Starting phenix.real_space_refine on Thu Feb 5 18:31:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9it2_60854/02_2026/9it2_60854.cif Found real_map, /net/cci-nas-00/data/ceres_data/9it2_60854/02_2026/9it2_60854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9it2_60854/02_2026/9it2_60854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9it2_60854/02_2026/9it2_60854.map" model { file = "/net/cci-nas-00/data/ceres_data/9it2_60854/02_2026/9it2_60854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9it2_60854/02_2026/9it2_60854.cif" } resolution = 2.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.066 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: 5 Type Number sf(0) Gaussians Ni 6 6.56 5 S 96 5.16 5 C 11772 2.51 5 N 3189 2.21 5 O 4028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19091 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 792 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 101, 784 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 101, 784 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} bond proxies already assigned to first conformer: 781 Chain: "B" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "C" Number of atoms: 4537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4537 Classifications: {'peptide': 598} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 575} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 792 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 101, 784 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 101, 784 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} bond proxies already assigned to first conformer: 781 Chain: "E" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "F" Number of atoms: 4537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4537 Classifications: {'peptide': 598} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 575} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 792 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 101, 784 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 101, 784 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} bond proxies already assigned to first conformer: 781 Chain: "H" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "I" Number of atoms: 4537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4537 Classifications: {'peptide': 598} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 575} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AMET A 70 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 70 " occ=0.50 residue: pdb=" N AMET D 70 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET D 70 " occ=0.50 residue: pdb=" N AMET G 70 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET G 70 " occ=0.50 Time building chain proxies: 4.62, per 1000 atoms: 0.24 Number of scatterers: 19091 At special positions: 0 Unit cell: (142.299, 140.553, 77.697, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ni 6 28.00 S 96 16.00 O 4028 8.00 N 3189 7.00 C 11772 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: 1.37 Conformation dependent library (CDL) restraints added in 927.8 milliseconds 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4428 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 39 sheets defined 34.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 4 through 26 removed outlier: 3.678A pdb=" N LEU A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU A 12 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE A 13 " --> pdb=" O GLN A 9 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'B' and resid 53 through 57 removed outlier: 3.574A pdb=" N VAL B 57 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 14 Processing helix chain 'C' and resid 148 through 156 Processing helix chain 'C' and resid 169 through 175 Processing helix chain 'C' and resid 179 through 192 removed outlier: 3.886A pdb=" N TRP C 183 " --> pdb=" O PRO C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 217 removed outlier: 3.768A pdb=" N GLN C 214 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 215 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 246 Processing helix chain 'C' and resid 261 through 270 removed outlier: 3.535A pdb=" N LYS C 270 " --> pdb=" O ILE C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 313 through 326 Processing helix chain 'C' and resid 332 through 341 removed outlier: 3.517A pdb=" N VAL C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 358 removed outlier: 3.914A pdb=" N ASP C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'C' and resid 375 through 392 Processing helix chain 'C' and resid 402 through 412 removed outlier: 3.740A pdb=" N LYS C 412 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 442 through 446 Processing helix chain 'C' and resid 483 through 485 No H-bonds generated for 'chain 'C' and resid 483 through 485' Processing helix chain 'C' and resid 486 through 493 removed outlier: 4.126A pdb=" N THR C 491 " --> pdb=" O GLY C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 505 Processing helix chain 'C' and resid 506 through 511 Processing helix chain 'C' and resid 527 through 531 Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 563 through 569 Processing helix chain 'D' and resid 4 through 26 removed outlier: 3.633A pdb=" N LEU D 11 " --> pdb=" O GLU D 7 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE D 13 " --> pdb=" O GLN D 9 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D 14 " --> pdb=" O LYS D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 50 Processing helix chain 'D' and resid 52 through 60 Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 72 through 77 Processing helix chain 'E' and resid 53 through 57 removed outlier: 3.542A pdb=" N VAL E 57 " --> pdb=" O LEU E 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 14 Processing helix chain 'F' and resid 148 through 156 Processing helix chain 'F' and resid 169 through 175 Processing helix chain 'F' and resid 179 through 192 removed outlier: 3.883A pdb=" N TRP F 183 " --> pdb=" O PRO F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 217 removed outlier: 3.787A pdb=" N GLN F 214 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE F 215 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'F' and resid 231 through 246 Processing