Starting phenix.real_space_refine on Fri Aug 7 14:10:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q0m_72099/08_2026/9q0m_72099.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q0m_72099/08_2026/9q0m_72099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q0m_72099/08_2026/9q0m_72099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q0m_72099/08_2026/9q0m_72099.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q0m_72099/08_2026/9q0m_72099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q0m_72099/08_2026/9q0m_72099.map" } resolution = 3.1 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= 0.002 sd= 0.078 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: 7 Type Number sf(0) Gaussians Fe 16 7.16 5 P 8 5.49 5 Mg 8 5.21 5 S 136 5.16 5 C 13832 2.51 5 N 3724 2.21 5 O 4144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 21868 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3810 Classifications: {'peptide': 490} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 462} Chain breaks: 1 Chain: "B" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3810 Classifications: {'peptide': 490} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 462} Chain breaks: 1 Chain: "C" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3810 Classifications: {'peptide': 490} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 462} Chain breaks: 1 Chain: "D" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3810 Classifications: {'peptide': 490} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 462} Chain breaks: 1 Chain: "E" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1601 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "F" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1601 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "G" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1601 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "H" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1601 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'AMP%rna2p': 1, 'SF4': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'AMP%rna2p': 1, 'SF4': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'AMP%rna2p': 1, 'SF4': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'AMP%rna2p': 1, 'SF4': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {' MG': 2, 'AMP%rna2p': 2} Classifications: {'RNA_mixed': 2, 'undetermined': 2} Modifications used: {'rna2p': 2} Link IDs: {'rna2p': 1, None: 2} Not linked: pdbres="AMP F 302 " pdbres=" MG F 303 " Not linked: pdbres=" MG F 303 " pdbres=" MG F 304 " Chain breaks: 1 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' MG': 2, 'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' MG': 2, 'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3716 SG CYS A 506 93.138 72.703 83.679 1.00 38.74 S ATOM 2076 SG CYS A 280 91.388 79.204 83.447 1.00 29.75 S ATOM 3698 SG CYS A 503 92.620 76.215 88.741 1.00 38.58 S ATOM 3221 SG CYS A 426 87.235 74.680 85.099 1.00 46.38 S ATOM 7526 SG CYS B 506 93.130 95.208 36.732 1.00 41.02 S ATOM 5886 SG CYS B 280 91.389 88.700 36.965 1.00 26.71 S ATOM 7508 SG CYS B 503 92.589 91.703 31.659 1.00 37.69 S ATOM 7031 SG CYS B 426 87.234 93.229 35.329 1.00 44.84 S ATOM 11336 SG CYS C 506 30.677 72.701 36.725 1.00 41.74 S ATOM 9696 SG CYS C 280 32.452 79.200 36.994 1.00 28.20 S ATOM 11318 SG CYS C 503 31.206 76.220 31.672 1.00 38.32 S ATOM 10841 SG CYS C 426 36.573 74.668 35.338 1.00 43.96 S ATOM 15146 SG CYS D 506 30.670 95.212 83.675 1.00 42.62 S ATOM 13506 SG CYS D 280 32.335 88.706 83.490 1.00 28.07 S ATOM 15128 SG CYS D 503 31.197 91.702 88.754 1.00 36.13 S ATOM 14651 SG CYS D 426 36.569 93.232 85.100 1.00 43.94 S Time building chain proxies: 5.27, per 1000 atoms: 0.24 Number of scatterers: 21868 At special positions: 0 Unit cell: (124.656, 168.752, 121.264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 16 26.01 S 136 16.00 P 8 15.00 Mg 8 11.99 O 4144 8.00 N 3724 7.00 C 13832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 995.3 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 601 " pdb="FE4 SF4 A 601 " - pdb=" SG CYS A 426 " pdb="FE3 SF4 A 601 " - pdb=" SG CYS A 503 " pdb="FE1 SF4 A 601 " - pdb=" SG CYS A 506 " pdb="FE2 SF4 A 601 " - pdb=" SG CYS A 280 " pdb=" SF4 B 601 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 426 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 503 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 280 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 506 " pdb=" SF4 C 601 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 426 " pdb="FE2 SF4 C 601 " - pdb=" SG CYS C 280 " pdb="FE3 SF4 C 601 " - pdb=" SG CYS C 503 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 506 " pdb=" SF4 D 601 " pdb="FE4 SF4 D 601 " - pdb=" SG CYS D 426 " pdb="FE2 SF4 D 601 " - pdb=" SG CYS D 280 " pdb="FE3 SF4 D 601 " - pdb=" SG CYS D 503 " pdb="FE1 SF4 D 601 " - pdb=" SG CYS D 506 " Number of angles added : 48 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 33 sheets defined 34.5% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 28 through 40 Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.918A pdb=" N ASN A 104 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS A 105 " --> pdb=" O LEU A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 105' Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.680A pdb=" N GLY A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.793A pdb=" N MET A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 235 through 242 removed outlier: 4.121A pdb=" N SER A 238 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 241 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.638A pdb=" N VAL A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 328 through 340 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 377 through 380 Processing helix chain 'A' and resid 397 through 408 removed outlier: 4.078A pdb=" N ILE A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 446 removed outlier: 6.176A pdb=" N ILE A 439 " --> pdb=" O GLU A 436 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA A 440 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 447 through 453 Processing helix chain 'A' and resid 461 