Starting phenix.real_space_refine on Tue Aug 26 03:44:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gts_51566/08_2025/9gts_51566.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gts_51566/08_2025/9gts_51566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gts_51566/08_2025/9gts_51566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gts_51566/08_2025/9gts_51566.map" model { file = "/net/cci-nas-00/data/ceres_data/9gts_51566/08_2025/9gts_51566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gts_51566/08_2025/9gts_51566.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.119 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 108 5.16 5 C 20892 2.51 5 N 5868 2.21 5 O 6132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33000 Number of models: 1 Model: "" Number of chains: 18 Chain: "1a" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "1f" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "1e" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "1d" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "1c" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "1b" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "2A" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2750 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 22, 'TRANS': 331} Chain breaks: 2 Chain: "0A" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 20, 'TRANS': 189} Chain breaks: 1 Chain: "2F" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2750 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 22, 'TRANS': 331} Chain breaks: 2 Chain: "0F" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 20, 'TRANS': 189} Chain breaks: 1 Chain: "2E" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2750 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 22, 'TRANS': 331} Chain breaks: 2 Chain: "0E" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 20, 'TRANS': 189} Chain breaks: 1 Chain: "2D" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2750 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 22, 'TRANS': 331} Chain breaks: 2 Chain: "0D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 20, 'TRANS': 189} Chain breaks: 1 Chain: "2C" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2750 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 22, 'TRANS': 331} Chain breaks: 2 Chain: "0C" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 20, 'TRANS': 189} Chain breaks: 1 Chain: "2B" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2750 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 22, 'TRANS': 331} Chain breaks: 2 Chain: "0B" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 20, 'TRANS': 189} Chain breaks: 1 Time building chain proxies: 7.66, per 1000 atoms: 0.23 Number of scatterers: 33000 At special positions: 0 Unit cell: (172.53, 192.765, 128.865, 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 108 16.00 O 6132 8.00 N 5868 7.00 C 20892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7800 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 47 sheets defined 33.7% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain '1a' and resid 76 through 87 Processing helix chain '1a' and resid 89 through 94 removed outlier: 3.520A pdb=" N ARG1a 94 " --> pdb=" O MET1a 90 " (cutoff:3.500A) Processing helix chain '1a' and resid 104 through 106 No H-bonds generated for 'chain '1a' and resid 104 through 106' Processing helix chain '1f' and resid 76 through 87 Processing helix chain '1f' and resid 89 through 94 Processing helix chain '1e' and resid 76 through 87 Processing helix chain '1e' and resid 89 through 94 Processing helix chain '1d' and resid 76 through 87 Processing helix chain '1d' and resid 89 through 94 Processing helix chain '1c' and resid 76 through 87 Processing helix chain '1c' and resid 89 through 94 Processing helix chain '1b' and resid 76 through 87 Processing helix chain '1b' and resid 89 through 94 Processing helix chain '2A' and resid 53 through 61 Processing helix chain '2A' and resid 69 through 80 Processing helix chain '2A' and resid 252 through 257 removed outlier: 3.537A pdb=" N GLU2A 257 " --> pdb=" O GLY2A 254 " (cutoff:3.500A) Processing helix