------------------| r_work (final): 0.3753 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.063452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.060371 restraints weight = 10101.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.061062 restraints weight = 3919.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.061514 restraints weight = 2151.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.061752 restraints weight = 1381.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.061905 restraints weight = 1030.637| |-----------------------------------------------------------------------------| r_work (final): 0.3142 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.087017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.078845 restraints weight = 10622.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.079719 restraints weight = 4973.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.080193 restraints weight = 3065.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080394 restraints weight = 2304.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.080475 restraints weight = 2015.617| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 1.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24268 Z= 0.143 Angle : 0.660 9.192 33658 Z= 0.380 Chirality : 0.042 0.218 3818 Planarity : 0.004 0.042 3470 Dihedral : 25.189 143.103 4884 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.17), residues: 2328 helix: 0.67 (0.14), residues: 1380 sheet: -0.51 (0.38), residues: 208 loop : -1.23 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 52 TYR 0.012 0.001 TYR G 604 PHE 0.025 0.002 PHE A 526 TRP 0.011 0.001 TRP K 48 HIS 0.003 0.000 HIS K 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.14 (24244) covalent geometry : angle 0.64421 / 0.38 (33640) hydrogen bonds : bond 0.08039 / 9.09 ( 1093) hydrogen bonds : angle 4.58726 / 6.14 ( 3022) metal coordination : bond 0.02049 / 2.38 ( 24) metal coordination : angle 6.27030 / 11.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.8641 (mtm) cc_final: 0.8193 (mtm) REVERT: A 372 LYS cc_start: 0.7198 (mmmt) cc_final: 0.6857 (mmmt) REVERT: A 425 LEU cc_start: 0.8901 (mt) cc_final: 0.8363 (mt) REVERT: A 442 MET cc_start: 0.6839 (pmm) cc_final: 0.6357 (tpp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0601 time to fit residues: 5.5235 Evaluate side-chains 41 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.172 Evaluate side-chains 14 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.025 Fit side-chains REVERT: K 4 MET cc_start: 0.5756 (tmm) cc_final: 0.5469 (tmm) REVERT: K 58 LEU cc_start: 0.5493 (tp) cc_final: 0.4634 (mp) REVERT: K 68 LEU cc_start: 0.8237 (mm) cc_final: 0.7994 (mm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0404 time to fit residues: 0.6415 Evaluate side-chains 12 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0132 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0163 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 57 optimal weight: 1.9990 chunk 123 optimal weight: 0.0050 chunk 225 optimal weight: 20.0000 chunk 216 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.096760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.080154 restraints weight = 21980.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.081717 restraints weight = 15258.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.082667 restraints weight = 11661.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.083392 restraints weight = 9754.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.083894 restraints weight = 8552.627| |-----------------------------------------------------------------------------| r_work (final): 0.3439 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.122739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.113104 restraints weight = 3086.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.114610 restraints weight = 2111.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.115721 restraints weight = 1597.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.116453 restraints weight = 1259.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.117059 restraints weight = 1047.181| |-----------------------------------------------------------------------------| r_work (final): 0.4079 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.100145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.094652 restraints weight = 819.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.096105 restraints weight = 455.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.097297 restraints weight = 281.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.097812 restraints weight = 183.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.098333 restraints weight = 137.495| |-----------------------------------------------------------------------------| r_work (final): 0.3725 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.063604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.060634 restraints weight = 10685.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.061312 restraints weight = 4117.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.061706 restraints weight = 2244.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.061955 restraints weight = 1501.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.062008 restraints weight = 1099.517| |-----------------------------------------------------------------------------| r_work (final): 0.3100 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.070054 restraints weight = 10139.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.071250 restraints weight = 4706.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.071847 restraints weight = 3243.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.072386 restraints weight = 2731.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.072574 restraints weight = 2460.185| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 1.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24268 Z= 0.143 Angle : 0.661 7.951 33658 Z= 0.379 Chirality : 0.042 0.215 3818 Planarity : 0.004 0.041 3470 Dihedral : 25.161 143.243 4884 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.17), residues: 2328 helix: 0.77 (0.14), residues: 1376 sheet: -0.35 (0.39), residues: 200 loop : -1.33 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 52 TYR 0.015 0.001 TYR C 225 PHE 0.033 0.002 PHE C 575 TRP 0.010 0.001 TRP K 48 HIS 0.002 0.000 HIS G 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (24244) covalent geometry : angle 0.64797 / 0.38 (33640) hydrogen bonds : bond 0.07802 / 8.82 ( 1093) hydrogen bonds : angle 4.63775 / 6.27 ( 3022) metal coordination : bond 0.01470 / 1.74 ( 24) metal coordination : angle 5.59120 / 10.