through 475 removed outlier: 4.541A pdb=" N GLY A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'B' and resid 28 through 40 Processing helix chain 'B' and resid 41 through 44 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.776A pdb=" N ASN B 104 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS B 105 " --> pdb=" O LEU B 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 101 through 105' Processing helix chain 'B' and resid 127 through 139 removed outlier: 3.634A pdb=" N GLY B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 157 removed outlier: 3.854A pdb=" N MET B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 214 through 219 removed outlier: 4.519A pdb=" N ASN B 218 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 214 through 219' Processing helix chain 'B' and resid 235 through 242 removed outlier: 4.122A pdb=" N SER B 238 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU B 240 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 241 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 removed outlier: 3.655A pdb=" N VAL B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 314 Processing helix chain 'B' and resid 328 through 340 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 377 through 380 Processing helix chain 'B' and resid 397 through 408 removed outlier: 4.100A pdb=" N ILE B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 446 removed outlier: 4.003A pdb=" N LEU B 438 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE B 439 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 440 " --> pdb=" O GLU B 437 " (cutoff:3.500A) Proline residue: B 443 - end of helix Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 461 through 476 removed outlier: 4.562A pdb=" N GLY B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 removed outlier: 3.530A pdb=" N SER B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 41 through 44 Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.528A pdb=" N CYS C 105 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 139 removed outlier: 3.693A pdb=" N LEU C 131 " --> pdb=" O ASN C 127 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.724A pdb=" N MET C 150 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 213 through 219 removed outlier: 4.161A pdb=" N ASN C 218 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 242 removed outlier: 4.119A pdb=" N SER C 238 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU C 240 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER C 241 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 286 removed outlier: 3.652A pdb=" N VAL C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 314 Processing helix chain 'C' and resid 328 through 340 Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 377 through 380 Processing helix chain 'C' and resid 397 through 408 removed outlier: 4.154A pdb=" N ILE C 401 " --> pdb=" O THR C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 446 removed outlier: 3.727A pdb=" N LEU C 438 " --> pdb=" O LYS C 435 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE C 439 " --> pdb=" O GLU C 436 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA C 440 " --> pdb=" O GLU C 437 " (cutoff:3.500A) Proline residue: C 443 - end of helix Processing helix chain 'C' and resid 447 through 453 Processing helix chain 'C' and resid 461 through 475 removed outlier: 4.589A pdb=" N GLY C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE C 475 " --> pdb=" O GLU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'D' and resid 28 through 40 Processing helix chain 'D' and resid 41 through 44 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 101 through 105 removed outlier: 3.614A pdb=" N ASN D 104 " --> pdb=" O GLU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 146 through 157 removed outlier: 3.748A pdb=" N MET D 150 " --> pdb=" O SER D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 180 Processing helix chain 'D' and resid 213 through 218 removed outlier: 3.782A pdb=" N ASN D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 242 removed outlier: 4.141A pdb=" N SER D 238 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU D 240 " --> pdb=" O CYS D 237 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER D 241 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 286 removed outlier: 3.633A pdb=" N VAL D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 314 Processing helix chain 'D' and resid 328 through 340 Processing helix chain 'D' and resid 366 through 371 Processing helix chain 'D' and resid 377 through 380 Processing helix chain 'D' and resid 397 through 408 removed outlier: 4.140A pdb=" N ILE D 401 " --> pdb=" O THR D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 446 removed outlier: 3.738A pdb=" N LEU D 438 " --> pdb=" O LYS D 435 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE D 439 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA D 440 " --> pdb=" O GLU D 437 " (cutoff:3.500A) Proline residue: D 443 - end of helix Processing helix chain 'D' and resid 447 through 453 Processing helix chain 'D' and resid 461 through 478 removed outlier: 4.801A pdb=" N GLY D 472 " --> pdb=" O SER D 468 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'E' and resid 104 through 118 Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'E' and resid 177 through 190 Processing helix chain 'E' and resid 195 through 207 Processing helix chain 'F' and resid 104 through 117 Processing helix chain 'F' and resid 152 through 156 Processing helix chain 'F' and resid 177 through 190 Processing helix chain 'F' and resid 195 through 207 Processing helix chain 'G' and resid 104 through 118 Processing helix chain 'G' and resid 177 through 190 Processing helix chain 'G' and resid 195 through 207 Processing helix chain 'H' and resid 104 through 118 Processing helix chain 'H' and resid 152 through 157 removed outlier: 4.093A pdb=" N ARG H 157 " --> pdb=" O ALA H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 190 removed outlier: 3.678A pdb=" N HIS H 190 " --> pdb=" O VAL H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 207 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 67 removed outlier: 3.840A