Starting phenix.real_space_refine on Fri Aug 7 17:37:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8edg_28034/08_2026/8edg_28034.cif Found real_map, /net/cci-nas-00/data/ceres_data/8edg_28034/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8edg_28034/08_2026/8edg_28034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8edg_28034/08_2026/8edg_28034.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8edg_28034/08_2026/8edg_28034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8edg_28034/08_2026/8edg_28034.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8edg_28034/08_2026/8edg_28034.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8edg_28034/08_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 5.88, per 1000 atoms: 0.25 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: 2.00 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 2.43 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: 2.71 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: 32642 1.92 - 3.85: 923 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: 1.620 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 26.550 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.660 ------------------------------------------------------------------------------- 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 : 0.687 11.018 33658 Z= 0.505 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 0.68348 / 0.50 (33640) hydrogen bonds : bond 0.17540 / 19.92 ( 1093) hydrogen bonds : angle 6.66273 / 8.56 ( 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 : 0.178 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: 0.0576 time to fit residues: 5.6480 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 : 0.173 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 : 0.016 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: 0.0466 time to fit residues: 1.0241 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 : 0.029 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 : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0057 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 : 0.003 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: 0.0153 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 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 : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0108 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 : 0.017 ------------------------------------------------------------------------------- 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: 20.0000 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 = 0.3661 r_free = 0.3661 target = 0.094655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.077815 restraints weight = 20175.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079283 restraints weight = 13922.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.080300 restraints weight = 10687.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.080896 restraints weight = 8841.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081387 restraints weight = 7844.126| |-----------------------------------------------------------------------------| r_work (final): 0.3390 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.123672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.113173 restraints weight = 2750.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.113172 restraints weight = 2733.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.113172 restraints weight = 2733.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.113172 restraints weight = 2733.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.113172 restraints weight = 2733.113| |-----------------------------------------------------------------------------| r_work (final): 0.4003 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.101081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.096830 restraints weight = 904.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.097997 restraints weight = 425.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.098882 restraints weight = 252.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.099428 restraints weight = 164.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.099766 restraints weight = 115.367| |-----------------------------------------------------------------------------| r_work (final): 0.3666 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.063511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.057924 restraints weight = 9128.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.059077 restraints weight = 3748.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.059810 restraints weight = 2286.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.060122 restraints weight = 1631.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.060432 restraints weight = 1378.940| |-----------------------------------------------------------------------------| r_work (final): 0.3029 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.085221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076690 restraints weight = 11310.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077543 restraints weight = 5374.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.078095 restraints weight = 3442.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.078095 restraints weight = 2562.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.078095 restraints weight = 2562.292| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 1.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 24268 Z= 0.228 Angle : 0.854 13.337 33658 Z= 0.476 Chirality : 0.049 0.230 3818 Planarity : 0.006 0.052 3470 Dihedral : 25.098 144.532 4884 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.86 % Allowed : 4.30 % Favored : 94.85 % Rotamer: Outliers : 1.49 % Allowed : 5.20 % Favored : 93.31 % 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: -0.54 (0.17), residues: 2328 helix: 0.43 (0.14), residues: 1378 sheet: -0.79 (0.31), residues: 240 loop : -1.63 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 70 TYR 0.020 0.002 TYR G 131 PHE 0.024 0.002 PHE C 124 TRP 0.028 0.002 TRP A 319 HIS 0.007 0.001 HIS K 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.23 (24244) covalent geometry : angle 0.81742 / 0.47 (33640) hydrogen bonds : bond 0.13285 / 15.02 ( 1093) hydrogen bonds : angle 5.41708 / 7.29 ( 3022) metal coordination : bond 0.02955 / 3.49 ( 24) metal coordination : angle 10.66779 / 19.36 ( 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 79 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8673 (tt0) cc_final: 0.8301 (tp30) REVERT: A 360 MET cc_start: 0.8721 (mtm) cc_final: 0.8318 (mtm) REVERT: A 392 VAL cc_start: 0.8382 (t) cc_final: 0.8181 (p) REVERT: A 422 