Starting phenix.real_space_refine on Fri Nov 21 04:06:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4w_48907/11_2025/9n4w_48907.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4w_48907/11_2025/9n4w_48907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n4w_48907/11_2025/9n4w_48907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4w_48907/11_2025/9n4w_48907.map" model { file = "/net/cci-nas-00/data/ceres_data/9n4w_48907/11_2025/9n4w_48907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4w_48907/11_2025/9n4w_48907.cif" } resolution = 2.5 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= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 200 5.16 5 C 27460 2.51 5 N 7700 2.21 5 O 7890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43250 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4325 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 26, 'TRANS': 521} Chain breaks: 1 Chain: "B" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4325 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 26, 'TRANS': 521} Chain breaks: 1 Chain: "C" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4325 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 26, 'TRANS': 521} Chain breaks: 1 Chain: "D" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4325 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 26, 'TRANS': 521} Chain breaks: 1 Chain: "E" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4325 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 26, 'TRANS': 521} Chain breaks: 1 Chain: "F" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4325 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 26, 'TRANS': 521} Chain breaks: 1 Chain: "G" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4325 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 26, 'TRANS': 521} Chain breaks: 1 Chain: "H" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4325 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 26, 'TRANS': 521} Chain breaks: 1 Chain: "I" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4325 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 26, 'TRANS': 521} Chain breaks: 1 Chain: "J" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4325 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 26, 'TRANS': 521} Chain breaks: 1 Time building chain proxies: 10.36, per 1000 atoms: 0.24 Number of scatterers: 43250 At special positions: 0 Unit cell: (182.65, 174.2, 92.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 200 16.00 O 7890 8.00 N 7700 7.00 C 27460 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: 3.71 Conformation dependent library (CDL) restraints added in 2.0 seconds 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10060 Finding SS restraints... Secondary structure from input PDB file: 300 helices and 30 sheets defined 61.5% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 9 through 12 Processing helix chain 'A' and resid 13 through 27 Processing helix chain 'A' and resid 30 through 37 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 62 through 77 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 119 through 139 Processing helix chain 'A' and resid 158 through 161 Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 173 through 176 Processing helix chain 'A' and resid 189 through 198 removed outlier: 3.620A pdb=" N PHE A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 233 Processing helix chain 'A' and resid 236 through 242 removed outlier: 4.977A pdb=" N TYR A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 290 through 311 Processing helix chain 'A' and resid 316 through 332 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 348 through 362 removed outlier: 3.690A pdb=" N HIS A 352 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 360 " --> pdb=" O MET A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 removed outlier: 3.602A pdb=" N LEU A 396 " --> pdb=" O TYR A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 438 Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 454 through 466 Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 482 through 505 Processing helix chain 'A' and resid 514 through 530 removed outlier: 3.714A pdb=" N LYS A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 550 Processing helix chain 'B' and resid 9 through 12 Processing helix chain 'B' and resid 13 through 27 Processing helix chain 'B' and resid 30 through 37 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 62 through 77 Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 119 through 139 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'B' and resid 173 through 176 Processing helix chain 'B' and resid 189 through 198 removed outlier: 3.621A pdb=" N PHE B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 233 Processing helix chain 'B' and resid 236 through 242 removed outlier: 4.979A pdb=" N TYR B 241 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 290 through 311 Processing helix chain 'B' and resid 316 through 332 Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 348 through 362 removed outlier: 3.690A pdb=" N HIS B 352 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 360 " --> pdb=" O MET B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 399 removed outlier: 3.602A pdb=" N LEU B 396 " --> pdb=" O TYR B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 438 Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 454 through 466 Proline residue: B 463 - end of helix Processing helix chain 'B' and resid 482 through 505 Processing helix chain 'B' and resid 514 through 530 removed outlier: 3.722A pdb=" N LYS B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 550 Processing helix chain 'C' and resid 9 through 12 Processing helix chain 'C' and resid 13 through 27 Processing helix chain 'C' and resid 30 through 37 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 62 through 77 Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 119 through 139 Processing helix chain 'C' and resid 158 through 161 Processing helix chain 'C' and resid 162 through 172 Processing helix chain 'C' and resid 173 through 176 Processing helix chain 'C' and resid 189 through 198 removed outlier: 3.638A pdb=" N PHE C 193 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 233 Processing helix chain 'C' and resid 236 through 242 removed outlier: 4.904A pdb=" N TYR C 241 " --> pdb=" O GLU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 290 through 311 Processing helix chain 'C' and resid 316 through 332 Processing helix chain 'C' and resid 343 through 347 Processing helix chain 'C' and resid 348 through 362 removed outlier: 3.682A pdb=" N HIS C 352 " --> pdb=" O ASN C 348 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER C 360 " --> pdb=" O MET C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 399 removed outlier: 3.605A pdb=" N LEU C 396 " --> pdb=" O TYR C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 438 Processing helix chain 'C' and resid 440 through 451 Processing helix chain 'C' and resid 454 through 466 Proline residue: C 463 - end of helix Processing helix chain 'C' and resid 482 through 505 Processing helix chain 'C' and resid 514 through 530 removed outlier: 3.734A pdb=" N LYS C 518 " --> pdb=" O VAL C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 550 Processing helix chain 'D' and resid 9 through 12 Processing helix chain 'D' and resid 13 through 27 Processing helix chain 'D' and resid 30 through 37 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 62 through 77 Processing helix chain 'D' and resid 77 through 88 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 119 through 139 Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'D' and resid 173 through 176 Processing helix chain 'D' and resid 189 through 198 removed outlier: 3.617A pdb=" N PHE D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 233 Processing helix chain 'D' and resid 236 through 242 removed outlier: 4.974A pdb=" N TYR D 241 " --> pdb=" O GLU D 238 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG D 242 " --> pdb=" O ARG D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 282 through 290 Processing helix chain 'D' and resid 290 through 311 Processing helix chain 'D' and resid 316 through 332 Processing helix chain 'D' and resid 343 through 347 Processing helix chain 'D' and resid 348 