chain '2A' and resid 268 through 276 removed outlier: 4.116A pdb=" N ALA2A 272 " --> pdb=" O PRO2A 268 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG2A 276 " --> pdb=" O ALA2A 272 " (cutoff:3.500A) Processing helix chain '2A' and resid 280 through 299 Processing helix chain '2A' and resid 312 through 322 Processing helix chain '2A' and resid 353 through 368 removed outlier: 4.074A pdb=" N GLY2A 359 " --> pdb=" O GLY2A 355 " (cutoff:3.500A) Processing helix chain '2A' and resid 390 through 398 removed outlier: 3.972A pdb=" N LEU2A 396 " --> pdb=" O GLY2A 392 " (cutoff:3.500A) Processing helix chain '2A' and resid 424 through 428 removed outlier: 3.501A pdb=" N ARG2A 428 " --> pdb=" O PRO2A 425 " (cutoff:3.500A) Processing helix chain '2A' and resid 429 through 447 removed outlier: 3.572A pdb=" N ARG2A 433 " --> pdb=" O TYR2A 429 " (cutoff:3.500A) Processing helix chain '2A' and resid 448 through 451 removed outlier: 3.924A pdb=" N VAL2A 451 " --> pdb=" O GLN2A 448 " (cutoff:3.500A) No H-bonds generated for 'chain '2A' and resid 448 through 451' Processing helix chain '2A' and resid 456 through 477 removed outlier: 4.066A pdb=" N ASN2A 473 " --> pdb=" O ALA2A 469 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU2A 474 " --> pdb=" O PHE2A 470 " (cutoff:3.500A) Processing helix chain '2A' and resid 484 through 488 Processing helix chain '0A' and resid 2 through 15 Processing helix chain '0A' and resid 31 through 36 Processing helix chain '0A' and resid 54 through 57 removed outlier: 3.632A pdb=" N ARG0A 57 " --> pdb=" O VAL0A 54 " (cutoff:3.500A) No H-bonds generated for 'chain '0A' and resid 54 through 57' Processing helix chain '0A' and resid 93 through 109 Processing helix chain '0A' and resid 120 through 125 Processing helix chain '0A' and resid 144 through 152 Processing helix chain '0A' and resid 203 through 213 Processing helix chain '2F' and resid 53 through 61 Processing helix chain '2F' and resid 69 through 80 Processing helix chain '2F' and resid 252 through 259 removed outlier: 3.543A pdb=" N GLU2F 257 " --> pdb=" O GLY2F 254 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA2F 258 " --> pdb=" O GLY2F 255 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE2F 259 " --> pdb=" O LEU2F 256 " (cutoff:3.500A) Processing helix chain '2F' and resid 268 through 276 removed outlier: 4.065A pdb=" N ALA2F 272 " --> pdb=" O PRO2F 268 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG2F 276 " --> pdb=" O ALA2F 272 " (cutoff:3.500A) Processing helix chain '2F' and resid 280 through 299 Processing helix chain '2F' and resid 312 through 322 Processing helix chain '2F' and resid 353 through 368 removed outlier: 4.051A pdb=" N GLY2F 359 " --> pdb=" O GLY2F 355 " (cutoff:3.500A) Processing helix chain '2F' and resid 390 through 398 removed outlier: 3.916A pdb=" N LEU2F 396 " --> pdb=" O GLY2F 392 " (cutoff:3.500A) Processing helix chain '2F' and resid 424 through 428 removed outlier: 3.527A pdb=" N ARG2F 428 " --> pdb=" O PRO2F 425 " (cutoff:3.500A) Processing helix chain '2F' and resid 429 through 447 removed outlier: 3.552A pdb=" N ARG2F 433 " --> pdb=" O TYR2F 429 " (cutoff:3.500A) Processing helix chain '2F' and resid 448 through 451 removed outlier: 3.678A pdb=" N VAL2F 451 " --> pdb=" O GLN2F 448 " (cutoff:3.500A) No H-bonds generated for 'chain '2F' and resid 448 through 451' Processing helix chain '2F' and resid 456 through 477 removed outlier: 4.156A pdb=" N ASN2F 473 " --> pdb=" O ALA2F 469 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU2F 474 " --> pdb=" O PHE2F 470 " (cutoff:3.500A) Processing helix chain '2F' and resid 484 through 488 Processing helix chain '2F' and resid 498 through 503 Processing helix chain '0F' and resid 2 through 16 Processing helix chain '0F' and resid 31 through 36 Processing helix chain '0F' and resid 54 through 57 Processing helix chain '0F' and resid 93 through 109 Processing helix chain '0F' and resid 120 through 125 Processing helix chain '0F' and resid 144 through 152 removed outlier: 3.700A pdb=" N LEU0F 151 " --> pdb=" O ILE0F 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY0F 152 " --> pdb=" O TRP0F 148 " (cutoff:3.500A) Processing helix