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8345 (ttm) cc_final: 0.7590 (mmt) REVERT: A 360 MET cc_start: 0.8588 (mtm) cc_final: 0.8203 (mtm) REVERT: A 372 LYS cc_start: 0.7251 (mmmt) cc_final: 0.6942 (mmmt) REVERT: A 425 LEU cc_start: 0.8923 (mt) cc_final: 0.8366 (mt) REVERT: A 442 MET cc_start: 0.6856 (pmm) cc_final: 0.6351 (tpp) REVERT: A 595 ASP cc_start: 0.8877 (m-30) cc_final: 0.8561 (m-30) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0490 time to fit residues: 4.3177 Evaluate side-chains 42 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.146 Evaluate side-chains 13 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.024 Fit side-chains REVERT: K 58 LEU cc_start: 0.5648 (tp) cc_final: 0.4701 (mp) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0283 time to fit residues: 0.4263 Evaluate side-chains 11 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.026 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0030 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0093 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0177 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 229 optimal weight: 0.0030 chunk 145 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 118 optimal weight: 0.0770 chunk 5 optimal weight: 20.0000 overall best weight: 0.4748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.097787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081507 restraints weight = 21497.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.082913 restraints weight = 15356.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.083871 restraints weight = 12037.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.084430 restraints weight = 10114.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.084883 restraints weight = 9041.008| |-----------------------------------------------------------------------------| r_work (final): 0.3455 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.124049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.113551 restraints weight = 3133.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.115043 restraints weight = 2276.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.116396 restraints weight = 1776.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.117002 restraints weight = 1403.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.117728 restraints weight = 1209.724| |-----------------------------------------------------------------------------| r_work (final): 0.4068 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.099543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.097356 restraints weight = 700.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.098420 restraints weight = 291.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.098888 restraints weight = 137.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.099162 restraints weight = 68.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.099337 restraints weight = 36.723| |-----------------------------------------------------------------------------| r_work (final): 0.3757 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.064286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.061354 restraints weight = 10483.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.062025 restraints weight = 3968.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.062449 restraints weight = 2141.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.062659 restraints weight = 1370.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.062659 restraints weight = 1039.184| |-----------------------------------------------------------------------------| r_work (final): 0.3153 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.088876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.069910 restraints weight = 10386.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.071185 restraints weight = 4816.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.071823 restraints weight = 3324.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.072186 restraints weight = 2764.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.072276 restraints weight = 2541.503| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 1.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24268 Z= 0.146 Angle : 0.661 7.123 33658 Z= 0.380 Chirality : 0.041 0.222 3818 Planarity : 0.004 0.041 3470 Dihedral : 25.118 143.474 4884 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.18), residues: 2328 helix: 0.81 (0.14), residues: 1380 sheet: -0.54 (0.40), residues: 200 loop : -1.29 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 573 TYR 0.013 0.001 TYR I 18 PHE 0.030 0.002 PHE E 433 TRP 0.012 0.001 TRP A 421 HIS 0.003 0.001 HIS E 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (24244) covalent geometry : angle 0.65094 / 0.38 (33640) hydrogen bonds : bond 0.07598 / 8.55 ( 1093) hydrogen bonds : angle 4.61698 / 6.21 ( 3022) metal coordination : bond 0.01393 / 1.65 ( 24) metal coordination : angle 4.95320 / 9.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7567 (mmmm) cc_final: 0.6749 (mttt) REVERT: A 360 MET cc_start: 0.8725 (mtm) cc_final: 0.8229 (mtm) REVERT: A 372 LYS cc_start: 0.7239 (mmmt) cc_final: 0.6851 (mmmt) REVERT: A 425 LEU cc_start: 0.8894 (mt) cc_final: 0.8434 (mt) REVERT: A 442 MET cc_start: 0.6770 (pmm) cc_final: 0.6205 (tpp) REVERT: A 595 ASP cc_start: 0.8848 (m-30) cc_final: 0.8512 (m-30) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0561 time to fit residues: 5.1451 Evaluate side-chains 45 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.159 Evaluate side-chains 13 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.025 Fit side-chains REVERT: K 58 LEU cc_start: 0.6089 (tp) cc_final: 0.5107 (mp) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0380 time to fit residues: 0.5699 Evaluate side-chains 12 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0018 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0140 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.008 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0158 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 237 optimal weight: 4.9990 chunk 230 optimal weight: 0.0060 chunk 47 optimal weight: 0.1980 chunk 123 optimal weight: 10.0000 chunk 228 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 81 optimal weight: 0.0870 chunk 231 optimal weight: 4.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 ASN A 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.098616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.082162 restraints weight = 21572.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.083349 restraints weight = 16813.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.084039 restraints weight = 13309.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.084167 restraints weight = 11445.