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7965 (pp20) REVERT: A 425 LEU cc_start: 0.8397 (mt) cc_final: 0.7951 (mt) outliers start: 8 outliers final: 2 residues processed: 78 average time/residue: 0.0691 time to fit residues: 6.9639 Evaluate side-chains 43 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.180 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: 0.7592 (tp) cc_final: 0.7186 (tp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0974 time to fit residues: 3.0438 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 : 0.023 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0036 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: 0.0152 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 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 : 0.015 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0195 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 136 optimal weight: 3.9990 chunk 160 optimal weight: 0.2980 chunk 242 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 249 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 177 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 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 = 0.3662 r_free = 0.3662 target = 0.094929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.077977 restraints weight = 20972.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079444 restraints weight = 14566.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.080455 restraints weight = 11136.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081140 restraints weight = 9214.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081450 restraints weight = 8100.645| |-----------------------------------------------------------------------------| r_work (final): 0.3393 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.126788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.113103 restraints weight = 2916.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.114464 restraints weight = 2341.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.115856 restraints weight = 2012.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.116242 restraints weight = 1810.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.117297 restraints weight = 1677.880| |-----------------------------------------------------------------------------| r_work (final): 0.4092 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.099761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.096704 restraints weight = 873.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.097790 restraints weight = 387.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.098477 restraints weight = 198.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.098890 restraints weight = 113.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.099096 restraints weight = 70.229| |-----------------------------------------------------------------------------| r_work (final): 0.3703 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.064389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.058919 restraints weight = 9556.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.060126 restraints weight = 3850.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.060857 restraints weight = 2282.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.061280 restraints weight = 1611.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.061549 restraints weight = 1263.390| |-----------------------------------------------------------------------------| r_work (final): 0.3072 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.086145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.077317 restraints weight = 10580.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.078141 restraints weight = 5321.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.078674 restraints weight = 3425.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.078985 restraints weight = 2623.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.079030 restraints weight = 2221.027| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 1.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24268 Z= 0.176 Angle : 0.781 17.447 33658 Z= 0.433 Chirality : 0.045 0.207 3818 Planarity : 0.006 0.149 3470 Dihedral : 25.141 141.234 4884 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.19 % Allowed : 4.55 % Favored : 95.26 % 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: -0.52 (0.17), residues: 2328 helix: 0.49 (0.14), residues: 1352 sheet: -0.81 (0.32), residues: 240 loop : -1.65 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 189 TYR 0.013 0.001 TYR G 604 PHE 0.028 0.002 PHE C 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 0.00332 / 0.18 (24244) covalent geometry : angle 0.73814 / 0.43 (33640) hydrogen bonds : bond 0.10496 / 11.89 ( 1093) hydrogen bonds : angle 5.00877 / 6.72 ( 3022) metal coordination : bond 0.02101 / 2.65 ( 24) metal coordination : angle 11.01625 / 20.07 ( 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 : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8570 (tt0) cc_final: 0.8304 (tp30) REVERT: A 360 MET cc_start: 0.8693 (mtm) cc_final: 0.8247 (mtm) REVERT: A 369 ARG cc_start: 0.6445 (ttt180) cc_final: 0.6074 (tpm170) REVERT: A 418 ARG cc_start: 0.7877 (pmt-80) cc_final: 0.7376 (ptm-80) REVERT: A 421 TRP cc_start: 0.7857 (t60) cc_final: 0.7614 (t60) outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.0833 time to fit residues: 8.0916 Evaluate side-chains 46 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.151 Evaluate side-chains 21 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.025 Fit side-chains REVERT: K 34 LEU cc_start: 0.7367 (tp) cc_final: 0.6587 (tp) REVERT: K 68 LEU cc_start: 0.8227 (mm) cc_final: 0.7968 (mm) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0949 time to fit residues: 2.0888 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 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 : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0147 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 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 : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0222 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 : 0.017 ------------------------------------------------------------------------------- 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: 10.0000 chunk 31 optimal weight: 0.0770 chunk 132 optimal weight: 9.9990 chunk 176 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 175 optimal weight: 0.0010 chunk 8 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 overall best weight: 0.6746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.095699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.079285 restraints weight = 20395.