through 362 removed outlier: 3.641A pdb=" N HIS D 352 " --> pdb=" O ASN D 348 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 360 " --> pdb=" O MET D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 399 removed outlier: 3.602A pdb=" N LEU D 396 " --> pdb=" O TYR D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 438 Processing helix chain 'D' and resid 440 through 451 Processing helix chain 'D' and resid 454 through 466 Proline residue: D 463 - end of helix Processing helix chain 'D' and resid 482 through 505 Processing helix chain 'D' and resid 514 through 530 removed outlier: 3.714A pdb=" N LYS D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 550 Processing helix chain 'E' and resid 9 through 12 Processing helix chain 'E' and resid 13 through 27 Processing helix chain 'E' and resid 30 through 37 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 62 through 77 Processing helix chain 'E' and resid 77 through 88 Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 119 through 139 Processing helix chain 'E' and resid 158 through 161 Processing helix chain 'E' and resid 162 through 172 Processing helix chain 'E' and resid 173 through 176 Processing helix chain 'E' and resid 189 through 198 removed outlier: 3.623A pdb=" N PHE E 193 " --> pdb=" O ASP E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 233 Processing helix chain 'E' and resid 236 through 242 removed outlier: 5.019A pdb=" N TYR E 241 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 258 removed outlier: 3.534A pdb=" N ALA E 254 " --> pdb=" O ASN E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 279 through 281 No H-bonds generated for 'chain 'E' and resid 279 through 281' Processing helix chain 'E' and resid 282 through 290 Processing helix chain 'E' and resid 290 through 311 Processing helix chain 'E' and resid 316 through 332 Processing helix chain 'E' and resid 343 through 347 Processing helix chain 'E' and resid 348 through 362 removed outlier: 3.679A pdb=" N HIS E 352 " --> pdb=" O ASN E 348 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER E 360 " --> pdb=" O MET E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 399 removed outlier: 3.584A pdb=" N LEU E 396 " --> pdb=" O TYR E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 438 Processing helix chain 'E' and resid 440 through 451 Processing helix chain 'E' and resid 454 through 466 Proline residue: E 463 - end of helix Processing helix chain 'E' and resid 482 through 505 Processing helix chain 'E' and resid 514 through 530 removed outlier: 3.705A pdb=" N LYS E 518 " --> pdb=" O VAL E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 550 Processing helix chain 'F' and resid 9 through 12 Processing helix chain 'F' and resid 13 through 27 Processing helix chain 'F' and resid 30 through 37 Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 62 through 77 Processing helix chain 'F' and resid 77 through 88 Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 119 through 139 Processing helix chain 'F' and resid 158 through 161 Processing helix chain 'F' and resid 162 through 172 Processing helix chain 'F' and resid 173 through 176 Processing helix chain 'F' and resid 189 through 198 removed outlier: 3.613A pdb=" N PHE F 193 " --> pdb=" O ASP F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 233 Processing helix chain 'F' and resid 236 through 242 removed outlier: 4.952A pdb=" N TYR F 241 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 258 Processing helix chain 'F' and resid 260 through 262 No H-bonds generated for 'chain 'F' and resid 260 through 262' Processing helix chain 'F' and resid 272 through 276 Processing helix chain 'F' and resid 279 through 281 No H-bonds generated for 'chain 'F' and resid 279 through 281' Processing helix chain 'F' and resid 282 through 290 Processing helix chain 'F' and resid 290 through 311 Processing helix chain 'F' and resid 316 through 332 Processing helix chain 'F' and resid 343 through 347 Processing helix chain 'F' and resid 348 through 362 removed outlier: 3.685A pdb=" N HIS F 352 " --> pdb=" O ASN F 348 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER F 360 " --> pdb=" O MET F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 399 removed outlier: 3.573A pdb=" N LEU F 396 " --> pdb=" O TYR F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 438 Processing helix chain 'F' and resid 440 through 451 Processing helix chain 'F' and resid 454 through 466 Proline residue: F 463 - end of helix Processing helix chain 'F' and resid 482 through 505 Processing helix chain 'F' and resid 514 through 530 removed outlier: 3.715A pdb=" N LYS F 518 " --> pdb=" O VAL F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 550 Processing helix chain 'G' and resid 9 through 12 Processing helix chain 'G' and resid 13 through 27 Processing helix chain 'G' and resid 30 through 37 Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 62 through 77 Processing helix chain 'G' and resid 77 through 88 Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 119 through 139 Processing helix chain 'G' and resid 158 through 161 Processing helix chain 'G' and resid 162 through 172 Processing helix chain 'G' and resid 173 through 176 Processing helix chain 'G' and resid 189 through 198 removed outlier: 3.613A pdb=" N PHE G 193 " --> pdb=" O ASP G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 233 Processing helix chain 'G' and resid 236 through 242 removed outlier: 4.958A pdb=" N TYR G 241 " --> pdb=" O GLU G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 258 Processing helix chain 'G' and resid 260 through 262 No H-bonds generated for 'chain 'G' and resid 260 through 262' Processing helix chain 'G' and resid 272 through 276 Processing helix chain 'G' and resid 279 through 281 No H-bonds generated for 'chain 'G' and resid 279 through 281' Processing helix chain 'G' and resid 282 through 290 Processing helix chain 'G' and resid 290 through 311 Processing helix chain 'G' and resid 316 through 332 Processing helix chain 'G' and resid 343 through 347 Processing helix chain 'G' and resid 348 through 362 removed outlier: 3.685A pdb=" N HIS G 352 " --> pdb=" O ASN G 348 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER G 360 " --> pdb=" O MET G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 399 removed outlier: 3.566A pdb=" N LEU G 396 " --> pdb=" O TYR G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 419 through 438 Processing helix chain 'G' and resid 440 through 451 Processing helix chain 'G' and resid 454 through 466 Proline residue: G 463 - end of helix Processing helix chain 'G' and resid 482 through 505 Processing helix chain 'G' and resid 514 through 530 removed outlier: 3.714A pdb=" N LYS G 518 " --> pdb=" O VAL G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 550 Processing helix chain 'H' and resid 9 through 12 Processing helix chain 'H' and resid 13 through 27 Processing helix chain 'H' and resid 30 through 37 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 62 through 77 Processing helix chain 'H' and resid 77 through 88 Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 119 through 139 Processing helix chain 'H' and resid 158 through 161 Processing helix chain 'H' and resid 162 through 172 Processing helix chain 'H' and resid 173 through 176 Processing helix chain 'H' and resid 189 through 198 removed outlier: 3.621A pdb=" N PHE H 193 " --> pdb=" O ASP H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 233 Processing helix chain 'H' and resid 236 through 242 removed outlier: 5.038A pdb=" N TYR H 241 " --> pdb=" O GLU H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 258 Processing helix chain 'H' and resid 260 through 262 No H-bonds generated for 'chain 'H' and resid 260 through 262' Processing helix chain 'H' and resid 272 through 276 Processing helix chain 'H' and resid 279 through 281 No H-bonds generated for 'chain 'H' and resid 279 through 281' Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 290 through 311 Processing helix chain 'H' and resid 316 through 332 Processing helix chain 'H' and resid 343 through 347 Processing helix chain 'H' and resid 348 through 362 removed outlier: 3.681A pdb=" N HIS H 352 " --> pdb=" O ASN H 348 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER H 360 " --> pdb=" O MET H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 392 through 