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.084374 restraints weight = 11292.999| |-----------------------------------------------------------------------------| r_work (final): 0.3449 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.123606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.112977 restraints weight = 3120.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.114482 restraints weight = 2147.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.115601 restraints weight = 1639.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.116576 restraints weight = 1335.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.117126 restraints weight = 1107.078| |-----------------------------------------------------------------------------| r_work (final): 0.4106 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.099454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.097047 restraints weight = 754.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.098123 restraints weight = 316.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.098612 restraints weight = 149.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.098993 restraints weight = 84.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.099110 restraints weight = 43.441| |-----------------------------------------------------------------------------| r_work (final): 0.3762 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.064560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.061717 restraints weight = 10132.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.062346 restraints weight = 4020.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.062765 restraints weight = 2124.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.062954 restraints weight = 1323.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.063000 restraints weight = 1025.634| |-----------------------------------------------------------------------------| r_work (final): 0.3161 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.089011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.070330 restraints weight = 10181.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.071540 restraints weight = 4728.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.072347 restraints weight = 3263.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.072642 restraints weight = 2666.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.072891 restraints weight = 2434.779| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 1.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24268 Z= 0.140 Angle : 0.658 7.919 33658 Z= 0.380 Chirality : 0.042 0.181 3818 Planarity : 0.004 0.041 3470 Dihedral : 25.079 144.463 4884 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.18), residues: 2328 helix: 0.81 (0.14), residues: 1380 sheet: -0.70 (0.39), residues: 200 loop : -1.19 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 149 TYR 0.012 0.001 TYR C 225 PHE 0.028 0.002 PHE G 433 TRP 0.011 0.001 TRP A 421 HIS 0.002 0.000 HIS I 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (24244) covalent geometry : angle 0.64862 / 0.38 (33640) hydrogen bonds : bond 0.07481 / 8.46 ( 1093) hydrogen bonds : angle 4.67019 / 6.31 ( 3022) metal coordination : bond 0.01270 / 1.51 ( 24) metal coordination : angle 4.75827 / 8.79 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7597 (mmmm) cc_final: 0.6892 (mtmt) REVERT: A 179 ILE cc_start: 0.7989 (mm) cc_final: 0.7746 (pt) REVERT: A 360 MET cc_start: 0.8760 (mtm) cc_final: 0.8257 (mtm) REVERT: A 425 LEU cc_start: 0.8935 (mt) cc_final: 0.8453 (mt) REVERT: A 442 MET cc_start: 0.6989 (pmm) cc_final: 0.6446 (tpp) REVERT: A 595 ASP cc_start: 0.8913 (m-30) cc_final: 0.8584 (m-30) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0520 time to fit residues: 4.9352 Evaluate side-chains 48 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.183 Evaluate side-chains 14 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.015 Fit side-chains REVERT: K 58 LEU cc_start: 0.6401 (tp) cc_final: 0.5269 (mp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0544 time to fit residues: 0.8281 Evaluate side-chains 11 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.025 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0019 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0161 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0161 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 245 optimal weight: 0.8980 chunk 193 optimal weight: 0.2980 chunk 26 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 81 optimal weight: 0.4980 chunk 231 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.098331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.081813 restraints weight = 22257.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.083025 restraints weight = 16831.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.083561 restraints weight = 12674.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.083620 restraints weight = 12018.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.083796 restraints weight = 11312.811| |-----------------------------------------------------------------------------| r_work (final): 0.3436 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.122642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.114044 restraints weight = 2569.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.114540 restraints weight = 2263.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.114540 restraints weight = 2012.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.114539 restraints weight = 2012.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.114539 restraints weight = 2012.494| |-----------------------------------------------------------------------------| r_work (final): 0.4013 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.099832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.097323 restraints weight = 749.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.098395 restraints weight = 322.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.098963 restraints weight = 155.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.099231 restraints weight = 80.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.099501 restraints weight = 50.878| |-----------------------------------------------------------------------------| r_work (final): 0.3734 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.064335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.061522 restraints weight = 10088.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.062145 restraints weight = 3885.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.062548 restraints weight = 2104.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.062779 restraints weight = 1338.