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.080727 restraints weight = 14053.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.081693 restraints weight = 10723.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.082351 restraints weight = 8866.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.082672 restraints weight = 7767.631| |-----------------------------------------------------------------------------| r_work (final): 0.3417 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.124805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.111749 restraints weight = 3220.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.112930 restraints weight = 2595.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.113887 restraints weight = 2217.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.114995 restraints weight = 1957.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.115336 restraints weight = 1743.427| |-----------------------------------------------------------------------------| r_work (final): 0.4002 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.129205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.125269 restraints weight = 860.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.126028 restraints weight = 408.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.126610 restraints weight = 270.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.126911 restraints weight = 195.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.127252 restraints weight = 159.688| |-----------------------------------------------------------------------------| r_work (final): 0.4126 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.064845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.059552 restraints weight = 9793.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.060712 restraints weight = 3920.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.061361 restraints weight = 2357.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.061767 restraints weight = 1678.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.061944 restraints weight = 1334.034| |-----------------------------------------------------------------------------| r_work (final): 0.3084 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.086706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.078040 restraints weight = 10879.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.078919 restraints weight = 5103.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.079277 restraints weight = 3247.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.079638 restraints weight = 2624.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079721 restraints weight = 2205.277| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 1.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24268 Z= 0.167 Angle : 0.727 13.839 33658 Z= 0.412 Chirality : 0.044 0.175 3818 Planarity : 0.005 0.110 3470 Dihedral : 25.187 141.472 4884 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.28 % Allowed : 3.53 % Favored : 96.19 % 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: -0.44 (0.17), residues: 2328 helix: 0.53 (0.14), residues: 1388 sheet: -0.70 (0.33), residues: 220 loop : -1.66 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K 63 TYR 0.011 0.001 TYR G 297 PHE 0.037 0.002 PHE A 526 TRP 0.024 0.001 TRP G 421 HIS 0.006 0.001 HIS K 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.17 (24244) covalent geometry : angle 0.69889 / 0.41 (33640) hydrogen bonds : bond 0.09340 / 10.56 ( 1093) hydrogen bonds : angle 4.87008 / 6.59 ( 3022) metal coordination : bond 0.02153 / 2.59 ( 24) metal coordination : angle 8.74587 / 15.94 ( 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: 1 poor density : 71 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6107 (mp0) cc_final: 0.5893 (mp0) REVERT: A 96 GLU cc_start: 0.8450 (tt0) cc_final: 0.8238 (tp30) REVERT: A 360 MET cc_start: 0.8663 (mtm) cc_final: 0.8227 (mtm) REVERT: A 418 ARG cc_start: 0.8034 (pmt-80) cc_final: 0.7479 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.0765 time to fit residues: 6.9270 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 : 0.169 Evaluate side-chains 19 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.025 Fit side-chains REVERT: K 34 LEU cc_start: 0.7365 (tp) cc_final: 0.6682 (tp) REVERT: K 68 LEU cc_start: 0.7966 (mm) cc_final: 0.7688 (mm) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.1094 time to fit residues: 2.1670 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 : 0.023 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: 0.0133 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: 0.0175 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 251 optimal weight: 8.9990 chunk 188 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 206 optimal weight: 0.4980 chunk 216 optimal weight: 0.0970 chunk 181 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** 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 = 0.3665 r_free = 0.3665 target = 0.095318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.078902 restraints weight = 20990.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.080380 restraints weight = 14563.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081365 restraints weight = 11098.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082014 restraints weight = 9201.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.082379 restraints weight = 8066.118| |-----------------------------------------------------------------------------| r_work (final): 0.3409 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.121992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.113316 restraints weight = 2549.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.114436 restraints weight = 1898.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.114998 restraints weight = 1495.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.115827 restraints weight = 1282.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.116540 restraints weight = 1098.470| |-----------------------------------------------------------------------------| r_work (final): 0.4055 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.098989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.097110 restraints weight = 768.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.097985 restraints weight = 289.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.098401 restraints weight = 114.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.098612 restraints weight = 54.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.098673 restraints weight = 30.369| |-----------------------------------------------------------------------------| r_work (final): 0.3663 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.064975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.059577 restraints weight = 9395.