399 removed outlier: 3.585A pdb=" N LEU H 396 " --> pdb=" O TYR H 392 " (cutoff:3.500A) Processing helix chain 'H' and resid 419 through 438 Processing helix chain 'H' and resid 440 through 451 Processing helix chain 'H' and resid 454 through 466 Proline residue: H 463 - end of helix Processing helix chain 'H' and resid 482 through 505 Processing helix chain 'H' and resid 514 through 530 removed outlier: 3.704A pdb=" N LYS H 518 " --> pdb=" O VAL H 514 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 550 Processing helix chain 'I' and resid 9 through 12 Processing helix chain 'I' and resid 13 through 27 Processing helix chain 'I' and resid 30 through 37 Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 62 through 77 Processing helix chain 'I' and resid 77 through 88 Processing helix chain 'I' and resid 101 through 106 Processing helix chain 'I' and resid 119 through 139 Processing helix chain 'I' and resid 158 through 161 Processing helix chain 'I' and resid 162 through 172 Processing helix chain 'I' and resid 173 through 176 Processing helix chain 'I' and resid 189 through 198 removed outlier: 3.613A pdb=" N PHE I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 233 Processing helix chain 'I' and resid 236 through 242 removed outlier: 4.978A pdb=" N TYR I 241 " --> pdb=" O GLU I 238 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG I 242 " --> pdb=" O ARG I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 258 Processing helix chain 'I' and resid 260 through 262 No H-bonds generated for 'chain 'I' and resid 260 through 262' Processing helix chain 'I' and resid 272 through 276 Processing helix chain 'I' and resid 279 through 281 No H-bonds generated for 'chain 'I' and resid 279 through 281' Processing helix chain 'I' and resid 282 through 290 Processing helix chain 'I' and resid 290 through 311 Processing helix chain 'I' and resid 316 through 332 Processing helix chain 'I' and resid 343 through 347 Processing helix chain 'I' and resid 348 through 362 removed outlier: 3.648A pdb=" N HIS I 352 " --> pdb=" O ASN I 348 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER I 360 " --> pdb=" O MET I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 392 through 399 removed outlier: 3.602A pdb=" N LEU I 396 " --> pdb=" O TYR I 392 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 438 Processing helix chain 'I' and resid 440 through 451 Processing helix chain 'I' and resid 454 through 466 Proline residue: I 463 - end of helix Processing helix chain 'I' and resid 482 through 505 Processing helix chain 'I' and resid 514 through 530 removed outlier: 3.717A pdb=" N LYS I 518 " --> pdb=" O VAL I 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 538 through 550 Processing helix chain 'J' and resid 9 through 12 Processing helix chain 'J' and resid 13 through 27 Processing helix chain 'J' and resid 30 through 37 Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 62 through 77 Processing helix chain 'J' and resid 77 through 88 Processing helix chain 'J' and resid 101 through 106 Processing helix chain 'J' and resid 119 through 139 Processing helix chain 'J' and resid 158 through 161 Processing helix chain 'J' and resid 162 through 172 Processing helix chain 'J' and resid 173 through 176 Processing helix chain 'J' and resid 189 through 198 removed outlier: 3.635A pdb=" N PHE J 193 " --> pdb=" O ASP J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 233 Processing helix chain 'J' and resid 236 through 242 removed outlier: 4.934A pdb=" N TYR J 241 " --> pdb=" O GLU J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 258 Processing helix chain 'J' and resid 260 through 262 No H-bonds generated for 'chain 'J' and resid 260 through 262' Processing helix chain 'J' and resid 272 through 276 Processing helix chain 'J' and resid 279 through 281 No H-bonds generated for 'chain 'J' and resid 279 through 281' Processing helix chain 'J' and resid 282 through 290 Processing helix chain 'J' and resid 290 through 311 Processing helix chain 'J' and resid 316 through 332 Processing helix chain 'J' and resid 343 through 347 Processing helix chain 'J' and resid 348 through 362 removed outlier: 3.683A pdb=" N HIS J 352 " --> pdb=" O ASN J 348 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER J 360 " --> pdb=" O MET J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 392 through 399 removed outlier: 3.606A pdb=" N LEU J 396 " --> pdb=" O TYR J 392 " (cutoff:3.500A) Processing helix chain 'J' and resid 419 through 438 Processing helix chain 'J' and resid 440 through 451 Processing helix chain 'J' and resid 454 through 466 Proline residue: J 463 - end of helix Processing helix chain 'J' and resid 482 through 505 Processing helix chain 'J' and resid 514 through 530 removed outlier: 3.733A pdb=" N LYS J 518 " --> pdb=" O VAL J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 550 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 185 removed outlier: 9.008A pdb=" N PHE A 265 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA A 246 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 49 Processing sheet with id=AA5, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 185 removed outlier: 9.008A pdb=" N PHE B 265 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA B 246 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 49 Processing sheet with id=AA8, first strand: chain 'C' and resid 113 through 114 Processing sheet with id=AA9, first strand: chain 'C' and resid 181 through 185 removed outlier: 9.028A pdb=" N PHE C 265 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA C 246 " --> pdb=" O PHE C 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 46 through 49 Processing sheet with id=AB2, first strand: chain 'D' and resid 113 through 114 Processing sheet with id=AB3, first strand: chain 'D' and resid 181 through 185 removed outlier: 9.007A pdb=" N PHE D 265 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA D 246 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 46 through 49 Processing sheet with id=AB5, first strand: chain 'E' and resid 113 through 114 Processing sheet with id=AB6, first strand: chain 'E' and resid 181 through 185 removed outlier: 9.002A pdb=" N PHE E 265 " --> pdb=" O PHE E 244 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA E 246 " --> pdb=" O PHE E 265 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 46 through 49 Processing sheet with id=AB8, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AB9, first strand: chain 'F' and resid 181 through 185 removed outlier: 9.007A pdb=" N PHE F 265 " --> pdb=" O PHE F 244 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA F 246 " --> pdb=" O PHE F 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 46 through 49 Processing sheet with id=AC2, first strand: chain 'G' and resid 113 through 114 Processing sheet with id=AC3, first strand: chain 'G' and resid 181 through 185 removed outlier: 9.010A pdb=" N PHE G 265 " --> pdb=" O PHE G 244 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA G 246 " --> pdb=" O PHE G 265 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 46 through 49 Processing sheet with id=AC5, first strand: chain 'H' and resid 113 through 114 Processing sheet with id=AC6, first strand: chain 'H' and resid 181 through 185 removed outlier: 9.014A pdb=" N PHE H 265 " --> pdb=" O PHE H 244 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA H 246 " --> pdb=" O PHE H 265 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 46 through 49 Processing sheet with id=AC8, first strand: chain 'I' and resid 113 through 114 Processing sheet with id=AC9, first strand: chain 'I' and resid 181 through 185 removed outlier: 8.985A pdb=" N PHE I 265 " --> pdb=" O PHE I 244 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA I 246 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 46 through 49 Processing sheet with id=AD2, first strand: chain 'J' and resid 113 through 114 Processing sheet with id=AD3, first strand: chain 'J' and resid 181 through 185 removed outlier: 9.031A pdb=" N PHE J 265 " --> pdb=" O PHE J 244 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA J 246 " --> pdb=" O PHE J 265 " (cutoff:3.500A) 2497 hydrogen bonds defined for protein. 