helix chain 'F' and resid 261 through 270 removed outlier: 3.544A pdb=" N LYS F 270 " --> pdb=" O ILE F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 313 through 326 removed outlier: 3.529A pdb=" N HIS F 326 " --> pdb=" O LEU F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 341 Processing helix chain 'F' and resid 344 through 358 removed outlier: 3.906A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU F 353 " --> pdb=" O ALA F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'F' and resid 375 through 392 Processing helix chain 'F' and resid 402 through 411 Processing helix chain 'F' and resid 414 through 421 removed outlier: 3.825A pdb=" N ALA F 418 " --> pdb=" O THR F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 446 Processing helix chain 'F' and resid 483 through 485 No H-bonds generated for 'chain 'F' and resid 483 through 485' Processing helix chain 'F' and resid 486 through 493 removed outlier: 4.232A pdb=" N THR F 491 " --> pdb=" O GLY F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 505 Processing helix chain 'F' and resid 506 through 511 Processing helix chain 'F' and resid 527 through 531 Processing helix chain 'F' and resid 553 through 557 Processing helix chain 'F' and resid 563 through 569 Processing helix chain 'G' and resid 4 through 26 removed outlier: 3.620A pdb=" N LEU G 11 " --> pdb=" O GLU G 7 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU G 12 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE G 13 " --> pdb=" O GLN G 9 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR G 14 " --> pdb=" O LYS G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 50 Processing helix chain 'G' and resid 52 through 60 removed outlier: 3.601A pdb=" N GLN G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'H' and resid 53 through 57 removed outlier: 3.502A pdb=" N VAL H 57 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 14 Processing helix chain 'I' and resid 148 through 156 Processing helix chain 'I' and resid 169 through 175 Processing helix chain 'I' and resid 179 through 192 removed outlier: 3.882A pdb=" N TRP I 183 " --> pdb=" O PRO I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 217 removed outlier: 4.005A pdb=" N GLN I 214 " --> pdb=" O PRO I 210 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE I 215 " --> pdb=" O ILE I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 231 through 246 Processing helix chain 'I' and resid 261 through 270 removed outlier: 3.663A pdb=" N LYS I 270 " --> pdb=" O ILE I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 296 removed outlier: 3.502A pdb=" N VAL I 294 " --> pdb=" O LEU I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 308 No H-bonds generated for 'chain 'I' and resid 306 through 308' Processing helix chain 'I' and resid 313 through 326 removed outlier: 3.511A pdb=" N LEU I 322 " --> pdb=" O HIS I 318 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET I 323 " --> pdb=" O LEU I 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 341 Processing helix chain 'I' and resid 344 through 358 removed outlier: 3.906A pdb=" N ASP I 352 " --> pdb=" O ILE I 348 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU I 353 " --> pdb=" O ALA I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 374 No H-bonds generated for 'chain 'I' and resid 372 through 374' Processing helix chain 'I' and resid 375 through 392 Processing helix chain 'I' and resid 402 through 412 removed outlier: 3.773A pdb=" N LYS I 412 " --> pdb=" O ARG I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 421 Processing helix chain 'I' and resid 442 through 446 Processing helix chain 'I' and resid 483 through 490 removed outlier: 6.606A pdb=" N GLY I 487 " --> pdb=" O GLY I 484 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ARG I 488 " --> pdb=" O THR I 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 499 through 505 Processing helix chain 'I' and resid 506 through 511 Processing helix chain 'I' and resid 527 through 531 Processing helix chain 'I' and resid 553 through 557 Processing helix chain 'I' and resid 563 through 569 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 86 Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 19 Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AA4, first strand: chain 'B' and resid 70 through 71 removed outlier: 4.396A pdb=" N PHE B 63 " --> pdb=" O ASP B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 49 Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AA7, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AA9, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 104 removed outlier: 5.109A pdb=" N ILE C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS C 96 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR C 89 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU C 81 " --> pdb=" O TYR C 89 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ALA C 91 " --> pdb=" O ASN C 79 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN C 79 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL C 76 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 104 removed outlier: 5.109A pdb=" N ILE C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS C 96 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR C 89 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU C 81 " --> pdb=" O TYR C 89 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ALA C 91 " --> pdb=" O ASN C 79 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN C 79 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TYR C 133 " --> pdb=" O ASN C 79 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU C 81 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ALA C 135 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N VAL C 83 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR C 452 " --> pdb=" O ALA C 440 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL C 453 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB4, first strand: chain 'C' and resid 137 through 143 removed outlier: 5.730A pdb=" N GLY C 137 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS C 141 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLY C 164 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N HIS C 143 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR C 159 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLY C 199 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL C 161 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU C 201 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ALA C 163 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N LYS C 203 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N GLY C 221 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE C 200 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N KCX C 223 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA C 202 " --> pdb=" O KCX C 223 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N HIS C 225 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU C 222 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N HIS C 252 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE C 224 " --> pdb=" O HIS C 252 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 249 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 274 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA C 302 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA C 276 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N THR C 304 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 137 through 143 removed outlier: 5.730A pdb=" N GLY C 137 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS C 141 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLY C 164 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N HIS C 143 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR C 159 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLY C 199 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL C 161 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU C 201 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ALA C 163 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N LYS C 203 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA C 198 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER C 496 " --> pdb=" O LEU C 518 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AB7, first strand: chain 'D' and resid 79 through 86 Processing sheet with id=AB8, first strand: chain 'E' and resid 70 through 71 removed outlier: 4.458A pdb=" N PHE E 63 " --> pdb=" O ASP E 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 46 through 49 Processing sheet with id=AC1, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AC2, first strand: chain 'F' and resid 2 through 4 Processing sheet with id=AC3, first strand: chain 'F' and resid 29 through 31 Processing sheet with id=AC4, first strand: chain 'F' and resid 66 through 67 Processing sheet with id=AC5, first strand: chain 'F' and resid 99 through 104 removed outlier: 5.135A pdb=" N ILE F 100 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS F 96 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TYR F 89 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU F 81 " --> pdb=" O TYR F 89 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA F 91 " --> pdb=" O ASN F 79 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN F 79 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL F 76 " --> pdb=" O SER F 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 99 through 104 removed outlier: 5.135A pdb=" N ILE F 100 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS F 96 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TYR F 89 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU F 81 " --> pdb=" O TYR F 89 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA F 91 " --> pdb=" O ASN F 79 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN F 79 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N TYR F 133 " --> pdb=" O ASN F 79 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU F 81 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ALA F 135 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N VAL F 83 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR F 452 " --> pdb=" O ALA F 440 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL F 453 " --> pdb=" O ALA F 460 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 106 through 107 Processing sheet with id=AC8, first strand: chain 'F' and resid 137 through 143 removed outlier: 5.692A pdb=" N GLY F 137 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS F 141 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLY F 164 " --> pdb=" O HIS F 141 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N HIS F 143 " --> pdb=" O GLY F 164 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR F 159 " --> pdb=" O ASN F 197 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N GLY F 199 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL F 161 " --> pdb=" O GLY F 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU F 201 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA F 163 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N LYS F 203 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY F 221 " --> pdb=" O PHE F 200 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU F 222 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N HIS F 252 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE F 224 " --> pdb=" O HIS F 252 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL F 249 " --> pdb=" O HIS F 275 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE F 274 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA F 302 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA F 276 " --> pdb=" O ALA F 302 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR F 304 " --> pdb=" O ALA F 276 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 137 through 143 removed outlier: 5.692A pdb=" N GLY F 137 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS F 141 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLY F 164 " --> pdb=" O HIS F 141 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N HIS F 143 " --> pdb=" O GLY F 164 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR F 159 " --> pdb=" O ASN F 197 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N GLY F 199 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL F 161 " --> pdb=" O GLY F 199 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU F 201 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA F 163 