pdb=" N SER A 47 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY A 229 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE A 208 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 112 removed outlier: 3.699A pdb=" N ASP A 267 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLU A 257 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N THR A 265 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 279 through 280 removed outlier: 6.114A pdb=" N PHE A 279 " --> pdb=" O CYS A 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 293 through 294 Processing sheet with id=AA5, first strand: chain 'A' and resid 320 through 323 removed outlier: 6.710A pdb=" N ILE A 385 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ARG A 416 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 387 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A 456 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 349 Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 67 removed outlier: 3.989A pdb=" N SER B 47 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY B 229 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 208 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 112 removed outlier: 3.746A pdb=" N ASP B 267 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU B 257 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR B 265 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 279 through 280 removed outlier: 6.137A pdb=" N PHE B 279 " --> pdb=" O CYS B 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AB2, first strand: chain 'B' and resid 320 through 323 removed outlier: 6.705A pdb=" N ILE B 385 " --> pdb=" O HIS B 414 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ARG B 416 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU B 387 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER B 456 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 347 through 349 Processing sheet with id=AB4, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AB5, first strand: chain 'C' and resid 61 through 67 removed outlier: 4.081A pdb=" N SER C 47 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY C 229 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE C 208 " --> pdb=" O TYR C 247 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 108 through 112 removed outlier: 3.721A pdb=" N ASP C 267 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU C 257 " --> pdb=" O THR C 265 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N THR C 265 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 279 through 280 removed outlier: 6.094A pdb=" N PHE C 279 " --> pdb=" O CYS C 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 293 through 294 Processing sheet with id=AB9, first strand: chain 'C' and resid 320 through 323 removed outlier: 6.727A pdb=" N ILE C 385 " --> pdb=" O HIS C 414 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ARG C 416 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU C 387 " --> pdb=" O ARG C 416 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER C 456 " --> pdb=" O VAL C 413 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 347 through 349 Processing sheet with id=AC2, first strand: chain 'C' and resid 357 through 358 Processing sheet with id=AC3, first strand: chain 'D' and resid 61 through 67 removed outlier: 3.925A pdb=" N SER D 47 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY D 229 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE D 208 " --> pdb=" O TYR D 247 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 108 through 112 removed outlier: 3.726A pdb=" N ASP D 267 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU D 257 " --> pdb=" O THR D 265 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR D 265 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 279 through 280 removed outlier: 6.353A pdb=" N PHE D 279 " --> pdb=" O CYS D 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 293 through 294 Processing sheet with id=AC7, first strand: chain 'D' and resid 320 through 323 removed outlier: 4.085A pdb=" N SER D 456 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 347 through 349 Processing sheet with id=AC9, first strand: chain 'D' and resid 357 through 358 Processing sheet with id=AD1, first strand: chain 'E' and resid 17 through 25 removed outlier: 6.323A pdb=" N ILE E 17 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N MET E 37 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 31 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU E 25 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 61 through 69 removed outlier: 17.493A pdb=" N VAL E 62 " --> pdb=" O GLN E 82 " (cutoff:3.500A) removed outlier: 14.650A pdb=" N GLN E 82 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 10.919A pdb=" N VAL E 64 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N VAL E 80 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY E 89 " --> pdb=" O ARG E 84 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 89 through 93 current: chain 'E' and resid 140 through 149 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 140 through 149 current: chain 'F' and resid 76 through 84 removed outlier: 3.578A pdb=" N GLY F 89 " --> pdb=" O ARG F 84 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 89 through 93 current: chain 'F' and resid 140 through 149 Processing sheet with id=AD3, first strand: chain 'F' and resid 17 through 25 removed outlier: 5.777A pdb=" N ILE F 17 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N MET F 37 " --> pdb=" O ILE F 17 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU F 31 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLU F 25 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 17 through 25 removed outlier: 5.981A pdb=" N ILE G 17 " --> pdb=" O MET G 37 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N MET G 37 " --> pdb=" O ILE G 17 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU G 31 " --> pdb=" O ILE G 23 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU G 25 " --> pdb=" O VAL G 29 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 61 through 69 removed outlier: 17.547A pdb=" N VAL G 62 " --> pdb=" O GLN G 82 " (cutoff:3.500A) removed outlier: 14.699A pdb=" N GLN G 82 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N VAL G 64 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL G 80 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY G 89 " --> pdb=" O ARG G 84 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 89 through 93 current: chain 'G' and resid 140 through 149 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 140 through 149 current: chain 'H' and resid 76 through 84 removed outlier: 3.575A pdb=" N GLY H 89 " --> pdb=" O ARG H 84 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 89 through 93 current: chain 'H' and resid 140 through 149 Processing sheet with id=AD6, first strand: chain 'H' and resid 17 through 25 removed outlier: 6.332A pdb=" N ILE H 17 " --> pdb=" O MET H 37 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET H 37 " --> pdb=" O ILE H 17 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU H 31 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLU H 25 " --> pdb=" O VAL H 29 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL H 29 " --> pdb=" O GLU H 25 " (cutoff:3.500A) 855 hydrogen bonds defined for protein. 2319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.19 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 9087 1.42 - 1.64: 13049 1.64 - 1.85: 164 1.85 - 2.07: 0 2.07 - 2.28: 48 Bond restraints: 22348 Sorted by residual: bond pdb=" C4 AMP A 602 " pdb=" C5 AMP A 602 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C4 AMP D 602 " pdb=" C5 AMP D 602 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 AMP B 602 " pdb=" C5 AMP B 602 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 AMP C 602 " pdb=" C5 AMP C 602 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 AMP F 301 " pdb=" C5 AMP F 301 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 22343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 29720 1.86 - 3.71: 533 3.71 - 5.57: 74 5.57 - 7.42: 33 7.42 - 9.28: 16 Bond angle restraints: 30376 Sorted by residual: angle pdb=" CA GLN A 106 " pdb=" C GLN A 106 " pdb=" O GLN A 106 " ideal model delta sigma weight residual 121.08 117.04 4.04 8.90e-01 1.26e+00 2.06e+01 angle pdb=" N LEU A 102 " pdb=" CA LEU A 102 " pdb=" C LEU A 102 " ideal model delta sigma weight residual 113.18 107.71 5.47 1.21e+00 6.83e-01 2.04e+01 angle pdb=" CA GLY A 115 " pdb=" C GLY A 115 " pdb=" O GLY A 115 " ideal model delta sigma weight residual 122.01 117.81 4.20 9.70e-01 1.06e+00 1.87e+01 angle pdb=" CA ALA A 118 " pdb=" C ALA A 118 " pdb=" O ALA A 118 " ideal model delta sigma weight residual 121.16 116.42 4.74 1.13e+00 7.83e-01 1.76e+01 angle pdb=" CA ILE A 89 " pdb=" C ILE A 89 " pdb=" O ILE A 89 " ideal model delta sigma weight residual 121.67 117.55 4.12 1.02e+00 9.61e-01 1.63e+01 ... (remaining 30371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.85: 13128 25.85 - 51.70: 301 51.70 - 77.56: 39 77.56 - 103.41: 10 103.41 - 129.26: 2 Dihedral angle restraints: 13480 sinusoidal: 5460 harmonic: 8020 Sorted by residual: dihedral pdb=" C5' AMP B 602 " pdb=" O5' AMP B 602 " pdb=" P AMP B 602 " pdb=" O3P AMP B 602 " ideal model delta sinusoidal sigma weight residual -60.00 69.26 -129.26 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" C5' AMP C 602 " pdb=" O5' AMP C 602 " pdb=" P AMP C 602 " pdb=" O3P AMP C 602 " ideal model delta sinusoidal sigma weight residual -60.00 68.66 -128.65 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" CA PRO C 325 " pdb=" C PRO C 325 " pdb=" N GLU C 326 " pdb=" CA GLU C 326 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 13477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2434 0.037 - 0.075: 604 0.075 - 0.112: 266 0.112 - 0.150: 139 0.150 - 0.187: 5 Chirality restraints: 3448 Sorted by residual: chirality pdb=" CA VAL A 110 " pdb=" N VAL A 110 " pdb=" C VAL A 110 " pdb=" CB VAL A 110 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA ILE A 89 " pdb=" N ILE A 89 " pdb=" C ILE A 89 " pdb=" CB ILE A 89 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA VAL A 109 " pdb=" N VAL A 109 " pdb=" C VAL A 109 " pdb=" CB VAL A 109 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 3445 not shown) Planarity restraints: 3880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 93 " 0.196 9.50e-02 1.11e+02 8.81e-02 4.88e+00 pdb=" NE ARG A 93 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 93 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 93 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 93 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 180 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO C 181 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 351 " -0.172 9.50e-02 1.11e+02 7.72e-02 3.77e+00 pdb=" NE ARG B 351 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 351 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 351 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 351 " -0.004 2.00e-02 2.50e+03 ... (remaining 3877 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 8 2.49 - 3.09: 14537 3.09 - 3.70: 30275 3.70 - 4.30: 47819 4.30 - 4.90: 81054 Nonbonded interactions: 173693 Sorted by model distance: nonbonded pdb=" OE2 GLU E 112 " pdb="MG MG E 301 " model vdw 1.889 2.170 nonbonded pdb=" OE2 GLU H 112 " pdb="MG MG H 302 " model vdw 1.913 2.170 nonbonded pdb=" OE2 GLU F 112 " pdb="MG MG F 303 " model vdw 1.935 2.170 nonbonded pdb=" O3P AMP G 301 " pdb="MG MG G 302 " model vdw 1.944 2.170 nonbonded pdb=" OE2 GLU G 112 " pdb="MG MG G 302 " model vdw 1.992 2.170 ... (remaining 173688 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 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 15 through 219) selection = (chain 'F' and resid 15 through 219) selection = (chain 'G' and resid 15 through 219) selection = (chain 'H' and resid 15 through 219) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 individual isotropic 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: 1.360 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: 0.410 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 24.010 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 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 0.111 22364 Z= 0.235 Angle : 0.681 9.281 30424 Z= 