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.060735 restraints weight = 3761.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.061374 restraints weight = 2256.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.061760 restraints weight = 1632.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.062027 restraints weight = 1324.587| |-----------------------------------------------------------------------------| r_work (final): 0.3086 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.088157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.068895 restraints weight = 10117.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.070035 restraints weight = 4919.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.070681 restraints weight = 3455.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.071225 restraints weight = 2922.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.071333 restraints weight = 2607.586| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 1.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24268 Z= 0.149 Angle : 0.679 9.671 33658 Z= 0.392 Chirality : 0.042 0.179 3818 Planarity : 0.004 0.043 3470 Dihedral : 25.182 141.747 4884 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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: -0.24 (0.17), residues: 2328 helix: 0.64 (0.14), residues: 1382 sheet: -0.68 (0.34), residues: 220 loop : -1.42 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 70 TYR 0.009 0.001 TYR G 604 PHE 0.013 0.002 PHE A 117 TRP 0.018 0.001 TRP I 48 HIS 0.001 0.000 HIS G 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (24244) covalent geometry : angle 0.66517 / 0.39 (33640) hydrogen bonds : bond 0.08545 / 9.62 ( 1093) hydrogen bonds : angle 4.73474 / 6.41 ( 3022) metal coordination : bond 0.01598 / 1.93 ( 24) metal coordination : angle 5.86782 / 10.57 ( 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 : 0.224 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6259 (mp0) cc_final: 0.6023 (mp0) REVERT: A 360 MET cc_start: 0.8653 (mtm) cc_final: 0.8217 (mtm) REVERT: A 418 ARG cc_start: 0.8003 (pmt-80) cc_final: 0.7364 (ptm-80) REVERT: A 425 LEU cc_start: 0.8907 (mt) cc_final: 0.8377 (mt) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0802 time to fit residues: 6.9331 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 : 0.172 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 : 0.027 Fit side-chains REVERT: K 68 LEU cc_start: 0.8110 (mm) cc_final: 0.7825 (mm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0383 time to fit residues: 0.6112 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 : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0148 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 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 : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0223 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 : 0.017 ------------------------------------------------------------------------------- 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: 3.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 232 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 199 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 0.2980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** 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 = 0.3666 r_free = 0.3666 target = 0.094762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.077972 restraints weight = 22496.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.079528 restraints weight = 15398.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.080584 restraints weight = 11587.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.081262 restraints weight = 9498.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.081738 restraints weight = 8299.056| |-----------------------------------------------------------------------------| r_work (final): 0.3400 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.119811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.114487 restraints weight = 2339.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.115241 restraints weight = 1660.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.115942 restraints weight = 1290.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.116529 restraints weight = 1057.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.116999 restraints weight = 845.367| |-----------------------------------------------------------------------------| r_work (final): 0.4063 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.098260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.096466 restraints weight = 643.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.097340 restraints weight = 265.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.097746 restraints weight = 113.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.097939 restraints weight = 56.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.098024 restraints weight = 28.472| |-----------------------------------------------------------------------------| r_work (final): 0.3663 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.062494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.059352 restraints weight = 10191.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.060067 restraints weight = 3948.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.060496 restraints weight = 2200.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.060684 restraints weight = 1463.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.060838 restraints weight = 1182.148| |-----------------------------------------------------------------------------| r_work (final): 0.3108 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.087951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.068654 restraints weight = 10103.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.069833 restraints weight = 4936.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.070647 restraints weight = 3519.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070940 restraints weight = 2883.