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N LYS F 203 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA F 198 " --> pdb=" O PHE F 497 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER F 496 " --> pdb=" O LEU F 518 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AD2, first strand: chain 'G' and resid 79 through 86 Processing sheet with id=AD3, first strand: chain 'H' and resid 70 through 71 removed outlier: 4.549A pdb=" N PHE H 63 " --> pdb=" O ASP H 71 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 46 through 49 Processing sheet with id=AD5, first strand: chain 'H' and resid 110 through 111 Processing sheet with id=AD6, first strand: chain 'I' and resid 66 through 67 Processing sheet with id=AD7, first strand: chain 'I' and resid 99 through 104 removed outlier: 5.088A pdb=" N ILE I 100 " --> pdb=" O LYS I 96 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LYS I 96 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR I 89 " --> pdb=" O LEU I 81 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU I 81 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ALA I 91 " --> pdb=" O ASN I 79 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN I 79 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL I 76 " --> pdb=" O SER I 126 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 99 through 104 removed outlier: 5.088A pdb=" N ILE I 100 " --> pdb=" O LYS I 96 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LYS I 96 " --> pdb=" O ILE I 100 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR I 89 " --> pdb=" O LEU I 81 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU I 81 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ALA I 91 " --> pdb=" O ASN I 79 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN I 79 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N TYR I 133 " --> pdb=" O ASN I 79 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU I 81 " --> pdb=" O TYR I 133 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ALA I 135 " --> pdb=" O LEU I 81 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N VAL I 83 " --> pdb=" O ALA I 135 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR I 452 " --> pdb=" O ALA I 440 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL I 453 " --> pdb=" O ALA I 460 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 106 through 107 Processing sheet with id=AE1, first strand: chain 'I' and resid 137 through 143 removed outlier: 6.512A pdb=" N GLY I 137 " --> pdb=" O THR I 160 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE I 162 " --> pdb=" O GLY I 137 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASP I 139 " --> pdb=" O ILE I 162 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY I 164 " --> pdb=" O ASP I 139 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N HIS I 141 " --> pdb=" O GLY I 164 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N GLY I 221 " --> pdb=" O ALA I 198 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE I 200 " --> pdb=" O GLY I 221 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N KCX I 223 " --> pdb=" O PHE I 200 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA I 202 " --> pdb=" O KCX I 223 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N HIS I 225 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU I 222 " --> pdb=" O ALA I 250 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N HIS I 252 " --> pdb=" O LEU I 222 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE I 224 " --> pdb=" O HIS I 252 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL I 249 " --> pdb=" O HIS I 275 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE I 274 " --> pdb=" O LEU I 300 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA I 302 " --> pdb=" O ILE I 274 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA I 276 " --> pdb=" O ALA I 302 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N THR I 304 " --> pdb=" O ALA I 276 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 137 through 143 removed outlier: 6.512A pdb=" N GLY I 137 " --> pdb=" O THR I 160 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE I 162 " --> pdb=" O GLY I 137 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASP I 139 " --> pdb=" O ILE I 162 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY I 164 " --> pdb=" O ASP I 139 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N HIS I 141 " --> pdb=" O GLY I 164 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA I 198 " --> pdb=" O PHE I 497 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER I 496 " --> pdb=" O LEU I 518 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 541 through 542 711 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6204 1.34 - 1.46: 3944 1.46 - 1.58: 8656 1.58 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 18978 Sorted by residual: bond pdb=" NZ KCX C 223 " pdb=" CX KCX C 223 " ideal model delta sigma weight residual 1.411 1.333 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" NZ KCX I 223 " pdb=" CX KCX I 223 " ideal model delta sigma weight residual 1.411 1.334 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" NZ KCX F 223 " pdb=" CX KCX F 223 " ideal model delta sigma weight residual 1.411 1.334 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" CE KCX F 223 " pdb=" NZ KCX F 223 " ideal model delta sigma weight residual 1.442 1.498 -0.056 2.00e-02 2.50e+03 7.73e+00 bond pdb=" CE KCX C 223 " pdb=" NZ KCX C 223 " ideal model delta sigma weight residual 1.442 1.497 -0.055 2.00e-02 2.50e+03 7.50e+00 ... (remaining 18973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 25334 1.89 - 3.77: 280 3.77 - 5.66: 39 5.66 - 7.54: 8 7.54 - 9.43: 10 Bond angle restraints: 25671 Sorted by residual: angle pdb=" N ASN C 305 " pdb=" CA ASN C 305 " pdb=" C ASN C 305 " ideal model delta sigma weight residual 109.81 117.59 -7.78 2.21e+00 2.05e-01 1.24e+01 angle pdb=" N ASN F 305 " pdb=" CA ASN F 305 " pdb=" C ASN F 305 " ideal model delta sigma weight residual 109.81 117.55 -7.74 2.21e+00 2.05e-01 1.23e+01 angle pdb=" N ASN I 305 " pdb=" CA ASN I 305 " pdb=" C ASN I 305 " ideal model delta sigma weight residual 109.81 117.50 -7.69 2.21e+00 2.05e-01 1.21e+01 angle pdb=" CB MET C 387 " pdb=" CG MET C 387 " pdb=" SD MET C 387 " ideal model delta sigma