0.345 Chirality : 0.046 0.187 3448 Planarity : 0.005 0.088 3880 Dihedral : 11.773 129.260 8328 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.08 % Allowed : 0.96 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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 (0.16), residues: 2756 helix: 1.50 (0.21), residues: 692 sheet: 0.53 (0.20), residues: 620 loop : -0.66 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 351 TYR 0.011 0.001 TYR A 335 PHE 0.009 0.001 PHE A 108 TRP 0.008 0.001 TRP D 169 HIS 0.007 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.23 (22348) covalent geometry : angle 0.65242 / 0.34 (30376) hydrogen bonds : bond 0.13411 / 9.80 ( 855) hydrogen bonds : angle 6.27878 / 4.52 ( 2319) metal coordination : bond 0.00164 / 0.13 ( 16) metal coordination : angle 4.93076 / 3.46 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 0.870 Fit side-chains REVERT: A 22 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8145 (mm-30) REVERT: A 226 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7255 (mt-10) REVERT: A 339 CYS cc_start: 0.7903 (p) cc_final: 0.7702 (p) REVERT: A 446 ASP cc_start: 0.7786 (m-30) cc_final: 0.7487 (m-30) REVERT: A 514 GLU cc_start: 0.7554 (pm20) cc_final: 0.7315 (pm20) REVERT: B 22 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8181 (mm-30) REVERT: B 264 GLN cc_start: 0.8292 (tt0) cc_final: 0.8082 (tt0) REVERT: B 446 ASP cc_start: 0.7867 (m-30) cc_final: 0.7536 (m-30) REVERT: B 514 GLU cc_start: 0.7492 (pm20) cc_final: 0.7225 (pm20) REVERT: C 226 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7226 (mm-30) REVERT: C 403 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7531 (ttmm) REVERT: C 446 ASP cc_start: 0.7745 (m-30) cc_final: 0.7521 (m-30) REVERT: C 510 LYS cc_start: 0.7943 (mtpp) cc_final: 0.7647 (mtmm) REVERT: D 403 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7601 (ttmm) REVERT: D 510 LYS cc_start: 0.7908 (mtpp) cc_final: 0.7520 (mttm) REVERT: E 154 GLU cc_start: 0.7507 (pm20) cc_final: 0.7270 (pm20) REVERT: F 138 ASN cc_start: 0.7175 (p0) cc_final: 0.6627 (t0) REVERT: F 152 ASP cc_start: 0.8354 (t70) cc_final: 0.8066 (t70) REVERT: F 161 LYS cc_start: 0.6383 (mtpt) cc_final: 0.5936 (tptt) REVERT: H 159 LYS cc_start: 0.6946 (tmmt) cc_final: 0.6679 (mmtm) outliers start: 2 outliers final: 0 residues processed: 310 average time/residue: 0.1826 time to fit residues: 84.1416 Evaluate side-chains 255 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN A 431 ASN B 127 ASN B 470 GLN C 104 ASN D 138 HIS G 138 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.141729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.101899 restraints weight = 21864.821| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.24 r_work: 0.2616 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22364 Z= 0.181 Angle : 0.666 9.491 30424 Z= 0.321 Chirality : 0.048 0.176 3448 Planarity : 0.005 0.050 3880 Dihedral : 6.647 83.659 3076 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.67 % Allowed : 4.98 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 0.21 (0.15), residues: 2756 helix: 1.37 (0.20), residues: 728 sheet: 0.55 (0.19), residues: 648 loop : -0.72 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 351 TYR 0.015 0.002 TYR D 459 PHE 0.011 0.002 PHE D 282 TRP 0.008 0.001 TRP B 169 HIS 0.007 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.18 (22348) covalent geometry : angle 0.63816 / 0.32 (30376) hydrogen bonds : bond 0.04794 / 3.27 ( 855) hydrogen bonds : angle 5.13618 / 3.69 ( 2319) metal coordination : bond 0.00385 / 0.29 ( 16) metal coordination : angle 4.84361 / 3.42 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 261 time to evaluate : 0.811 Fit side-chains REVERT: A 127 ASN cc_start: 0.7998 (p0) cc_final: 0.6611 (m-40) REVERT: A 226 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7577 (mt-10) REVERT: A 446 ASP cc_start: 0.7940 (m-30) cc_final: 0.7698 (m-30) REVERT: B 277 VAL cc_start: 0.8882 (m) cc_final: 0.8636 (t) REVERT: B 446 ASP cc_start: 0.7941 (m-30) cc_final: 0.7655 (m-30) REVERT: B 514 GLU cc_start: 0.7610 (pm20) cc_final: 0.7403 (pm20) REVERT: C 226 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7635 (mm-30) REVERT: C 403 LYS cc_start: 0.8634 (ttmt) cc_final: 0.8231 (ttmm) REVERT: D 93 ARG cc_start: 0.8910 (ttt90) cc_final: 0.8654 (ttt-90) REVERT: D 403 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8267 (ttmm) REVERT: E 152 ASP cc_start: 0.8521 (t70) cc_final: 0.8168 (t70) REVERT: F 138 ASN cc_start: 0.7471 (p0) cc_final: 0.6602 (t0) REVERT: F 161 LYS cc_start: 0.6515 (mtpt) cc_final: 0.6113 (tptt) REVERT: H 149 ASN cc_start: 0.9097 (t0) cc_final: 0.8884 (t0) outliers start: 16 outliers final: 14 residues processed: 269 average time/residue: 0.1709 time to fit residues: 68.7522 Evaluate side-chains 259 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 245 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 194 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 38 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 216 optimal weight: 40.0000 chunk 265 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 252 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 431 ASN B 127 ASN B 350 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.141863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.101282 restraints weight = 21932.497| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.44 r_work: 0.2562 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22364 Z= 0.153 Angle : 0.634 8.722 30424 Z= 0.302 Chirality : 0.047 0.162 3448 Planarity : 0.005 0.048 3880 Dihedral : 6.253 54.406 3076 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.01 % Allowed : 6.07 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 0.29 (0.15), residues: 2756 helix: 1.42 (0.20), residues: 728 sheet: 0.67 (0.19), residues: 648 loop : -0.71 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 198 TYR 0.014 0.002 TYR D 459 PHE 0.010 0.002 PHE D 282 TRP 0.009 0.001 TRP D 169 HIS 0.006 0.001 HIS C 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.15 (22348) covalent geometry : angle 0.60202 / 0.30 (30376) hydrogen bonds : bond 0.04360 / 2.98 ( 855) hydrogen bonds : angle 4.97505 / 