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.062886 restraints weight = 999.359| |-----------------------------------------------------------------------------| r_work (final): 0.3164 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.088745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.072148 restraints weight = 10208.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.072558 restraints weight = 6386.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072800 restraints weight = 4758.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072901 restraints weight = 3793.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.073167 restraints weight = 3674.436| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 1.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24268 Z= 0.144 Angle : 0.663 7.710 33658 Z= 0.382 Chirality : 0.041 0.181 3818 Planarity : 0.004 0.041 3470 Dihedral : 25.036 143.820 4884 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.18), residues: 2328 helix: 0.84 (0.14), residues: 1380 sheet: -0.91 (0.39), residues: 200 loop : -1.16 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 573 TYR 0.011 0.001 TYR E 604 PHE 0.026 0.002 PHE E 433 TRP 0.010 0.001 TRP A 421 HIS 0.003 0.001 HIS E 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (24244) covalent geometry : angle 0.65566 / 0.38 (33640) hydrogen bonds : bond 0.07475 / 8.47 ( 1093) hydrogen bonds : angle 4.66123 / 6.19 ( 3022) metal coordination : bond 0.01250 / 1.48 ( 24) metal coordination : angle 4.41718 / 8.15 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7471 (mmmm) cc_final: 0.6651 (mtmt) REVERT: A 120 MET cc_start: 0.8346 (ttm) cc_final: 0.7528 (mmt) REVERT: A 202 ASN cc_start: 0.8548 (m-40) cc_final: 0.7531 (t0) REVERT: A 360 MET cc_start: 0.8664 (mtm) cc_final: 0.8202 (mtm) REVERT: A 372 LYS cc_start: 0.7044 (mmmt) cc_final: 0.6562 (mmmt) REVERT: A 425 LEU cc_start: 0.8921 (mt) cc_final: 0.8458 (mt) REVERT: A 442 MET cc_start: 0.7018 (pmm) cc_final: 0.6442 (tpp) REVERT: A 595 ASP cc_start: 0.8804 (m-30) cc_final: 0.8491 (m-30) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0563 time to fit residues: 5.2505 Evaluate side-chains 50 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.190 Evaluate side-chains 13 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.028 Fit side-chains REVERT: K 24 HIS cc_start: -0.1975 (t-90) cc_final: -0.2193 (t-90) REVERT: K 58 LEU cc_start: 0.6155 (tp) cc_final: 0.5119 (mp) REVERT: K 68 LEU cc_start: 0.8332 (mm) cc_final: 0.8101 (mm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0420 time to fit residues: 0.6240 Evaluate side-chains 11 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.024 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0029 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0132 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0161 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 80 optimal weight: 0.0020 chunk 206 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 127 optimal weight: 0.6980 chunk 223 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.098477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.082037 restraints weight = 22492.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.083187 restraints weight = 17712.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.083835 restraints weight = 14314.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.084519 restraints weight = 11953.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.084497 restraints weight = 12221.535| |-----------------------------------------------------------------------------| r_work (final): 0.3448 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.122681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.113790 restraints weight = 2385.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.114593 restraints weight = 1935.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.115590 restraints weight = 1645.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.116374 restraints weight = 1401.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.116934 restraints weight = 1210.290| |-----------------------------------------------------------------------------| r_work (final): 0.4061 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.102410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.096901 restraints weight = 785.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.098552 restraints weight = 452.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099628 restraints weight = 280.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.100330 restraints weight = 183.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.100752 restraints weight = 126.255| |-----------------------------------------------------------------------------| r_work (final): 0.3769 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.064823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.062043 restraints weight = 10540.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.062687 restraints weight = 4017.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.063025 restraints weight = 2109.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063231 restraints weight = 1409.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.063391 restraints weight = 1076.822| |-----------------------------------------------------------------------------| r_work (final): 0.3176 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.089051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.070272 restraints weight = 10610.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.071473 restraints weight = 4904.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.072027 restraints weight = 3412.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.072650 restraints weight = 2886.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072782 restraints weight = 2558.395| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 1.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24268 Z= 0.137 Angle : 0.643 6.965 33658 Z= 0.372 Chirality : 0.041 0.187 3818 Planarity : 0.004 0.041 3470 Dihedral : 24.991 143.197 4884 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.18), residues: 2328 helix: 0.91 (0.14), residues: 1380 sheet: -1.05 (0.38), residues: 200 loop : -1.09 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 205 TYR 0.017 0.001 TYR K 18 PHE 0.022 0.002 PHE E 433 TRP 0.016 0.001 TRP C 319 HIS 0.003 0.000 HIS E 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (24244) covalent geometry : angle 0.63532 / 0.37 (33640) hydrogen bonds : bond 0.07259 / 8.26 ( 1093) hydrogen bonds : angle 4.67879 / 6.25 ( 3022) metal coordination : bond 0.01194 / 1.41 ( 24) metal coordination : angle 4.19337 / 7.72 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2065.58 seconds wall clock time: 37 minutes 13.16 seconds (2233.16 seconds total)