7047 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: 11.37 Time building geometry restraints manager: 4.83 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: 14484 1.34 - 1.46: 9477 1.46 - 1.58: 20069 1.58 - 1.69: 0 1.69 - 1.81: 340 Bond restraints: 44370 Sorted by residual: bond pdb=" CG1 ILE D 503 " pdb=" CD1 ILE D 503 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 2.00e+00 bond pdb=" CG1 ILE I 503 " pdb=" CD1 ILE I 503 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.94e+00 bond pdb=" CG1 ILE I 281 " pdb=" CD1 ILE I 281 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.28e+00 bond pdb=" CG LEU G 167 " pdb=" CD1 LEU G 167 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 bond pdb=" CG LEU F 167 " pdb=" CD1 LEU F 167 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.28e-01 ... (remaining 44365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 58360 1.28 - 2.57: 1442 2.57 - 3.85: 269 3.85 - 5.13: 131 5.13 - 6.42: 38 Bond angle restraints: 60240 Sorted by residual: angle pdb=" C GLY J 385 " pdb=" N CYS J 386 " pdb=" CA CYS J 386 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.55e+00 angle pdb=" C GLY C 385 " pdb=" N CYS C 386 " pdb=" CA CYS C 386 " ideal model delta sigma weight residual 121.54 126.78 -5.24 1.91e+00 2.74e-01 7.53e+00 angle pdb=" C GLY H 385 " pdb=" N CYS H 386 " pdb=" CA CYS H 386 " ideal model delta sigma weight residual 121.54 126.77 -5.23 1.91e+00 2.74e-01 7.50e+00 angle pdb=" C GLY A 385 " pdb=" N CYS A 386 " pdb=" CA CYS A 386 " ideal model delta sigma weight residual 121.54 126.77 -5.23 1.91e+00 2.74e-01 7.50e+00 angle pdb=" C GLY B 385 " pdb=" N CYS B 386 " pdb=" CA CYS B 386 " ideal model delta sigma weight residual 121.54 126.75 -5.21 1.91e+00 2.74e-01 7.43e+00 ... (remaining 60235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 22613 17.18 - 34.36: 2535 34.36 - 51.55: 783 51.55 - 68.73: 126 68.73 - 85.91: 43 Dihedral angle restraints: 26100 sinusoidal: 10380 harmonic: 15720 Sorted by residual: dihedral pdb=" CA TYR D 275 " pdb=" C TYR D 275 " pdb=" N SER D 276 " pdb=" CA SER D 276 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA TYR F 275 " pdb=" C TYR F 275 " pdb=" N SER F 276 " pdb=" CA SER F 276 " ideal model delta harmonic sigma weight residual -180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA TYR G 275 " pdb=" C TYR G 275 " pdb=" N SER G 276 " pdb=" CA SER G 276 " ideal model delta harmonic sigma weight residual -180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 26097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3600 0.028 - 0.056: 1786 0.056 - 0.084: 652 0.084 - 0.111: 297 0.111 - 0.139: 105 Chirality restraints: 6440 Sorted by residual: chirality pdb=" CA MET E 358 " pdb=" N MET E 358 " pdb=" C MET E 358 " pdb=" CB MET E 358 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA VAL A 247 " pdb=" N VAL A 247 " pdb=" C VAL A 247 " pdb=" CB VAL A 247 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE F 208 " pdb=" N ILE F 208 " pdb=" C ILE F 208 " pdb=" CB ILE F 208 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 6437 not shown) Planarity restraints: 7870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 453 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO F 454 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO F 454 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 454 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 453 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO J 454 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO J 454 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO J 454 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 453 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO I 454 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO I 454 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 454 " 0.029 5.00e-02 4.00e+02 ... (remaining 7867 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 2172 2.73 - 3.27: 42842 3.27 - 3.81: 80157 3.81 - 4.36: 102549 4.36 - 4.90: 168521 Nonbonded interactions: 396241 Sorted by model distance: nonbonded pdb=" O MET G 356 " pdb=" OG SER G 360 " model vdw 2.184 3.040 nonbonded pdb=" O MET J 356 " pdb=" OG SER J 360 " model vdw 2.185 3.040 nonbonded pdb=" O MET F 356 " pdb=" OG SER F 360 " model vdw 2.185 3.040 nonbonded pdb=" O MET C 356 " pdb=" OG SER C 360 " model vdw 2.186 3.040 nonbonded pdb=" O MET B 356 " pdb=" OG SER B 360 " model vdw 2.188 3.040 ... (remaining 396236 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.910 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 43.500 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.110 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:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 44370 Z= 0.158 Angle : 0.546 6.418 60240 Z= 0.279 Chirality : 0.041 0.139 6440 Planarity : 0.005 0.053 7870 Dihedral : 16.080 85.911 16040 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.28 % Allowed : 17.81 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.11), residues: 5440 helix: 1.31 (0.09), residues: 2800 sheet: -0.36 (0.23), residues: 570 loop : -0.50 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 96 TYR 0.020 0.002 TYR H 145 PHE 0.012 0.001 PHE J 509 TRP 0.017 0.001 TRP B 327 HIS 0.006 0.001 HIS D 124 Details of bonding type rmsd covalent geometry : bond 0.00360 (44370) covalent geometry : angle 0.54585 (60240) hydrogen bonds : bond 0.13441 ( 2497) hydrogen bonds : angle 6.16280 ( 7047) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 591 time to evaluate : 1.652 Fit side-chains REVERT: H 80 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7884 (mp-120) outliers start: 58 outliers final: 49 residues processed: 642 average time/residue: 0.8967 time to fit residues: 691.7636 Evaluate side-chains 627 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 577 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 390 HIS Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 390 HIS Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 390 HIS Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 390 HIS Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 390 HIS Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 390 HIS Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 376 THR Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 480 THR Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 57 SER Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 390 HIS Chi-restraints excluded: chain I residue 477 VAL Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 390 HIS Chi-restraints excluded: chain J residue 477 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 0.9990 chunk 497 optimal weight: 0.7980 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 0.1980 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS B 117 HIS C 20 GLN C 117 HIS D 117 HIS D 224 GLN E 117 HIS F 117 HIS G 117 HIS H 20 GLN H 117 HIS I 117 HIS I 224 GLN J 117 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.149603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119645 restraints weight = 42860.544| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.40 r_work: 0.3245 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.0651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 44370 Z= 0.121 Angle : 0.506 5.845 60240 Z= 0.263 Chirality : 0.040 0.131 6440 Planarity : 0.004 0.038 7870 Dihedral : 4.889 69.463 6086 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.87 % Allowed : 15.19 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.11), residues: 5440 helix: 1.67 (0.10), residues: 2860 sheet: -0.74 (0.22), residues: 570 loop : -0.43 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 96 TYR 0.010 0.001 TYR J 145 PHE 0.009 0.001 PHE I 509 TRP 0.015 0.001 TRP B 327 HIS 0.005 0.001 HIS H 124 Details of bonding type rmsd covalent geometry : bond 0.00254 (44370) covalent geometry : angle 0.50603 (60240) hydrogen bonds : bond 0.04343 ( 2497) hydrogen bonds : angle 4.84973 ( 7047) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 632 time to evaluate : 1.706 Fit side-chains REVERT: C 80 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: C 256 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7094 (pm20) REVERT: D 242 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7806 (mtt180) REVERT: D 251 ILE cc_start: 0.7936 (mt) cc_final: 0.7678 (mt) REVERT: D 422 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: E 492 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8578 (tp) REVERT: F 170 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7478 (mm-30) REVERT: G 170 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7463 (mm-30) REVERT: H 242 ARG cc_start: 0.8134 (mtt180) cc_final: 0.7922 (mtt180) REVERT: H 492 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8580 (tp) REVERT: I 353 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8606 (mp) REVERT: I 422 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: J 80 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7866 (mp10) REVERT: J 256 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7108 (pm20) outliers start: 130 outliers final: 18 residues processed: 708 average time/residue: 0.8941 time to fit residues: 757.6722 Evaluate side-chains 627 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 598 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 422 GLN Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain H residue 492 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 422 GLN Chi-restraints excluded: chain I residue 477 VAL Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 256 GLU Chi-restraints excluded: chain J residue 353 LEU Chi-restraints excluded: chain J residue 477 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 211 optimal weight: 0.8980 chunk 305 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 346 optimal weight: 8.9990 chunk 26 optimal weight: 0.1980 chunk 244 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 446 optimal weight: 0.9980 chunk 377 optimal weight: 0.9980 chunk 351 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 117 HIS A 224 GLN A 389 GLN B 20 GLN B 117 HIS B 224 GLN B 389 GLN C 117 HIS D 117 HIS D 224 GLN E 117 HIS F 117 HIS G 117 HIS H 117 HIS I 117 HIS I 224 GLN J 117 HIS J 389 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.150111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120143 restraints weight = 42708.715| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.40 r_work: 0.3250 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 44370 Z= 0.120 Angle : 0.500 4.936 60240 Z= 0.257 Chirality : 0.040 0.135 6440 Planarity : 0.004 0.037 7870 Dihedral : 4.044 22.582 6014 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.25 % Allowed : 15.89 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.11), residues: 5440 helix: 1.81 (0.10), residues: 2860 sheet: -0.88 (0.22), residues: 570 loop : -0.37 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 96 TYR 0.011 0.001 TYR F 493 PHE 0.008 0.001 PHE I 509 TRP 0.016 0.001 TRP A 327 HIS 0.005 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00256 (44370) covalent geometry : angle 0.49953 (60240) hydrogen bonds : bond 0.04163 ( 2497) hydrogen bonds : angle 4.65945 ( 7047) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 640 time to evaluate : 1.848 Fit side-chains REVERT: A 227 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7055 (ttm-80) REVERT: A 422 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7314 (mp-120) REVERT: B 227 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7029 (ttm-80) REVERT: B 422 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7323 (mp-120) REVERT: C 80 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: C 197 THR cc_start: 0.7331 (p) cc_final: 0.7117 (p) REVERT: C 256 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7114 (pm20) REVERT: E 492 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8614 (tp) REVERT: F 167 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8070 (tp) REVERT: F 250 ASN cc_start: 0.7931 (t0) cc_final: 0.7720 (t0) REVERT: F 422 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7262 (mp-120) REVERT: G 79 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6740 (mt-10) REVERT: G 167 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8080 (tp) REVERT: G 170 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: G 250 ASN cc_start: 0.7946 (t0) cc_final: 0.7733 (t0) REVERT: G 422 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7259 (mp-120) REVERT: H 492 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8615 (tp) REVERT: I 242 ARG cc_start: 0.8018 (mtt180) cc_final: 0.7780 (mtt180) REVERT: I 251 ILE cc_start: 0.7913 (mt) cc_final: 0.7661 (mt) REVERT: I 353 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8598 (mp) REVERT: J 80 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: J 256 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7124 (pm20) outliers start: 102 outliers final: 23 residues processed: 697 average time/residue: 0.9156 time to fit residues: 763.9397 Evaluate side-chains 639 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 599 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain H residue 480 THR Chi-restraints excluded: chain H residue 492 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 477 VAL Chi-restraints excluded: chain I residue 478 MET Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 256 GLU Chi-restraints excluded: chain J residue 353 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 124 optimal weight: 4.9990 chunk 255 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 334 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 366 optimal weight: 2.9990 chunk 287 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 439 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS A 224 GLN B 117 HIS B 224 GLN C 117 HIS D 117 HIS D 224 GLN E 117 HIS G 117 HIS H 117 HIS I 117 HIS I 224 GLN J 117 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.145064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.114615 restraints weight = 42798.770| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.41 r_work: 0.3176 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 44370 Z= 0.243 Angle : 0.613 7.069 60240 Z= 0.312 Chirality : 0.045 0.142 6440 Planarity : 0.005 0.042 7870 Dihedral : 4.508 28.398 6012 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.67 % Allowed : 16.47 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.11), residues: 5440 helix: 1.57 (0.10), residues: 2770 sheet: -0.89 (0.23), residues: 570 loop : -0.60 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 143 TYR 0.018 0.002 TYR F 493 PHE 0.013 0.002 PHE I 509 TRP 0.017 0.002 TRP B 327 HIS 0.008 0.001 HIS D 124 Details of bonding type rmsd covalent geometry : bond 0.00564 (44370) covalent geometry : angle 0.61279 (60240) hydrogen bonds : bond 0.05282 ( 2497) hydrogen bonds : angle 4.99619 ( 7047) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 598 time to evaluate : 1.763 Fit side-chains REVERT: A 250 ASN cc_start: 0.7772 (t0) cc_final: 0.7474 (t0) REVERT: B 250 ASN cc_start: 0.7766 (t0) cc_final: 0.7465 (t0) REVERT: C 250 ASN cc_start: 0.7758 (t0) cc_final: 0.7528 (t0) REVERT: D 250 ASN cc_start: 0.7804 (t0) cc_final: 0.7465 (t0) REVERT: E 206 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7979 (tp) REVERT: E 250 ASN cc_start: 0.7992 (t0) cc_final: 0.7731 (t0) REVERT: F 167 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8078 (tp) REVERT: G 167 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8088 (tp) REVERT: H 206 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7975 (tp) REVERT: H 250 ASN cc_start: 0.7785 (t0) cc_final: 0.7371 (t0) REVERT: I 242 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7867 (mtt180) REVERT: I 251 ILE cc_start: 0.7973 (mt) cc_final: 0.7736 (mt) REVERT: J 250 ASN cc_start: 0.7733 (t0) cc_final: 0.7509 (t0) outliers start: 121 outliers final: 29 residues processed: 670 average time/residue: 0.8861 time to fit residues: 710.9310 Evaluate side-chains 613 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 580 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 477 VAL Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain J residue 353 LEU Chi-restraints excluded: chain J residue 376 THR Chi-restraints excluded: chain J residue 477 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 328 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 263 optimal weight: 0.0970 chunk 215 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 255 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 289 optimal weight: 0.0970 chunk 273 optimal weight: 2.9990 chunk 519 optimal weight: 2.