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070940 restraints weight = 2643.889| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 1.4028 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= 0.150 Angle : 0.673 9.616 33658 Z= 0.387 Chirality : 0.042 0.207 3818 Planarity : 0.004 0.043 3470 Dihedral : 25.176 141.787 4884 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % 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: -0.11 (0.17), residues: 2328 helix: 0.71 (0.14), residues: 1400 sheet: -0.62 (0.38), residues: 208 loop : -1.33 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 52 TYR 0.011 0.001 TYR G 436 PHE 0.027 0.002 PHE A 526 TRP 0.015 0.002 TRP C 182 HIS 0.003 0.001 HIS E 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (24244) covalent geometry : angle 0.65544 / 0.39 (33640) hydrogen bonds : bond 0.08241 / 9.32 ( 1093) hydrogen bonds : angle 4.66449 / 6.27 ( 3022) metal coordination : bond 0.02071 / 2.39 ( 24) metal coordination : angle 6.68681 / 12.35 ( 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 66 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7143 (tm-30) REVERT: A 360 MET cc_start: 0.8656 (mtm) cc_final: 0.8182 (mtm) REVERT: A 372 LYS cc_start: 0.7155 (mmmt) cc_final: 0.6849 (mmmt) REVERT: A 418 ARG cc_start: 0.7877 (pmt-80) cc_final: 0.7608 (ptm-80) REVERT: A 425 LEU cc_start: 0.8910 (mt) cc_final: 0.8372 (mt) REVERT: A 442 MET cc_start: 0.6885 (pmm) cc_final: 0.6007 (tpp) REVERT: A 572 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8070 (tm-30) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0656 time to fit residues: 5.6874 Evaluate side-chains 40 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.176 Evaluate side-chains 15 residues out of total 68 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.026 Fit side-chains REVERT: K 58 LEU cc_start: 0.5033 (tp) cc_final: 0.4314 (mp) REVERT: K 68 LEU cc_start: 0.8107 (mm) cc_final: 0.7873 (mm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0230 time to fit residues: 0.4242 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 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0032 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: 0.0139 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 : 0.016 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0172 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 57 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 225 optimal weight: 7.9990 chunk 216 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 99 optimal weight: 0.0010 chunk 76 optimal weight: 0.1980 chunk 246 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** 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 = 0.096030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.079423 restraints weight = 21710.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.080944 restraints weight = 15252.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.081940 restraints weight = 11684.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.082574 restraints weight = 9731.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082998 restraints weight = 8594.969| |-----------------------------------------------------------------------------| r_work (final): 0.3420 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.120539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.111831 restraints weight = 3254.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.113329 restraints weight = 2170.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.114641 restraints weight = 1587.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.115428 restraints weight = 1203.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.115956 restraints weight = 962.716| |-----------------------------------------------------------------------------| r_work (final): 0.4033 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.098750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.096631 restraints weight = 748.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.097598 restraints weight = 299.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.098036 restraints weight = 138.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.098360 restraints weight = 74.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.098459 restraints weight = 38.151| |-----------------------------------------------------------------------------| r_work (final): 0.3660 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.063180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.060156 restraints weight = 10795.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.060858 restraints weight = 4083.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.061305 restraints weight = 2221.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.061552 restraints weight = 1424.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.061683 restraints weight = 1053.216| |-----------------------------------------------------------------------------| r_work (final): 0.3092 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.088629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.069629 restraints weight = 10095.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.070806 restraints weight = 4767.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.071414 restraints weight = 3303.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.071961 restraints weight = 2810.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.072095 restraints weight = 2507.184| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 1.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24268 Z= 0.144 Angle : 0.664 7.322 33658 Z= 0.382 Chirality : 0.042 0.200 3818 Planarity : 0.004 0.041 3470 Dihedral : 25.170 142.070 4884 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: 0.06 (0.17), residues: 2328 helix: 0.85 (0.14), residues: 1376 sheet: -0.26 (0.39), residues: 200 loop : -1.30 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 418 TYR 0.011 0.001 TYR I 18 PHE 0.039 0.002 PHE C 575 TRP 0.014 0.001 TRP A 421 HIS 0.004 0.000 HIS E 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (24244) covalent geometry : angle 0.65339 / 0.38 (33640) hydrogen bonds : bond 0.07833 / 8.90 ( 1093) hydrogen bonds : angle 4.64184 / 6.28 ( 3022) metal coordination : bond 0.01477 / 1.75 ( 24) metal coordination : angle 5.19262 / 9.65 ( 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 : 0.214 Fit side-chains revert: symmetry clash REVERT: A 360 MET cc_start: 0.8599 (mtm) cc_final: 0.8113 (mtm) REVERT: A 372 LYS cc_start: 0.7203 (mmmt) cc_final: 0.6800 (mmmt) REVERT: A 418 ARG cc_start: 0.7949 (pmt-80) cc_final: 0.7258 (ptm-80) REVERT: A 425 LEU cc_start: 0.8917 (mt) cc_final: 0.8384 (mt) REVERT: A 442 MET cc_start: 0.6913 (pmm) cc_final: 0.6208 (tpp) REVERT: A 572 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8526 (mm-30) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0692 time to fit residues: 5.9248 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 : 0.183 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 : 0.027 Fit side-chains REVERT: K 18 TYR cc_start: 0.4318 (m-10) cc_final: 0.3921 (m-10) REVERT: K 49 VAL cc_start: 0.3754 (m) cc_final: 0.3225 (m) REVERT: K 58 LEU cc_start: 0.5603 (tp) cc_final: 0.4672 (mp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0384 time to fit residues: 0.6165 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 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 : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0138 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: 0.0176 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: 0.0060 chunk 145 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 169 optimal weight: 0.4980 chunk 246 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 0.0470 chunk 132 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 overall best weight: 0.4494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 ASN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.096881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.080312 restraints weight = 22154.