weight residual 112.70 122.13 -9.43 3.00e+00 1.11e-01 9.88e+00 angle pdb=" CA PRO F 538 " pdb=" CB PRO F 538 " pdb=" CG PRO F 538 " ideal model delta sigma weight residual 104.50 98.83 5.67 1.90e+00 2.77e-01 8.91e+00 ... (remaining 25666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10209 17.95 - 35.90: 928 35.90 - 53.85: 195 53.85 - 71.80: 46 71.80 - 89.75: 25 Dihedral angle restraints: 11403 sinusoidal: 4476 harmonic: 6927 Sorted by residual: dihedral pdb=" CA LEU F 591 " pdb=" C LEU F 591 " pdb=" N ALA F 592 " pdb=" CA ALA F 592 " ideal model delta harmonic sigma weight residual -180.00 -157.90 -22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU I 591 " pdb=" C LEU I 591 " pdb=" N ALA I 592 " pdb=" CA ALA I 592 " ideal model delta harmonic sigma weight residual -180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ILE C 308 " pdb=" C ILE C 308 " pdb=" N PRO C 309 " pdb=" CA PRO C 309 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 11400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2230 0.047 - 0.094: 519 0.094 - 0.141: 185 0.141 - 0.188: 0 0.188 - 0.235: 3 Chirality restraints: 2937 Sorted by residual: chirality pdb=" CA ASN F 305 " pdb=" N ASN F 305 " pdb=" C ASN F 305 " pdb=" CB ASN F 305 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ASN C 305 " pdb=" N ASN C 305 " pdb=" C ASN C 305 " pdb=" CB ASN C 305 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASN I 305 " pdb=" N ASN I 305 " pdb=" C ASN I 305 " pdb=" CB ASN I 305 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2934 not shown) Planarity restraints: 3312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 308 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO C 309 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 309 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 309 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 287 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO F 288 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO F 288 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 288 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 287 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO C 288 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 288 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 288 " 0.028 5.00e-02 4.00e+02 ... (remaining 3309 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 221 2.56 - 3.14: 15709 3.14 - 3.73: 33350 3.73 - 4.31: 51013 4.31 - 4.90: 78497 Nonbonded interactions: 178790 Sorted by model distance: nonbonded pdb=" NE2 HIS F 141 " pdb="NI NI F 603 " model vdw 1.972 2.260 nonbonded pdb=" NE2 HIS I 141 " pdb="NI NI I 603 " model vdw 1.974 2.260 nonbonded pdb=" NE2 HIS C 141 " pdb="NI NI C 603 " model vdw 1.975 2.260 nonbonded pdb=" NE2 HIS C 278 " pdb="NI NI C 602 " model vdw 1.976 2.260 nonbonded pdb=" ND1 HIS C 252 " pdb="NI NI C 602 " model vdw 1.981 2.260 ... (remaining 178785 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' and (resid 1 through 69 or resid 71 through 101)) selection = (chain 'D' and (resid 1 through 69 or resid 71 through 101)) selection = (chain 'G' and (resid 1 through 69 or resid 71 through 101)) } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } 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=0.50 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: 4.190 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.080 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.002 0.078 18978 Z= 0.121 Angle : 0.540 9.429 25671 Z= 0.286 Chirality : 0.044 0.235 2937 Planarity : 0.004 0.104 3312 Dihedral : 15.240 89.755 6975 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.94 % Favored : 96.93 % Rotamer: Outliers : 0.85 % Allowed : 8.95 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2421 helix: 0.28 (0.20), residues: 699 sheet: 0.07 (0.26), residues: 354 loop : -0.23 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 342 TYR 0.015 0.001 TYR I 452 PHE 0.009 0.001 PHE I 200 TRP 0.014 0.002 TRP F 183 HIS 0.004 0.001 HIS F 385 Details of bonding type rmsd covalent geometry : bond 0.00245 (18978) covalent geometry : angle 0.53956 (25671) hydrogen bonds : bond 0.18895 ( 676) hydrogen bonds : angle 7.04088 ( 1842) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 0.806 Fit side-chains REVERT: B 75 LYS cc_start: 0.7700 (mtmm) cc_final: 0.7387 (mmmt) outliers start: 17 outliers final: 14 residues processed: 248 average time/residue: 0.6630 time to fit residues: 182.4202 Evaluate side-chains 244 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 230 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 455 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122333 restraints weight = 43753.788| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.41 r_work: 0.3253 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18978 Z= 0.137 Angle : 0.586 8.378 25671 Z= 0.317 Chirality : 0.047 0.237 2937 Planarity : 0.004 0.069 3312 Dihedral : 6.159 51.918 2647 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.74 % Favored : 97.14 % Rotamer: Outliers : 1.41 % Allowed : 8.30 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.17), residues: 2421 helix: 0.53 (0.20), residues: 693 sheet: 0.12 (0.26), residues: 354 loop : -0.23 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 405 TYR 0.019 0.002 TYR F 452 PHE 0.014 0.001 PHE C 200 TRP 0.015 0.002 TRP F 441 HIS 0.005 0.001 HIS F 421 Details of bonding type rmsd covalent geometry : bond 0.00281 (18978) covalent geometry : angle 0.58627 (25671) hydrogen bonds : bond 0.05534 ( 676) hydrogen bonds : angle 5.24403 ( 1842) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 0.747 Fit side-chains REVERT: B 75 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7362 (mmmt) REVERT: C 322 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6983 (mt) REVERT: C 543 ASP cc_start: 0.8314 (t70) cc_final: 0.8096 (t70) REVERT: C 582 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7480 (t0) REVERT: E 93 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7428 (mm-30) REVERT: F 566 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6497 (mm-30) REVERT: F 582 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7438 (t0) REVERT: I 308 ILE cc_start: 0.6033 (OUTLIER) cc_final: 0.5709 (mm) outliers start: 28 outliers final: 