3.57 ( 2319) metal coordination : bond 0.00213 / 0.17 ( 16) metal coordination : angle 5.06388 / 3.56 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 249 time to evaluate : 0.731 Fit side-chains REVERT: A 127 ASN cc_start: 0.8004 (p0) cc_final: 0.6671 (m-40) REVERT: A 446 ASP cc_start: 0.7975 (m-30) cc_final: 0.7732 (m-30) REVERT: B 22 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8326 (tp30) REVERT: B 262 ASN cc_start: 0.9127 (p0) cc_final: 0.8775 (p0) REVERT: B 277 VAL cc_start: 0.8886 (m) cc_final: 0.8640 (t) REVERT: B 446 ASP cc_start: 0.7976 (m-30) cc_final: 0.7700 (m-30) REVERT: B 514 GLU cc_start: 0.7638 (pm20) cc_final: 0.7363 (pm20) REVERT: C 226 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7618 (mm-30) REVERT: C 403 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8176 (ttmm) REVERT: D 93 ARG cc_start: 0.8926 (ttt90) cc_final: 0.8663 (ttt-90) REVERT: E 159 LYS cc_start: 0.6551 (mmtm) cc_final: 0.6294 (mmtm) REVERT: F 138 ASN cc_start: 0.7286 (p0) cc_final: 0.6419 (t0) REVERT: F 161 LYS cc_start: 0.6560 (mtpt) cc_final: 0.6094 (mmtp) REVERT: H 149 ASN cc_start: 0.9120 (t0) cc_final: 0.8877 (t0) outliers start: 24 outliers final: 15 residues processed: 262 average time/residue: 0.1617 time to fit residues: 63.3741 Evaluate side-chains 254 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 239 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 194 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 116 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 176 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS B 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.140030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.096630 restraints weight = 21895.362| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.09 r_work: 0.2610 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22364 Z= 0.210 Angle : 0.692 9.670 30424 Z= 0.333 Chirality : 0.049 0.182 3448 Planarity : 0.006 0.049 3880 Dihedral : 6.323 53.434 3076 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.21 % Allowed : 7.29 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 0.12 (0.15), residues: 2756 helix: 1.19 (0.19), residues: 728 sheet: 0.66 (0.19), residues: 648 loop : -0.81 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 198 TYR 0.016 0.002 TYR D 459 PHE 0.012 0.002 PHE C 282 TRP 0.010 0.001 TRP B 169 HIS 0.008 0.001 HIS D 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.21 (22348) covalent geometry : angle 0.66145 / 0.33 (30376) hydrogen bonds : bond 0.05102 / 3.49 ( 855) hydrogen bonds : angle 5.04703 / 3.64 ( 2319) metal coordination : bond 0.00125 / 0.08 ( 16) metal coordination : angle 5.19941 / 3.68 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.796 Fit side-chains REVERT: A 127 ASN cc_start: 0.8007 (p0) cc_final: 0.6689 (m-40) REVERT: A 226 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7591 (mt-10) REVERT: B 22 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8226 (tp30) REVERT: B 257 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: B 262 ASN cc_start: 0.9111 (p0) cc_final: 0.8688 (p0) REVERT: B 446 ASP cc_start: 0.7815 (m-30) cc_final: 0.7594 (m-30) REVERT: C 226 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7539 (mm-30) REVERT: D 93 ARG cc_start: 0.8915 (ttt90) cc_final: 0.8652 (ttt-90) REVERT: E 159 LYS cc_start: 0.6564 (mmtm) cc_final: 0.6311 (mmtm) REVERT: F 60 ASP cc_start: 0.7888 (m-30) cc_final: 0.7535 (m-30) REVERT: F 138 ASN cc_start: 0.7286 (p0) cc_final: 0.6372 (t0) REVERT: F 161 LYS cc_start: 0.6485 (mtpt) cc_final: 0.5991 (mmtp) outliers start: 29 outliers final: 20 residues processed: 257 average time/residue: 0.1621 time to fit residues: 62.5742 Evaluate side-chains 253 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 194 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 265 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 1 optimal weight: 0.0270 chunk 153 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 192 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 GLN B 127 ASN B 470 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.143205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.105008 restraints weight = 21755.431| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.03 r_work: 0.2621 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22364 Z= 0.110 Angle : 0.589 9.054 30424 Z= 0.275 Chirality : 0.045 0.156 3448 Planarity : 0.005 0.048 3880 Dihedral : 5.964 52.808 3076 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.88 % Allowed : 8.38 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 0.43 (0.15), residues: 2756 helix: 1.57 (0.20), residues: 728 sheet: 0.81 (0.19), residues: 648 loop : -0.68 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 130 TYR 0.011 0.001 TYR C 286 PHE 0.008 0.001 PHE F 216 TRP 0.009 0.001 TRP D 169 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (22348) covalent geometry : angle 0.54938 / 0.27 (30376) hydrogen bonds : bond 0.03500 / 2.37 ( 855) hydrogen bonds : angle 4.75608 / 3.43 ( 2319) metal coordination : bond 0.00172 / 0.13 ( 16) metal coordination : angle 5.36263 / 3.78 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.754 Fit side-chains REVERT: A 226 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7562 (mt-10) REVERT: B 22 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8225 (tp30) REVERT: B 262 ASN cc_start: 0.9117 (p0) cc_final: 0.8763 (p0) REVERT: B 446 ASP cc_start: 0.7882 (m-30) cc_final: 0.7651 (m-30) REVERT: C 226 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7601 (mm-30) REVERT: D 93 ARG cc_start: 0.8870 (ttt90) cc_final: 0.8583 (ttt-90) REVERT: E 159 LYS cc_start: 0.6643 (mmtm) cc_final: 0.6410 (mmtm) REVERT: F 60 ASP cc_start: 0.7881 (m-30) cc_final: 0.7485 (m-30) REVERT: F 161 LYS cc_start: 0.6569 (mtpt) cc_final: 0.6111 (mmtp) outliers start: 21 outliers final: 18 residues processed: 259 average time/residue: 0.1649 time to fit residues: 64.1053 Evaluate side-chains 251 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 233 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 194 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 191 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 20 optimal