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 117 HIS A 224 GLN B 117 HIS B 224 GLN C 20 GLN C 117 HIS D 20 GLN D 117 HIS D 224 GLN E 117 HIS F 117 HIS G 117 HIS H 20 GLN H 117 HIS I 20 GLN I 117 HIS I 224 GLN J 117 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.151276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121366 restraints weight = 42595.752| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.41 r_work: 0.3276 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 44370 Z= 0.103 Angle : 0.481 5.619 60240 Z= 0.250 Chirality : 0.039 0.132 6440 Planarity : 0.004 0.039 7870 Dihedral : 3.999 21.301 6012 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.27 % Allowed : 16.98 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.11), residues: 5440 helix: 1.71 (0.10), residues: 2920 sheet: -0.95 (0.22), residues: 570 loop : -0.38 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 96 TYR 0.016 0.001 TYR E 145 PHE 0.008 0.001 PHE G 29 TRP 0.017 0.001 TRP C 270 HIS 0.005 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00207 (44370) covalent geometry : angle 0.48137 (60240) hydrogen bonds : bond 0.03894 ( 2497) hydrogen bonds : angle 4.56169 ( 7047) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 626 time to evaluate : 2.010 Fit side-chains REVERT: A 227 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7133 (ttm-80) REVERT: A 250 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7279 (t0) REVERT: A 422 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7276 (mp-120) REVERT: B 227 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.7159 (ttm-80) REVERT: B 250 ASN cc_start: 0.7618 (OUTLIER) cc_final: 0.7276 (t0) REVERT: B 422 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7280 (mp-120) REVERT: C 250 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7249 (t0) REVERT: D 250 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7328 (t0) REVERT: D 422 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: E 250 ASN cc_start: 0.7834 (t0) cc_final: 0.7633 (t0) REVERT: E 492 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8539 (tp) REVERT: F 79 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6823 (mt-10) REVERT: F 167 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8057 (tp) REVERT: F 250 ASN cc_start: 0.7672 (t0) cc_final: 0.7187 (t0) REVERT: F 422 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7199 (mp-120) REVERT: G 79 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6773 (mt-10) REVERT: G 167 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8086 (tp) REVERT: G 250 ASN cc_start: 0.7687 (t0) cc_final: 0.7201 (t0) REVERT: G 422 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7192 (mp-120) REVERT: H 250 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7209 (t0) REVERT: H 492 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8510 (tp) REVERT: I 242 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7863 (mtt180) REVERT: I 353 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8578 (mp) REVERT: I 422 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7292 (mp10) REVERT: J 197 THR cc_start: 0.7318 (p) cc_final: 0.7117 (p) REVERT: J 250 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7262 (t0) outliers start: 103 outliers final: 21 residues processed: 683 average time/residue: 0.8334 time to fit residues: 683.8782 Evaluate side-chains 639 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 597 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 422 GLN Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 250 ASN Chi-restraints excluded: chain D residue 422 GLN Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain H residue 250 ASN Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 480 THR Chi-restraints excluded: chain H residue 492 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 422 GLN Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 250 ASN Chi-restraints excluded: chain J residue 353 LEU Chi-restraints excluded: chain J residue 477 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 130 optimal weight: 8.9990 chunk 231 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 335 optimal weight: 4.9990 chunk 413 optimal weight: 3.9990 chunk 421 optimal weight: 8.9990 chunk 534 optimal weight: 3.9990 chunk 402 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 117 HIS A 224 GLN A 389 GLN B 20 GLN B 117 HIS B 224 GLN B 389 GLN C 117 HIS C 389 GLN D 117 HIS D 224 GLN D 389 GLN E 117 HIS F 117 HIS H 20 GLN H 117 HIS I 117 HIS I 224 GLN I 389 GLN J 117 HIS J 389 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.146325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.116016 restraints weight = 42885.270| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.39 r_work: 0.3198 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 44370 Z= 0.204 Angle : 0.581 6.393 60240 Z= 0.295 Chirality : 0.044 0.139 6440 Planarity : 0.005 0.039 7870 Dihedral : 4.335 16.307 6010 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.49 % Allowed : 17.35 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.11), residues: 5440 helix: 1.74 (0.10), residues: 2780 sheet: -0.98 (0.22), residues: 570 loop : -0.53 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 105 TYR 0.017 0.002 TYR E 493 PHE 0.012 0.002 PHE I 509 TRP 0.017 0.002 TRP B 327 HIS 0.008 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00469 (44370) covalent geometry : angle 0.58124 (60240) hydrogen bonds : bond 0.04892 ( 2497) hydrogen bonds : angle 4.85273 ( 7047) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 589 time to evaluate : 1.734 Fit side-chains REVERT: A 227 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7141 (ttm-80) REVERT: A 250 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7408 (t0) REVERT: B 227 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7132 (ttm-80) REVERT: B 250 ASN cc_start: 0.7746 (OUTLIER) cc_final: 0.7388 (t0) REVERT: C 250 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7356 (t0) REVERT: D 242 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7862 (mtt180) REVERT: D 250 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7382 (t0) REVERT: D 256 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7071 (pm20) REVERT: E 250 ASN cc_start: 0.7948 (t0) cc_final: 0.7678 (t0) REVERT: F 79 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6779 (mt-10) REVERT: F 167 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8067 (tp) REVERT: F 250 ASN cc_start: 0.7794 (t0) cc_final: 0.7253 (t0) REVERT: G 167 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8083 (tp) REVERT: G 250 ASN cc_start: 0.7805 (t0) cc_final: 0.7283 (t0) REVERT: H 250 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7257 (t0) REVERT: I 251 ILE cc_start: 0.8018 (mt) cc_final: 0.7787 (mt) REVERT: I 256 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7143 (pm20) REVERT: I 353 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8663 (mp) REVERT: J 250 ASN cc_start: 0.7665 (OUTLIER) cc_final: 0.7366 (t0) outliers start: 113 outliers final: 39 residues processed: 655 average time/residue: 0.7807 time to fit residues: 615.5996 Evaluate side-chains 638 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 585 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 250 ASN Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 245 ILE Chi-restraints excluded: chain F residue 353 LEU Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 353 LEU Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 250 ASN Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 256 GLU Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain I residue 477 VAL Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain J residue 250 ASN Chi-restraints excluded: chain J residue 353 LEU Chi-restraints excluded: chain J residue 376 THR Chi-restraints excluded: chain J residue 477 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 47 optimal weight: 1.9990 chunk 339 optimal weight: 1.9990 chunk 514 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 527 optimal weight: 4.9990 chunk 441 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 378 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS A 224 GLN B 117 HIS B 224 GLN C 117 HIS D 117 HIS E 117 HIS F 117 HIS G 117 HIS H 117 HIS I 117 HIS J 117 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.146269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116152 restraints weight = 42628.655| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.38 r_work: 0.3195 