12 residues processed: 251 average time/residue: 0.6774 time to fit residues: 188.8945 Evaluate side-chains 243 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 226 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 455 LYS Chi-restraints excluded: chain I residue 471 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 211 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 212 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 554 ASN I 492 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.143899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.125031 restraints weight = 30501.860| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.16 r_work: 0.3291 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18978 Z= 0.117 Angle : 0.542 8.267 25671 Z= 0.293 Chirality : 0.045 0.238 2937 Planarity : 0.004 0.058 3312 Dihedral : 5.746 51.281 2636 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.81 % Rotamer: Outliers : 1.21 % Allowed : 8.60 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2421 helix: 0.68 (0.20), residues: 693 sheet: 0.19 (0.26), residues: 351 loop : -0.25 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 23 TYR 0.017 0.001 TYR I 452 PHE 0.012 0.001 PHE I 200 TRP 0.014 0.002 TRP F 441 HIS 0.005 0.001 HIS F 421 Details of bonding type rmsd covalent geometry : bond 0.00240 (18978) covalent geometry : angle 0.54249 (25671) hydrogen bonds : bond 0.04770 ( 676) hydrogen bonds : angle 4.97129 ( 1842) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.672 Fit side-chains REVERT: B 24 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: B 75 LYS cc_start: 0.7830 (mtmm) cc_final: 0.7384 (mmmt) REVERT: C 322 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6957 (mt) REVERT: C 543 ASP cc_start: 0.8309 (t70) cc_final: 0.8103 (t70) REVERT: C 582 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7464 (t0) REVERT: F 244 LYS cc_start: 0.7889 (mttt) cc_final: 0.7657 (mtmp) REVERT: F 566 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6509 (mm-30) REVERT: F 582 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7419 (t0) REVERT: I 207 MET cc_start: 0.7871 (mmp) cc_final: 0.7568 (mmp) REVERT: I 308 ILE cc_start: 0.5836 (OUTLIER) cc_final: 0.5522 (mm) outliers start: 24 outliers final: 12 residues processed: 247 average time/residue: 0.6634 time to fit residues: 182.2475 Evaluate side-chains 237 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 219 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 455 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 104 optimal weight: 0.0270 chunk 193 optimal weight: 6.9990 chunk 182 optimal weight: 0.0770 chunk 207 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 554 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.143483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.124623 restraints weight = 30063.058| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.16 r_work: 0.3286 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18978 Z= 0.121 Angle : 0.552 8.376 25671 Z= 0.297 Chirality : 0.046 0.230 2937 Planarity : 0.004 0.052 3312 Dihedral : 5.728 51.126 2635 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.81 % Rotamer: Outliers : 1.31 % Allowed : 8.65 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2421 helix: 0.72 (0.20), residues: 693 sheet: 0.19 (0.26), residues: 351 loop : -0.26 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 23 TYR 0.018 0.001 TYR F 452 PHE 0.013 0.001 PHE I 200 TRP 0.013 0.002 TRP F 441 HIS 0.005 0.001 HIS F 421 Details of bonding type rmsd covalent geometry : bond 0.00249 (18978) covalent geometry : angle 0.55179 (25671) hydrogen bonds : bond 0.04781 ( 676) hydrogen bonds : angle 4.91980 ( 1842) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.742 Fit side-chains REVERT: B 24 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: B 75 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7371 (mmmt) REVERT: C 322 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6961 (mt) REVERT: C 543 ASP cc_start: 0.8327 (t70) cc_final: 0.8113 (t70) REVERT: C 582 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7472 (t0) REVERT: F 244 LYS cc_start: 0.7951 (mttt) cc_final: 0.7698 (mtmp) REVERT: F 566 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6570 (mm-30) REVERT: F 582 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7429 (t0) REVERT: I 308 ILE cc_start: 0.5895 (OUTLIER) cc_final: 0.5577 (mm) outliers start: 26 outliers final: 13 residues processed: 243 average time/residue: 0.6867 time to fit residues: 185.6693 Evaluate side-chains 245 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 455 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 99 optimal weight: 0.1980 chunk 43 optimal weight: 7.9990 chunk 211 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 222 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 554 ASN G 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.145083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.126198 restraints weight = 31098.484| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.18 r_work: 0.3305 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18978 Z= 0.108 Angle : 0.525 8.326 25671 Z= 0.283 Chirality : 0.045 0.230 2937 Planarity : 0.004 0.052 3312 Dihedral : 5.585 50.780 2635 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.19 % Favored : 96.68 % Rotamer: Outliers : 1.11 % Allowed : 9.10 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.17), residues: 2421 helix: 0.83 (0.20), residues: 693 sheet: 0.24 (0.26), residues: 351 loop : -0.23 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 23 TYR 0.016 0.001 TYR I 452 PHE 0.011 0.001 PHE I 200 TRP 0.013 0.002 TRP F 441 HIS 0.004 0.001 HIS I 385 Details of bonding type rmsd covalent geometry : bond 0.00223 (18978) covalent geometry : angle 0.52527 (25671) hydrogen bonds : bond 0.04324 ( 676) hydrogen bonds : angle 4.79222 ( 1842) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 0.508 Fit side-chains REVERT: B 75 LYS cc_start: 0.7821 (mtmm) cc_final: 0.7377 (mmmt) REVERT: C 322 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6934 (mt) REVERT: C 543 ASP cc_start: 0.8335 (t70) cc_final: 0.8118 (t70) REVERT: E 93 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7510 (mm-30) REVERT: F 244 LYS cc_start: 