weight: 0.0000 chunk 7 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 ASN B 127 ASN B 470 GLN G 138 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.141122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.102755 restraints weight = 21900.219| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.02 r_work: 0.2551 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22364 Z= 0.147 Angle : 0.626 8.992 30424 Z= 0.295 Chirality : 0.046 0.159 3448 Planarity : 0.005 0.049 3880 Dihedral : 6.061 52.875 3076 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.21 % Allowed : 8.79 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 0.31 (0.15), residues: 2756 helix: 1.33 (0.19), residues: 752 sheet: 0.80 (0.19), residues: 648 loop : -0.72 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 137 TYR 0.013 0.002 TYR D 459 PHE 0.010 0.002 PHE D 282 TRP 0.009 0.001 TRP A 169 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (22348) covalent geometry : angle 0.58927 / 0.29 (30376) hydrogen bonds : bond 0.04181 / 2.84 ( 855) hydrogen bonds : angle 4.82904 / 3.48 ( 2319) metal coordination : bond 0.00124 / 0.10 ( 16) metal coordination : angle 5.34570 / 3.77 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.853 Fit side-chains REVERT: A 226 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7646 (mt-10) REVERT: B 22 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8256 (tp30) REVERT: B 262 ASN cc_start: 0.9146 (p0) cc_final: 0.8783 (p0) REVERT: C 226 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7657 (mm-30) REVERT: D 93 ARG cc_start: 0.8954 (ttt90) cc_final: 0.8677 (ttt-90) REVERT: E 159 LYS cc_start: 0.6617 (mmtm) cc_final: 0.6408 (mmtm) REVERT: F 60 ASP cc_start: 0.7895 (m-30) cc_final: 0.7500 (m-30) REVERT: F 161 LYS cc_start: 0.6477 (mtpt) cc_final: 0.5960 (mmtp) outliers start: 29 outliers final: 23 residues processed: 252 average time/residue: 0.1641 time to fit residues: 62.1709 Evaluate side-chains 256 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 194 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 69 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 ASN B 470 GLN G 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.142200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.103657 restraints weight = 21848.623| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.01 r_work: 0.2583 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22364 Z= 0.120 Angle : 0.597 9.113 30424 Z= 0.278 Chirality : 0.045 0.157 3448 Planarity : 0.005 0.048 3880 Dihedral : 5.936 52.845 3076 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.13 % Allowed : 9.09 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 0.41 (0.15), residues: 2756 helix: 1.43 (0.20), residues: 752 sheet: 0.84 (0.19), residues: 648 loop : -0.66 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 130 TYR 0.013 0.001 TYR C 286 PHE 0.009 0.001 PHE C 282 TRP 0.008 0.001 TRP A 169 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (22348) covalent geometry : angle 0.55680 / 0.28 (30376) hydrogen bonds : bond 0.03669 / 2.49 ( 855) hydrogen bonds : angle 4.72370 / 3.41 ( 2319) metal coordination : bond 0.00154 / 0.13 ( 16) metal coordination : angle 5.42772 / 3.84 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 0.810 Fit side-chains REVERT: A 226 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7630 (mt-10) REVERT: B 257 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8527 (tt0) REVERT: B 262 ASN cc_start: 0.9137 (p0) cc_final: 0.8756 (p0) REVERT: C 226 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7624 (mm-30) REVERT: D 93 ARG cc_start: 0.8916 (ttt90) cc_final: 0.8632 (ttt-90) REVERT: E 159 LYS cc_start: 0.6572 (mmtm) cc_final: 0.6366 (mmtm) REVERT: F 60 ASP cc_start: 0.7877 (m-30) cc_final: 0.7448 (m-30) REVERT: F 161 LYS cc_start: 0.6412 (mtpt) cc_final: 0.5890 (mmtp) outliers start: 27 outliers final: 24 residues processed: 253 average time/residue: 0.1615 time to fit residues: 61.4227 Evaluate side-chains 258 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 194 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 153 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 231 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 175 optimal weight: 0.6980 chunk 193 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 431 ASN B 127 ASN B 470 GLN C 350 ASN D 153 GLN G 138 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.141075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.103123 restraints weight = 21918.965| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.97 r_work: 0.2539 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22364 Z= 0.151 Angle : 0.629 9.109 30424 Z= 0.295 Chirality : 0.047 0.158 3448 Planarity : 0.005 0.050 3880 Dihedral : 6.048 52.835 3076 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.42 % Allowed : 9.09 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 0.30 (0.15), residues: 2756 helix: 1.30 (0.19), residues: 752 sheet: 0.81 (0.19), residues: 648 loop : -0.72 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 130 TYR 0.013 0.002 TYR D 459 PHE 0.011 0.002 PHE D 282 TRP 0.008 0.001 TRP B 169 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 (22348) covalent geometry : angle 0.59123 / 0.29 (30376) hydrogen bonds : bond 0.04193 / 2.85 ( 855) hydrogen bonds : angle 4.81007 / 3.47 ( 2319) metal coordination : bond 0.00108 / 0.09 ( 16) metal coordination : angle 5.40851 / 3.83 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.638 Fit side-chains REVERT: A 226 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7675 (mt-10) REVERT: B 257 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8544 (tt0) REVERT: B 262 ASN cc_start: 0.9170 (p0) cc_final: 0.8792 (p0) REVERT: C 226 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7699 (mm-30) REVERT: D 93 ARG cc_start: 0.8957 (ttt90) cc_final: 0.8680 (ttt-90) REVERT: E 159 LYS cc_start: 0.6611 (mmtm) cc_final: 0.6400 (mmtm) REVERT: F 60 ASP cc_start: 0.7958 (m-30) cc_final: 0.7564 (m-30) REVERT: F 161 LYS cc_start: 0.6483 (mtpt) cc_final: 0.5971 (mmtp) outliers start: 34 outliers final: 28 residues processed: 258 average time/residue: 0.1747 time to fit residues: 