chain '0F' and resid 203 through 214 removed outlier: 3.537A pdb=" N ARG0F 214 " --> pdb=" O ALA0F 210 " (cutoff:3.500A) Processing helix chain '2E' and resid 53 through 61 Processing helix chain '2E' and resid 69 through 80 Processing helix chain '2E' and resid 252 through 257 removed outlier: 3.530A pdb=" N GLU2E 257 " --> pdb=" O GLY2E 254 " (cutoff:3.500A) Processing helix chain '2E' and resid 268 through 276 removed outlier: 4.099A pdb=" N ALA2E 272 " --> pdb=" O PRO2E 268 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG2E 276 " --> pdb=" O ALA2E 272 " (cutoff:3.500A) Processing helix chain '2E' and resid 280 through 299 Processing helix chain '2E' and resid 312 through 322 Processing helix chain '2E' and resid 353 through 368 removed outlier: 4.048A pdb=" N GLY2E 359 " --> pdb=" O GLY2E 355 " (cutoff:3.500A) Processing helix chain '2E' and resid 390 through 398 removed outlier: 3.861A pdb=" N LEU2E 396 " --> pdb=" O GLY2E 392 " (cutoff:3.500A) Processing helix chain '2E' and resid 424 through 428 removed outlier: 3.576A pdb=" N ARG2E 428 " --> pdb=" O PRO2E 425 " (cutoff:3.500A) Processing helix chain '2E' and resid 429 through 447 removed outlier: 3.576A pdb=" N ARG2E 433 " --> pdb=" O TYR2E 429 " (cutoff:3.500A) Processing helix chain '2E' and resid 448 through 451 removed outlier: 3.884A pdb=" N VAL2E 451 " --> pdb=" O GLN2E 448 " (cutoff:3.500A) No H-bonds generated for 'chain '2E' and resid 448 through 451' Processing helix chain '2E' and resid 456 through 477 removed outlier: 3.514A pdb=" N TRP2E 460 " --> pdb=" O ASP2E 456 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN2E 473 " --> pdb=" O ALA2E 469 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU2E 474 " --> pdb=" O PHE2E 470 " (cutoff:3.500A) Processing helix chain '2E' and resid 484 through 488 Processing helix chain '2E' and resid 499 through 504 Processing helix chain '0E' and resid 2 through 16 Processing helix chain '0E' and resid 31 through 36 Processing helix chain '0E' and resid 54 through 57 removed outlier: 3.634A pdb=" N ARG0E 57 " --> pdb=" O VAL0E 54 " (cutoff:3.500A) No H-bonds generated for 'chain '0E' and resid 54 through 57' Processing helix chain '0E' and resid 93 through 109 Processing helix chain '0E' and resid 120 through 125 Processing helix chain '0E' and resid 144 through 152 Processing helix chain '0E' and resid 203 through 214 Processing helix chain '2D' and resid 53 through 61 Processing helix chain '2D' and resid 69 through 82 removed outlier: 4.026A pdb=" N GLY2D 82 " --> pdb=" O PHE2D 78 " (cutoff:3.500A) Processing helix chain '2D' and resid 252 through 257 removed outlier: 3.545A pdb=" N GLU2D 257 " --> pdb=" O GLY2D 254 " (cutoff:3.500A) Processing helix chain '2D' and resid 269 through 276 removed outlier: 3.747A pdb=" N ARG2D 276 " --> pdb=" O ALA2D 272 " (cutoff:3.500A) Processing helix chain '2D' and resid 280 through 299 Processing helix chain '2D' and resid 312 through 322 Processing helix chain '2D' and resid 353 through 368 removed outlier: 4.098A pdb=" N GLY2D 359 " --> pdb=" O GLY2D 355 " (cutoff:3.500A) Processing helix chain '2D' and resid 390 through 398 removed outlier: 3.977A pdb=" N LEU2D 396 " --> pdb=" O GLY2D 392 " (cutoff:3.500A) Processing helix chain '2D' and resid 424 through 428 Processing helix chain '2D' and resid 429 through 447 removed outlier: 3.569A pdb=" N ARG2D 433 " --> pdb=" O TYR2D 429 " (cutoff:3.500A) Processing helix chain '2D' and resid 448 through 451 removed outlier: 3.841A pdb=" N VAL2D 451 " --> pdb=" O GLN2D 448 " (cutoff:3.500A) No H-bonds generated for 'chain '2D' and resid 448 through 451' Processing helix chain '2D' and resid 456 through 477 removed outlier: 4.079A pdb=" N ASN2D 473 " --> pdb=" O ALA2D 469 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU2D 474 " --> pdb=" O PHE2D 470 " (cutoff:3.500A) Processing helix chain '2D' and resid 484 through 488 Processing helix chain '2D' and resid 499 through 504 Processing helix chain '0D' and resid 2 through 15 Processing helix chain '0D' and resid 31 through 36 Processing helix chain '0D' and resid 54 through 57 removed outlier: 3.560A pdb=" N ARG0D 57 " --> pdb=" O VAL0D 54 " (cutoff:3.500A) No