0.7948 (mttt) cc_final: 0.7712 (mtmp) REVERT: F 566 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6538 (mm-30) REVERT: F 582 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7412 (t0) REVERT: I 383 MET cc_start: 0.8652 (ttp) cc_final: 0.8266 (ttp) outliers start: 22 outliers final: 16 residues processed: 251 average time/residue: 0.6871 time to fit residues: 192.0554 Evaluate side-chains 238 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 455 LYS Chi-restraints excluded: chain I residue 463 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 71 optimal weight: 0.3980 chunk 12 optimal weight: 7.9990 chunk 223 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 196 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 554 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.142392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.122868 restraints weight = 37690.120| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.31 r_work: 0.3259 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18978 Z= 0.140 Angle : 0.583 8.446 25671 Z= 0.314 Chirality : 0.047 0.228 2937 Planarity : 0.004 0.055 3312 Dihedral : 5.848 51.777 2635 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.82 % Favored : 97.06 % Rotamer: Outliers : 1.21 % Allowed : 9.10 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2421 helix: 0.74 (0.20), residues: 693 sheet: 0.18 (0.26), residues: 351 loop : -0.29 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 594 TYR 0.020 0.002 TYR F 452 PHE 0.015 0.002 PHE F 200 TRP 0.013 0.002 TRP F 441 HIS 0.006 0.001 HIS I 421 Details of bonding type rmsd covalent geometry : bond 0.00292 (18978) covalent geometry : angle 0.58302 (25671) hydrogen bonds : bond 0.05139 ( 676) hydrogen bonds : angle 4.96842 ( 1842) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.629 Fit side-chains REVERT: B 75 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7383 (mmmt) REVERT: C 322 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6939 (mt) REVERT: C 543 ASP cc_start: 0.8343 (t70) cc_final: 0.8109 (t70) REVERT: C 582 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7497 (t0) REVERT: E 93 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7503 (mm-30) REVERT: F 582 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7452 (t0) REVERT: I 170 ASP cc_start: 0.7435 (m-30) cc_final: 0.7228 (m-30) REVERT: I 308 ILE cc_start: 0.6071 (OUTLIER) cc_final: 0.5775 (mm) outliers start: 24 outliers final: 15 residues processed: 241 average time/residue: 0.6796 time to fit residues: 181.9847 Evaluate side-chains 244 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 455 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 0.0060 chunk 165 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 492 ASN F 554 ASN I 492 ASN I 539 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.120049 restraints weight = 45311.404| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.43 r_work: 0.3222 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18978 Z= 0.187 Angle : 0.665 8.813 25671 Z= 0.360 Chirality : 0.049 0.239 2937 Planarity : 0.005 0.060 3312 Dihedral : 6.241 53.735 2635 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 1.26 % Allowed : 9.10 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2421 helix: 0.46 (0.19), residues: 699 sheet: 0.08 (0.26), residues: 351 loop : -0.36 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 594 TYR 0.020 0.002 TYR F 452 PHE 0.019 0.002 PHE F 200 TRP 0.014 0.003 TRP F 441 HIS 0.008 0.002 HIS I 421 Details of bonding type rmsd covalent geometry : bond 0.00393 (18978) covalent geometry : angle 0.66501 (25671) hydrogen bonds : bond 0.06116 ( 676) hydrogen bonds : angle 5.24145 ( 1842) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.755 Fit side-chains REVERT: B 75 LYS cc_start: 0.7866 (mtmm) cc_final: 0.7395 (mmmt) REVERT: C 322 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6791 (mp) REVERT: C 582 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7441 (t0) REVERT: E 93 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7451 (mm-30) REVERT: F 582 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7441 (t0) REVERT: I 322 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6639 (mp) REVERT: I 387 MET cc_start: 0.8616 (mmp) cc_final: 0.8413 (mmp) outliers start: 25 outliers final: 14 residues processed: 245 average time/residue: 0.7011 time to fit residues: 191.0176 Evaluate side-chains 243 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 225 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain I residue 322 LEU Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 455 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 170 optimal weight: 0.0060 chunk 211 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 65 optimal weight: 0.2980 chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 162 optimal weight: 0.0870 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 492 ASN F 554 ASN I 492 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.145132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.126066 restraints weight = 33795.252| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.23 r_work: 0.3302 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18978 Z= 0.105 Angle : 0.526 8.296 25671 Z= 0.283 Chirality : 0.045 0.231 2937 Planarity : 0.004 0.054 3312 Dihedral : 5.659 53.693 2635 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.64 % Rotamer: Outliers : 0.90 % Allowed : 9.45 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2421 helix: 0.79 (0.20), residues: 693 sheet: 0.21 (0.26), residues: 351 loop : -0.27 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 23 TYR 0.015 0.001 TYR I 452 PHE 0.011 0.001 PHE I 200 TRP 0.015 0.002 TRP F 441 HIS 0.005 0.001 HIS C 385 Details of bonding type rmsd covalent geometry : bond 0.00217 (18978) covalent geometry : angle 0.52602 (25671) hydrogen bonds : bond 0.04158 ( 676) hydrogen bonds : angle 4.82199 ( 1842) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 0.640 Fit side-chains REVERT: B 75 LYS cc_start: 0.7820 (mtmm) cc_final: 0.7358 (mmmt) REVERT: C 322 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6856 (mt) REVERT: C 582 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7471 (t0) REVERT: F 566 