67.6275 Evaluate side-chains 260 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 231 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 194 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 194 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 ASN B 470 GLN G 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.142296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.105411 restraints weight = 21877.005| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.84 r_work: 0.2579 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22364 Z= 0.116 Angle : 0.593 9.106 30424 Z= 0.276 Chirality : 0.045 0.163 3448 Planarity : 0.005 0.048 3880 Dihedral : 5.922 52.820 3076 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.05 % Allowed : 9.38 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 0.43 (0.15), residues: 2756 helix: 1.45 (0.20), residues: 752 sheet: 0.86 (0.19), residues: 648 loop : -0.66 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 93 TYR 0.013 0.001 TYR B 286 PHE 0.008 0.001 PHE F 216 TRP 0.008 0.001 TRP B 169 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (22348) covalent geometry : angle 0.55329 / 0.28 (30376) hydrogen bonds : bond 0.03592 / 2.44 ( 855) hydrogen bonds : angle 4.70187 / 3.39 ( 2319) metal coordination : bond 0.00153 / 0.12 ( 16) metal coordination : angle 5.41511 / 3.84 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.756 Fit side-chains REVERT: A 226 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7632 (mt-10) REVERT: B 257 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8545 (tt0) REVERT: B 262 ASN cc_start: 0.9149 (p0) cc_final: 0.8777 (p0) REVERT: C 226 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7689 (mm-30) REVERT: D 93 ARG cc_start: 0.8917 (ttt90) cc_final: 0.8634 (ttt-90) REVERT: E 159 LYS cc_start: 0.6647 (mmtm) cc_final: 0.6440 (mmtm) REVERT: F 60 ASP cc_start: 0.7949 (m-30) cc_final: 0.7566 (m-30) REVERT: F 161 LYS cc_start: 0.6535 (mtpt) cc_final: 0.6061 (mmtp) outliers start: 25 outliers final: 23 residues processed: 249 average time/residue: 0.1682 time to fit residues: 62.3490 Evaluate side-chains 253 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 194 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 76 optimal weight: 0.3980 chunk 21 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 148 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN B 127 ASN B 470 GLN C 350 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.147702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.107366 restraints weight = 21494.965| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.40 r_work: 0.2697 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22364 Z= 0.145 Angle : 0.623 9.149 30424 Z= 0.292 Chirality : 0.046 0.158 3448 Planarity : 0.005 0.049 3880 Dihedral : 6.024 52.862 3076 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.26 % Allowed : 9.30 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 0.33 (0.15), residues: 2756 helix: 1.33 (0.19), residues: 752 sheet: 0.83 (0.19), residues: 648 loop : -0.72 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 130 TYR 0.013 0.002 TYR D 459 PHE 0.011 0.002 PHE D 282 TRP 0.008 0.001 TRP B 169 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.14 (22348) covalent geometry : angle 0.58527 / 0.29 (30376) hydrogen bonds : bond 0.04095 / 2.79 ( 855) hydrogen bonds : angle 4.77886 / 3.45 ( 2319) metal coordination : bond 0.00101 / 0.08 ( 16) metal coordination : angle 5.42494 / 3.84 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5512 Ramachandran restraints generated. 2756 Oldfield, 0 Emsley, 2756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.849 Fit side-chains REVERT: A 226 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7641 (mt-10) REVERT: B 257 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: B 262 ASN cc_start: 0.9163 (p0) cc_final: 0.8771 (p0) REVERT: C 226 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7665 (mm-30) REVERT: D 93 ARG cc_start: 0.8959 (ttt90) cc_final: 0.8680 (ttt-90) REVERT: E 159 LYS cc_start: 0.6600 (mmtm) cc_final: 0.6389 (mmtm) REVERT: F 60 ASP cc_start: 0.7959 (m-30) cc_final: 0.7561 (m-30) REVERT: F 161 LYS cc_start: 0.6434 (mtpt) cc_final: 0.5909 (mmtp) REVERT: H 154 GLU cc_start: 0.7512 (pm20) cc_final: 0.7292 (pm20) outliers start: 30 outliers final: 29 residues processed: 254 average time/residue: 0.1734 time to fit residues: 65.3603 Evaluate side-chains 264 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 194 ASP Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 194 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 26 optimal weight: 0.0060 chunk 57 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 259 optimal weight: 30.0000 chunk 222 optimal weight: 6.9990 chunk 199 optimal weight: 30.0000 chunk 159 optimal weight: 0.0050 overall best weight: 2.0016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 ASN B 470 GLN C 350 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.141560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.103229 restraints weight = 21913.900| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.99 r_work: 0.2579 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22364 Z= 0.125 Angle : 0.609 9.087 30424 Z= 0.285 Chirality : 0.045 0.157 3448 Planarity : 0.005 0.049 3880 Dihedral : 5.985 52.797 3076 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.21 % Allowed : 9.46 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.15 % 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: 0.37 (0.15), residues: 2756 helix: 1.39 (0.20), residues: 752 sheet: 0.85 (0.19), residues: 648 loop : -0.70 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 130 TYR 0.013 0.001 TYR B 286 PHE 0.009 0.001 PHE D 282 TRP 0.009 0.001 TRP B 169 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (22348) covalent geometry : angle 0.57002 / 0.28 (30376) hydrogen bonds : bond 0.03834 / 2.60 ( 855) hydrogen bonds : angle 4.74224 / 3.42 ( 2319) metal coordination : bond 0.00126 / 0.10 ( 16) metal coordination : angle 5.43118 / 3.84 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4544.63 seconds wall clock time: 78 minutes 41.34 seconds (4721.34 seconds total)