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.081810 restraints weight = 15573.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.082827 restraints weight = 11986.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.083491 restraints weight = 9953.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.083967 restraints weight = 8746.921| |-----------------------------------------------------------------------------| r_work (final): 0.3439 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.119929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.111416 restraints weight = 2511.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.112265 restraints weight = 1995.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.112473 restraints weight = 1672.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.113371 restraints weight = 1569.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.113718 restraints weight = 1342.102| |-----------------------------------------------------------------------------| r_work (final): 0.4001 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.098139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.096038 restraints weight = 699.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.097079 restraints weight = 290.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.097514 restraints weight = 131.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.097808 restraints weight = 69.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.097900 restraints weight = 34.284| |-----------------------------------------------------------------------------| r_work (final): 0.3746 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.063628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.060660 restraints weight = 10538.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.061339 restraints weight = 3996.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.061782 restraints weight = 2158.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.061998 restraints weight = 1364.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.062048 restraints weight = 1027.393| |-----------------------------------------------------------------------------| r_work (final): 0.3121 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.088948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069640 restraints weight = 10415.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.070885 restraints weight = 4927.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.071735 restraints weight = 3455.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.072043 restraints weight = 2823.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.072137 restraints weight = 2572.250| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 1.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24268 Z= 0.146 Angle : 0.663 7.207 33658 Z= 0.382 Chirality : 0.041 0.190 3818 Planarity : 0.004 0.040 3470 Dihedral : 25.136 142.579 4884 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: 0.81 (0.14), residues: 1380 sheet: -0.47 (0.39), residues: 200 loop : -1.25 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 149 TYR 0.010 0.001 TYR I 18 PHE 0.029 0.002 PHE C 433 TRP 0.011 0.001 TRP A 421 HIS 0.002 0.000 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (24244) covalent geometry : angle 0.65217 / 0.38 (33640) hydrogen bonds : bond 0.07696 / 8.73 ( 1093) hydrogen bonds : angle 4.61581 / 6.24 ( 3022) metal coordination : bond 0.01416 / 1.68 ( 24) metal coordination : angle 5.25522 / 9.67 ( 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 75 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 180 ASP cc_start: 0.6985 (t0) cc_final: 0.6742 (t70) REVERT: A 360 MET cc_start: 0.8623 (mtm) cc_final: 0.8222 (mtm) REVERT: A 372 LYS cc_start: 0.7398 (mmmt) cc_final: 0.7047 (mmmt) REVERT: A 418 ARG cc_start: 0.7879 (pmt-80) cc_final: 0.7346 (ptm-80) REVERT: A 425 LEU cc_start: 0.8906 (mt) cc_final: 0.8394 (mt) REVERT: A 442 MET cc_start: 0.6754 (pmm) cc_final: 0.6194 (tpp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0608 time to fit residues: 6.1377 Evaluate side-chains 46 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.179 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 49 VAL cc_start: 0.4136 (m) cc_final: 0.3690 (m) REVERT: K 58 LEU cc_start: 0.5169 (tp) cc_final: 0.4445 (mp) REVERT: K 68 LEU cc_start: 0.8093 (mm) cc_final: 0.7749 (mm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0215 time to fit residues: 0.3547 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 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: 0.0131 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 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: 0.0162 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 237 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 228 optimal weight: 0.0980 chunk 48 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 231 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 591 GLN ** 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 = 0.3715 r_free = 0.3715 target = 0.097103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.080506 restraints weight = 22929.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.081962 restraints weight = 16253.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.082995 restraints weight = 12705.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.083683 restraints weight = 10641.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.083969 restraints weight = 9382.407| |-----------------------------------------------------------------------------| r_work (final): 0.3445 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.121736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.114130 restraints weight = 2391.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.115083 restraints weight = 1949.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.115599 restraints weight = 1636.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.115800 restraints weight = 1429.