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6547 (mm-30) REVERT: F 582 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7421 (t0) outliers start: 18 outliers final: 10 residues processed: 238 average time/residue: 0.6809 time to fit residues: 180.1632 Evaluate side-chains 233 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 220 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 274 ILE Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 455 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 154 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 0.0010 chunk 203 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 211 optimal weight: 0.0970 chunk 220 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 182 optimal weight: 0.8980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 554 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.146502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.126950 restraints weight = 41129.206| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.38 r_work: 0.3309 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18978 Z= 0.101 Angle : 0.514 8.963 25671 Z= 0.275 Chirality : 0.045 0.223 2937 Planarity : 0.003 0.052 3312 Dihedral : 5.473 51.203 2633 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.40 % Favored : 96.48 % Rotamer: Outliers : 0.75 % Allowed : 9.80 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.17), residues: 2421 helix: 0.91 (0.20), residues: 693 sheet: 0.24 (0.26), residues: 351 loop : -0.22 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 80 TYR 0.015 0.001 TYR I 452 PHE 0.010 0.001 PHE I 200 TRP 0.014 0.002 TRP F 441 HIS 0.005 0.001 HIS C 385 Details of bonding type rmsd covalent geometry : bond 0.00209 (18978) covalent geometry : angle 0.51445 (25671) hydrogen bonds : bond 0.03946 ( 676) hydrogen bonds : angle 4.69427 ( 1842) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 226 time to evaluate : 0.684 Fit side-chains REVERT: B 75 LYS cc_start: 0.7820 (mtmm) cc_final: 0.7357 (mmmt) REVERT: C 322 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6933 (mt) REVERT: C 582 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7467 (t0) REVERT: F 566 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6519 (mm-30) REVERT: F 582 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7420 (t0) REVERT: I 207 MET cc_start: 0.7770 (mmp) cc_final: 0.7412 (mmp) outliers start: 15 outliers final: 10 residues processed: 236 average time/residue: 0.7124 time to fit residues: 187.0281 Evaluate side-chains 234 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 221 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 455 LYS Chi-restraints excluded: chain I residue 471 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 70 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 1 optimal weight: 0.0050 chunk 85 optimal weight: 3.9990 chunk 212 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 554 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.142261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122442 restraints weight = 41403.635| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.38 r_work: 0.3250 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18978 Z= 0.146 Angle : 0.600 9.416 25671 Z= 0.322 Chirality : 0.047 0.227 2937 Planarity : 0.004 0.058 3312 Dihedral : 5.869 51.661 2633 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.90 % Favored : 96.97 % Rotamer: Outliers : 0.90 % Allowed : 9.85 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2421 helix: 0.76 (0.20), residues: 693 sheet: 0.13 (0.26), residues: 351 loop : -0.28 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 594 TYR 0.020 0.002 TYR F 452 PHE 0.016 0.002 PHE F 200 TRP 0.013 0.002 TRP F 441 HIS 0.006 0.001 HIS I 421 Details of bonding type rmsd covalent geometry : bond 0.00305 (18978) covalent geometry : angle 0.59962 (25671) hydrogen bonds : bond 0.05244 ( 676) hydrogen bonds : angle 4.97219 ( 1842) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 224 time to evaluate : 0.745 Fit side-chains REVERT: B 75 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7392 (mmmt) REVERT: C 258 GLU cc_start: 0.8032 (tt0) cc_final: 0.7671 (tt0) REVERT: C 322 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6710 (mp) REVERT: C 582 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7511 (t0) REVERT: F 582 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7458 (t0) REVERT: I 308 ILE cc_start: 0.6156 (OUTLIER) cc_final: 0.5886 (mm) outliers start: 18 outliers final: 12 residues processed: 236 average time/residue: 0.6884 time to fit residues: 180.7175 Evaluate side-chains 236 residues out of total 1983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain F residue 582 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain I residue 308 ILE Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 455 LYS Chi-restraints excluded: chain I residue 471 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 193 optimal weight: 0.4980 chunk 184 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 156 optimal weight: 0.0470 chunk 33 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 554 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.145286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.126473 restraints weight = 30506.082| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.17 r_work: 0.3310 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18978 Z= 0.108 Angle : 0.535 9.141 25671 Z= 0.285 Chirality : 0.045 0.230 2937 Planarity : 0.004 0.054 3312 Dihedral : 5.585 51.602 2633 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.28 % Favored : 96.60 % Rotamer: Outliers : 0.75 % Allowed : 9.90 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2421 helix: 0.86 (0.20), residues: 693 sheet: 0.22 (0.26), residues: 351 loop : -0.23 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 52 TYR 0.015 0.001 TYR I 452 PHE 0.011 0.001 PHE I 200 TRP 0.014 0.002 TRP F 441 HIS 0.005 0.001 HIS C 385 Details of bonding type rmsd covalent geometry : bond 0.00224 (18978) covalent geometry : angle 0.53471 (25671) hydrogen bonds : bond 0.04225 ( 676) hydrogen bonds : angle 4.76710 ( 1842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9568.34 seconds wall clock time: 163 minutes 22.04 seconds (9802.04 seconds total)