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 44370 Z= 0.198 Angle : 0.580 6.573 60240 Z= 0.295 Chirality : 0.043 0.135 6440 Planarity : 0.005 0.039 7870 Dihedral : 4.385 16.136 6010 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.54 % Allowed : 17.37 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.11), residues: 5440 helix: 1.63 (0.10), residues: 2780 sheet: -0.99 (0.22), residues: 570 loop : -0.61 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 143 TYR 0.017 0.002 TYR E 145 PHE 0.011 0.002 PHE I 509 TRP 0.017 0.002 TRP A 327 HIS 0.007 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00455 (44370) covalent geometry : angle 0.57983 (60240) hydrogen bonds : bond 0.04873 ( 2497) hydrogen bonds : angle 4.88382 ( 7047) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 593 time to evaluate : 1.332 Fit side-chains REVERT: A 250 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7436 (t0) REVERT: B 227 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7085 (ttm-80) REVERT: B 250 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7443 (t0) REVERT: C 242 ARG cc_start: 0.8089 (mtt-85) cc_final: 0.7887 (mtp180) REVERT: C 250 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7405 (t0) REVERT: D 250 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7406 (t0) REVERT: D 256 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7152 (pm20) REVERT: E 206 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7981 (tp) REVERT: E 242 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7729 (mtt180) REVERT: E 250 ASN cc_start: 0.8025 (t0) cc_final: 0.7749 (t0) REVERT: E 267 MET cc_start: 0.8301 (mtt) cc_final: 0.8058 (mtt) REVERT: F 167 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8108 (tp) REVERT: F 250 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7202 (t0) REVERT: F 422 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7355 (mp-120) REVERT: G 167 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8083 (tp) REVERT: G 250 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7244 (t0) REVERT: G 422 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7359 (mp-120) REVERT: H 206 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7981 (tp) REVERT: H 250 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7282 (t0) REVERT: I 251 ILE cc_start: 0.8037 (mt) cc_final: 0.7797 (mt) REVERT: I 353 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8669 (mp) REVERT: J 242 ARG cc_start: 0.8161 (mtt-85) cc_final: 0.7943 (mtt-85) REVERT: J 250 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7411 (t0) outliers start: 115 outliers final: 45 residues processed: 664 average time/residue: 0.6732 time to fit residues: 538.3833 Evaluate side-chains 645 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 583 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 250 ASN Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 310 ARG Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 245 ILE Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 250 ASN Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain H residue 206 LEU Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 250 ASN Chi-restraints excluded: chain H residue 270 TRP Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 310 ARG Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 477 VAL Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain J residue 250 ASN Chi-restraints excluded: chain J residue 353 LEU Chi-restraints excluded: chain J residue 376 THR Chi-restraints excluded: chain J residue 477 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 88 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 430 optimal weight: 0.0070 chunk 494 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 391 optimal weight: 1.9990 chunk 530 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 443 optimal weight: 4.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS A 224 GLN B 117 HIS B 224 GLN C 117 HIS D 117 HIS D 224 GLN E 117 HIS F 117 HIS G 117 HIS H 117 HIS I 117 HIS I 224 GLN J 117 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.149813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119736 restraints weight = 42848.412| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.42 r_work: 0.3246 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 44370 Z= 0.118 Angle : 0.507 7.143 60240 Z= 0.260 Chirality : 0.040 0.133 6440 Planarity : 0.004 0.039 7870 Dihedral : 4.057 16.069 6010 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.94 % Allowed : 18.06 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.11), residues: 5440 helix: 1.75 (0.10), residues: 2860 sheet: -1.02 (0.22), residues: 570 loop : -0.48 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 96 TYR 0.014 0.001 TYR E 145 PHE 0.008 0.001 PHE E 509 TRP 0.017 0.001 TRP A 270 HIS 0.005 0.001 HIS F 124 Details of bonding type rmsd covalent geometry : bond 0.00250 (44370) covalent geometry : angle 0.50721 (60240) hydrogen bonds : bond 0.04079 ( 2497) hydrogen bonds : angle 4.63289 ( 7047) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 592 time to evaluate : 1.004 Fit side-chains REVERT: A 227 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7145 (ttm-80) REVERT: A 250 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7322 (t0) REVERT: B 250 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7308 (t0) REVERT: C 250 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.7263 (t0) REVERT: D 242 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7830 (mtt180) REVERT: D 250 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.7272 (t0) REVERT: D 256 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: E 250 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7603 (t0) REVERT: E 492 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8615 (tp) REVERT: F 79 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6732 (mt-10) REVERT: F 167 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8043 (tp) REVERT: F 250 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7086 (t0) REVERT: F 422 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7256 (mp-120) REVERT: G 79 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6779 (mt-10) REVERT: G 167 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8063 (tp) REVERT: G 250 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7100 (t0) REVERT: G 422 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7262 (mp-120) REVERT: H 250 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7176 (t0) REVERT: H 492 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8613 (tp) REVERT: I 242 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7862 (mtt180) REVERT: I 353 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8609 (mp) REVERT: J 250 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.7271 (t0) outliers start: 88 outliers final: 27 residues processed: 643 average time/residue: 0.5181 time to fit residues: 403.1376 Evaluate side-chains 632 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 585 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 250 ASN Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain F residue 79 GLU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 250 ASN Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 250 ASN Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 492 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 477 VAL Chi-restraints excluded: chain J residue 250 ASN Chi-restraints excluded: chain J residue 353 LEU Chi-restraints excluded: chain J residue 376 THR Chi-restraints excluded: chain J residue 477 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 453 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 288 optimal weight: 4.9990 chunk 396 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 505 optimal weight: 1.9990 chunk 528 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 240 optimal weight: 0.0060 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS A 224 GLN A 389 GLN B 117 HIS B 224 GLN B 389 GLN C 117 HIS C 389 GLN D 117 HIS D 224 GLN E 117 HIS F 117 HIS G 117 HIS H 117 HIS I 117 HIS I 224 GLN J 117 HIS J 389 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121080 restraints weight = 42282.822| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.40 r_work: 0.3268 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 44370 Z= 0.111 