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.115800 restraints weight = 1328.382| |-----------------------------------------------------------------------------| r_work (final): 0.4061 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.097937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.095707 restraints weight = 765.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.096722 restraints weight = 317.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.097282 restraints weight = 149.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.097595 restraints weight = 73.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.097743 restraints weight = 37.058| |-----------------------------------------------------------------------------| r_work (final): 0.3680 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.063172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.060239 restraints weight = 10208.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.060884 restraints weight = 3933.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.061295 restraints weight = 2147.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.061445 restraints weight = 1386.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.061596 restraints weight = 1145.846| |-----------------------------------------------------------------------------| r_work (final): 0.3091 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.088714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069646 restraints weight = 10145.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.070890 restraints weight = 4775.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.071722 restraints weight = 3326.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.072008 restraints weight = 2728.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.072172 restraints weight = 2498.417| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 1.4185 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= 0.146 Angle : 0.676 7.040 33658 Z= 0.393 Chirality : 0.043 0.230 3818 Planarity : 0.004 0.041 3470 Dihedral : 25.092 142.968 4884 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 0.78 (0.14), residues: 1376 sheet: -0.53 (0.40), residues: 200 loop : -1.21 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 573 TYR 0.011 0.001 TYR K 18 PHE 0.028 0.002 PHE E 433 TRP 0.008 0.001 TRP A 421 HIS 0.002 0.001 HIS G 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (24244) covalent geometry : angle 0.66659 / 0.39 (33640) hydrogen bonds : bond 0.07716 / 8.79 ( 1093) hydrogen bonds : angle 4.66156 / 6.29 ( 3022) metal coordination : bond 0.01208 / 1.42 ( 24) metal coordination : angle 4.82397 / 8.73 ( 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 66 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7399 (mmmm) cc_final: 0.6620 (mttt) REVERT: A 120 MET cc_start: 0.8316 (ttm) cc_final: 0.7484 (ttm) REVERT: A 179 ILE cc_start: 0.7896 (mm) cc_final: 0.7677 (pt) REVERT: A 360 MET cc_start: 0.8608 (mtm) cc_final: 0.8211 (mtm) REVERT: A 418 ARG cc_start: 0.7740 (pmt-80) cc_final: 0.7540 (ptm-80) REVERT: A 425 LEU cc_start: 0.8932 (mt) cc_final: 0.8438 (mt) REVERT: A 442 MET cc_start: 0.6956 (pmm) cc_final: 0.6438 (tpp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0643 time to fit residues: 5.6584 Evaluate side-chains 47 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.184 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 : 0.026 Fit side-chains REVERT: K 49 VAL cc_start: 0.4153 (m) cc_final: 0.3704 (m) REVERT: K 58 LEU cc_start: 0.5873 (tp) cc_final: 0.4896 (mp) REVERT: K 68 LEU cc_start: 0.8197 (mm) cc_final: 0.7912 (mm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0226 time to fit residues: 0.3701 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 : 0.026 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 : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0033 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 : 0.003 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: 0.0150 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 : 0.017 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0210 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 245 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 221 optimal weight: 0.6980 chunk 184 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 197 HIS ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.097648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.080814 restraints weight = 22897.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.082407 restraints weight = 15989.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.083410 restraints weight = 12319.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.083986 restraints weight = 10333.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.084559 restraints weight = 9197.849| |-----------------------------------------------------------------------------| r_work (final): 0.3461 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.122567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.117258 restraints weight = 2334.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.118140 restraints weight = 1714.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.118558 restraints weight = 1336.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.119552 restraints weight = 1150.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.120010 restraints weight = 894.468| |-----------------------------------------------------------------------------| r_work (final): 0.4109 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.101187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.095530 restraints weight = 843.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096957 restraints weight = 487.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.098193 restraints weight = 317.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.098795 restraints weight = 209.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.099336 restraints weight = 152.390| |-----------------------------------------------------------------------------| r_work (final): 0.3683 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.060819 restraints weight = 9229.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.061916 restraints weight = 3946.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.062552 restraints weight = 2391.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.062962 restraints weight = 1729.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.063206 restraints weight = 1381.537| |-----------------------------------------------------------------------------| r_work (final): 0.3085 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.088871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.070101 restraints weight = 10072.