Angle : 0.506 8.008 60240 Z= 0.258 Chirality : 0.040 0.136 6440 Planarity : 0.004 0.039 7870 Dihedral : 3.943 16.222 6010 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.59 % Allowed : 18.57 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.11), residues: 5440 helix: 1.69 (0.10), residues: 2920 sheet: -1.01 (0.22), residues: 570 loop : -0.39 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 96 TYR 0.013 0.001 TYR E 145 PHE 0.008 0.001 PHE C 8 TRP 0.018 0.001 TRP G 270 HIS 0.005 0.001 HIS F 124 Details of bonding type rmsd covalent geometry : bond 0.00234 (44370) covalent geometry : angle 0.50553 (60240) hydrogen bonds : bond 0.03930 ( 2497) hydrogen bonds : angle 4.55752 ( 7047) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 595 time to evaluate : 0.901 Fit side-chains REVERT: A 250 ASN cc_start: 0.7646 (OUTLIER) cc_final: 0.7284 (t0) REVERT: B 250 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7279 (t0) REVERT: C 80 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: C 250 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.7231 (t0) REVERT: D 250 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7257 (t0) REVERT: D 256 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7166 (pm20) REVERT: E 250 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7599 (t0) REVERT: E 492 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8605 (tp) REVERT: F 167 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8055 (tp) REVERT: F 250 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7105 (t0) REVERT: G 79 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6780 (mt-10) REVERT: G 167 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8071 (tp) REVERT: G 250 ASN cc_start: 0.7624 (OUTLIER) cc_final: 0.7089 (t0) REVERT: H 250 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7138 (t0) REVERT: H 492 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8641 (tp) REVERT: I 353 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8601 (mp) REVERT: J 80 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7821 (mp10) REVERT: J 250 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.7223 (t0) REVERT: J 522 LYS cc_start: 0.8166 (mmtp) cc_final: 0.7582 (mmtm) outliers start: 72 outliers final: 28 residues processed: 637 average time/residue: 0.4820 time to fit residues: 371.8207 Evaluate side-chains 627 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 581 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 250 ASN Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 478 MET Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 250 ASN Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 250 ASN Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 492 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 478 MET Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 250 ASN Chi-restraints excluded: chain J residue 353 LEU Chi-restraints excluded: chain J residue 477 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 351 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 401 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 chunk 455 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 465 optimal weight: 0.5980 chunk 238 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS B 117 HIS C 117 HIS D 117 HIS D 224 GLN E 117 HIS F 117 HIS G 117 HIS H 117 HIS I 117 HIS I 224 GLN J 117 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120475 restraints weight = 42632.843| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.40 r_work: 0.3256 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 44370 Z= 0.121 Angle : 0.519 8.810 60240 Z= 0.264 Chirality : 0.041 0.133 6440 Planarity : 0.004 0.038 7870 Dihedral : 3.973 16.559 6010 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.17 % Allowed : 18.90 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.11), residues: 5440 helix: 1.66 (0.10), residues: 2920 sheet: -1.01 (0.22), residues: 570 loop : -0.39 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 96 TYR 0.013 0.001 TYR E 145 PHE 0.009 0.001 PHE C 8 TRP 0.017 0.001 TRP F 270 HIS 0.005 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00262 (44370) covalent geometry : angle 0.51925 (60240) hydrogen bonds : bond 0.04055 ( 2497) hydrogen bonds : angle 4.59958 ( 7047) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10880 Ramachandran restraints generated. 5440 Oldfield, 0 Emsley, 5440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 583 time to evaluate : 0.905 Fit side-chains REVERT: A 227 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.7207 (ttm-80) REVERT: A 250 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7308 (t0) REVERT: B 250 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7303 (t0) REVERT: C 80 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: C 239 ARG cc_start: 0.6261 (ttm170) cc_final: 0.5857 (tpt170) REVERT: C 250 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.7243 (t0) REVERT: D 250 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7257 (t0) REVERT: E 250 ASN cc_start: 0.7842 (OUTLIER) cc_final: 0.7610 (t0) REVERT: E 492 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8646 (tp) REVERT: F 167 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8081 (tp) REVERT: F 250 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7092 (t0) REVERT: G 167 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8032 (tp) REVERT: G 250 ASN cc_start: 0.7636 (OUTLIER) cc_final: 0.7100 (t0) REVERT: H 250 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7134 (t0) REVERT: H 492 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8648 (tp) REVERT: I 353 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8609 (mp) REVERT: J 80 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7832 (mp10) REVERT: J 250 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.7255 (t0) outliers start: 53 outliers final: 27 residues processed: 611 average time/residue: 0.4863 time to fit residues: 359.8603 Evaluate side-chains 621 residues out of total 4530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 577 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 80 GLN Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 250 ASN Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 250 ASN Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 250 ASN Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 492 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain I residue 477 VAL Chi-restraints excluded: chain J residue 80 GLN Chi-restraints excluded: chain J residue 250 ASN Chi-restraints excluded: chain J residue 353 LEU Chi-restraints excluded: chain J residue 376 THR Chi-restraints excluded: chain J residue 477 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 482 optimal weight: 5.9990 chunk 478 optimal weight: 0.0970 chunk 128 optimal weight: 3.9990 chunk 316 optimal weight: 0.3980 chunk 495 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 252 optimal weight: 0.0050 chunk 538 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 458 optimal weight: 0.8980 chunk 372 optimal weight: 0.6980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS A 224 GLN A 389 GLN B 117 HIS C 117 HIS D 117 HIS D 224 GLN E 117 HIS F 117 HIS G 117 HIS H 20 GLN H 117 HIS I 117 HIS J 117 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.154320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125900 restraints weight = 42983.728| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.31 r_work: 0.3329 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 44370 Z= 0.094 Angle : 0.484 9.075 60240 Z= 0.247 Chirality : 0.039 0.160 6440 Planarity : 0.004 0.039 7870 Dihedral : 3.750 16.073 6010 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.97 % Allowed : 19.12 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.12), residues: 5440 helix: 1.82 (0.10), residues: 2920 sheet: -1.03 (0.22), residues: 570 loop : -0.30 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 96 TYR 0.011 0.001 TYR C 4 PHE 0.009 0.001 PHE C 8 TRP 0.015 0.001 TRP J 327 HIS 0.004 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00188 (44370) covalent geometry : angle 0.48404 (60240) hydrogen bonds : bond 0.03559 ( 2497) hydrogen bonds : angle 4.42725 ( 7047) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16070.40 seconds wall clock time: 273 minutes 14.42 seconds (16394.42 seconds total)