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.071287 restraints weight = 4672.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.071910 restraints weight = 3271.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.072074 restraints weight = 2764.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072121 restraints weight = 2599.043| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 1.4199 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 : 0.665 7.001 33658 Z= 0.382 Chirality : 0.042 0.197 3818 Planarity : 0.004 0.041 3470 Dihedral : 25.067 142.402 4884 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 0.05 (0.18), residues: 2328 helix: 0.86 (0.14), residues: 1376 sheet: -0.62 (0.40), residues: 200 loop : -1.23 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 189 TYR 0.010 0.001 TYR G 436 PHE 0.024 0.002 PHE E 433 TRP 0.010 0.001 TRP A 421 HIS 0.001 0.000 HIS G 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (24244) covalent geometry : angle 0.65513 / 0.38 (33640) hydrogen bonds : bond 0.07568 / 8.66 ( 1093) hydrogen bonds : angle 4.58752 / 6.16 ( 3022) metal coordination : bond 0.01332 / 1.57 ( 24) metal coordination : angle 4.89361 / 8.95 ( 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 64 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7461 (mmmm) cc_final: 0.6628 (mttt) REVERT: A 104 ARG cc_start: 0.7860 (mtp180) cc_final: 0.7503 (ttp80) REVERT: A 120 MET cc_start: 0.8386 (ttm) cc_final: 0.7396 (ttm) REVERT: A 179 ILE cc_start: 0.7931 (mm) cc_final: 0.7690 (pt) REVERT: A 360 MET cc_start: 0.8617 (mtm) cc_final: 0.8226 (mtm) REVERT: A 372 LYS cc_start: 0.7036 (mmmt) cc_final: 0.6545 (mmmt) REVERT: A 425 LEU cc_start: 0.8931 (mt) cc_final: 0.8457 (mt) REVERT: A 442 MET cc_start: 0.6834 (pmm) cc_final: 0.6543 (tpp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0721 time to fit residues: 5.9835 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 : 0.173 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 49 VAL cc_start: 0.4473 (m) cc_final: 0.4091 (m) REVERT: K 58 LEU cc_start: 0.5185 (tp) cc_final: 0.4531 (mp) REVERT: K 68 LEU cc_start: 0.7903 (mm) cc_final: 0.7473 (mm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0208 time to fit residues: 0.3411 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 : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0137 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: 0.0160 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 80 optimal weight: 0.0870 chunk 206 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 193 optimal weight: 0.0270 chunk 16 optimal weight: 30.0000 chunk 127 optimal weight: 0.3980 chunk 223 optimal weight: 2.9990 chunk 121 optimal weight: 0.0020 chunk 239 optimal weight: 2.9990 chunk 50 optimal weight: 0.0170 overall best weight: 0.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 38 GLN ** 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 = 0.3738 r_free = 0.3738 target = 0.098762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.083037 restraints weight = 22903.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.083843 restraints weight = 19124.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.084823 restraints weight = 14612.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.085006 restraints weight = 12742.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.085116 restraints weight = 12110.504| |-----------------------------------------------------------------------------| r_work (final): 0.3463 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.122928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.115127 restraints weight = 2367.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.115697 restraints weight = 1934.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.116466 restraints weight = 1666.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.116689 restraints weight = 1459.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.117023 restraints weight = 1360.509| |-----------------------------------------------------------------------------| r_work (final): 0.4069 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.102567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.096790 restraints weight = 789.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.098586 restraints weight = 464.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.099429 restraints weight = 283.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.100221 restraints weight = 198.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.100689 restraints weight = 138.526| |-----------------------------------------------------------------------------| r_work (final): 0.3728 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.064658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.061854 restraints weight = 10578.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.062508 restraints weight = 3977.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.062840 restraints weight = 2091.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063104 restraints weight = 1410.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.063161 restraints weight = 1000.720| |-----------------------------------------------------------------------------| r_work (final): 0.3171 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.089453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.070293 restraints weight = 10512.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.071448 restraints weight = 4891.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.072372 restraints weight = 3409.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.072704 restraints weight = 2786.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.072803 restraints weight = 2542.648| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 1.4293 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= 0.146 Angle : 0.669 7.129 33658 Z= 0.385 Chirality : 0.042 0.207 3818 Planarity : 0.004 0.041 3470 Dihedral : 25.033 142.603 4884 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -0.05 (0.18), residues: 2328 helix: 0.79 (0.14), residues: 1376 sheet: -0.88 (0.39), residues: 200 loop : -1.22 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 205 TYR 0.009 0.001 TYR A 436 PHE 0.023 0.002 PHE C 433 TRP 0.015 0.002 TRP A 182 HIS 0.003 0.000 HIS E 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (24244) covalent geometry : angle 0.66025 / 0.38 (33640) hydrogen bonds : bond 0.07555 / 8.69 ( 1093) hydrogen bonds : angle 4.60666 / 6.17 ( 3022) metal coordination : bond 0.01242 / 1.48 ( 24) metal coordination : angle 4.73472 / 8.72 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2373.16 seconds wall clock time: 42 minutes 38.21 seconds (2558.21 seconds total)