H-bonds generated for 'chain '0D' and resid 54 through 57' Processing helix chain '0D' and resid 93 through 109 Processing helix chain '0D' and resid 120 through 125 Processing helix chain '0D' and resid 144 through 152 Processing helix chain '0D' and resid 203 through 213 Processing helix chain '2C' and resid 53 through 61 Processing helix chain '2C' and resid 68 through 80 removed outlier: 4.570A pdb=" N HIS2C 72 " --> pdb=" O TYR2C 68 " (cutoff:3.500A) Processing helix chain '2C' and resid 252 through 257 removed outlier: 3.546A pdb=" N GLU2C 257 " --> pdb=" O GLY2C 254 " (cutoff:3.500A) Processing helix chain '2C' and resid 268 through 276 removed outlier: 4.063A pdb=" N ALA2C 272 " --> pdb=" O PRO2C 268 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG2C 276 " --> pdb=" O ALA2C 272 " (cutoff:3.500A) Processing helix chain '2C' and resid 280 through 299 Processing helix chain '2C' and resid 312 through 322 Processing helix chain '2C' and resid 353 through 369 removed outlier: 4.065A pdb=" N GLY2C 359 " --> pdb=" O GLY2C 355 " (cutoff:3.500A) Processing helix chain '2C' and resid 390 through 398 removed outlier: 3.909A pdb=" N LEU2C 396 " --> pdb=" O GLY2C 392 " (cutoff:3.500A) Processing helix chain '2C' and resid 424 through 428 removed outlier: 3.550A pdb=" N ARG2C 428 " --> pdb=" O PRO2C 425 " (cutoff:3.500A) Processing helix chain '2C' and resid 429 through 447 removed outlier: 3.553A pdb=" N ARG2C 433 " --> pdb=" O TYR2C 429 " (cutoff:3.500A) Processing helix chain '2C' and resid 448 through 451 removed outlier: 3.679A pdb=" N VAL2C 451 " --> pdb=" O GLN2C 448 " (cutoff:3.500A) No H-bonds generated for 'chain '2C' and resid 448 through 451' Processing helix chain '2C' and resid 456 through 477 removed outlier: 4.138A pdb=" N ASN2C 473 " --> pdb=" O ALA2C 469 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU2C 474 " --> pdb=" O PHE2C 470 " (cutoff:3.500A) Processing helix chain '2C' and resid 484 through 488 Processing helix chain '2C' and resid 501 through 506 Processing helix chain '0C' and resid 2 through 16 removed outlier: 5.400A pdb=" N GLU0C 7 " --> pdb=" O HIS0C 3 " (cutoff:3.500A) Processing helix chain '0C' and resid 31 through 36 Processing helix chain '0C' and resid 54 through 57 Processing helix chain '0C' and resid 93 through 109 Processing helix chain '0C' and resid 120 through 125 Processing helix chain '0C' and resid 144 through 152 Processing helix chain '0C' and resid 203 through 214 removed outlier: 3.548A pdb=" N ARG0C 214 " --> pdb=" O ALA0C 210 " (cutoff:3.500A) Processing helix chain '2B' and resid 53 through 61 Processing helix chain '2B' and resid 69 through 80 Processing helix chain '2B' and resid 252 through 257 removed outlier: 3.534A pdb=" N GLU2B 257 " --> pdb=" O GLY2B 254 " (cutoff:3.500A) Processing helix chain '2B' and resid 268 through 276 removed outlier: 4.115A pdb=" N ALA2B 272 " --> pdb=" O PRO2B 268 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG2B 276 " --> pdb=" O ALA2B 272 " (cutoff:3.500A) Processing helix chain '2B' and resid 280 through 299 Processing helix chain '2B' and resid 312 through 322 Processing helix chain '2B' and resid 353 through 368 removed outlier: 4.050A pdb=" N GLY2B 359 " --> pdb=" O GLY2B 355 " (cutoff:3.500A) Processing helix chain '2B' and resid 390 through 398 removed outlier: 3.964A pdb=" N LEU2B 396 " --> pdb=" O GLY2B 392 " (cutoff:3.500A) Processing helix chain '2B' and resid 424 through 428 removed outlier: 3.575A pdb=" N ARG2B 428 " --> pdb=" O PRO2B 425 " (cutoff:3.500A) Processing helix chain '2B' and resid 429 through 447 removed outlier: 3.561A pdb=" N ARG2B 433 " --> pdb=" O TYR2B 429 " (cutoff:3.500A) Processing helix chain '2B' and resid 448 through 451 removed outlier: 3.808A pdb=" N VAL2B 451 " --> pdb=" O GLN2B 448 " (cutoff:3.500A) No H-bonds generated for 'chain '2B' and resid 448 through 451' Processing helix chain '2B' and resid 456 through 477 removed outlier: 4.110A pdb=" N ASN2B 473 " --> pdb=" O ALA2B 469 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU2B 474 " --> pdb=" O PHE2B 470 " (cutoff:3.500A) Processing helix chain '2B' and resid 484 through 488 Processing helix chain '2B' and resid 499 through 504 Processing helix chain '0B' and resid 2 through 16 removed outlier: 4.023A pdb=" N GLU0B 7 " --> pdb=" O HIS0B 3 " (cutoff:3.500A) Processing helix chain '0B' and resid 31 through 36 Processing helix chain '0B' and resid 54 through 57 removed outlier: 3.714A pdb=" N ARG0B 57 " --> pdb=" O VAL0B 54 " (cutoff:3.500A) No H-bonds generated for 'chain '0B' and resid 54 through 57' Processing helix chain '0B' and resid 93 through 109 Processing helix chain '0B' and resid 120 through 125 Processing helix chain '0B' and resid 144 through 151 Processing helix chain '0B' and resid 203 through 214 Processing sheet with id=AA1, first strand: chain '1a' and resid 14 through 19 removed outlier: 4.365A pdb=" N ASN1a 14 " --> pdb=" O MET1a 102 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA1a 97 " --> pdb=" O ARG1a 115 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ARG1a 115 " --> pdb=" O ALA1a 97 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE1a 99 " --> pdb=" O ASN1a 113 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN1a 113 " --> pdb=" O ILE1a 99 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL1a 101 " --> pdb=" O ARG1a 111 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG1a 111 " --> pdb=" O VAL1a 101 " (cutoff:3.500A) removed outlier: 28.085A pdb=" N TRP1a 112 " --> pdb=" O ASN1f 45 " (cutoff:3.500A) removed outlier: 25.053A pdb=" N ASN1f 45 " --> pdb=" O TRP1a 112 " (cutoff:3.500A) removed outlier: 21.358A pdb=" N LEU1a 114 " --> pdb=" O GLN1f 43 " (cutoff:3.500A) removed outlier: 18.328A pdb=" N GLN1f 43 " --> pdb=" O LEU1a 114 " (cutoff:3.500A) removed outlier: 16.087A pdb=" N ASN1a 116 " --> pdb=" O ARG1f 41 " (cutoff:3.500A) removed outlier: 11.983A pdb=" N ARG1f 41 " --> pdb=" O ASN1a 116 " (cutoff:3.500A) removed outlier: 12.619A pdb=" N TRP1a 118 " --> pdb=" O VAL1f 39 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N VAL1f 39 " --> pdb=" O TRP1a 118 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N SER1a 120 " --> pdb=" O GLN1f 37 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU1f 33 " --> pdb=" O ALA1a 124 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLU1f 36 " --> pdb=" O ALA1f 61 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ALA1f 61 " --> pdb=" O GLU1f 36 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASP1f 38 " --> pdb=" O GLY1f 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1a' and resid 145 through 148 removed outlier: 3.742A pdb=" N GLU1a 145 " --> pdb=" O ARG1a 115 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N CYS1a 119 " --> pdb=" O VAL1a 142 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL1a 142 " --> pdb=" O CYS1a 119 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS1a 121 " --> pdb=" O THR1a 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1a' and resid 34 through 35 removed outlier: 5.497A pdb=" N ARG1b 111 " --> pdb=" O VAL1b 101 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL1b 101 " --> pdb=" O ARG1b 111 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASN1b 113 " --> pdb=" O ILE1b 99 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE1b 99 " --> pdb=" O ASN1b 113 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ARG1b 115 " --> pdb=" O ALA1b 97 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA1b 97 " --> pdb=" O ARG1b 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1c' and resid 127 through 128 removed outlier: 6.048A pdb=" N VAL1b 142 " --> pdb=" O CYS1b 119 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N CYS1b 119 " --> pdb=" O VAL1b 142 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU1b 145 " --> pdb=" O ARG1b 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1a' and resid 37 through 39 removed outlier: 5.029A pdb=" N VAL1a 60 " --> pdb=" O ASP1a 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1a' and resid 42 through 45 removed outlier: 3.624A pdb=" N GLN1a 44 " --> pdb=" O ASN1a 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1a' and resid 127 through 128 removed outlier: 7.142A pdb=" N THR1f 136 " --> pdb=" O ALA1f 124 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA1f 124 " --> pdb=" O THR1f 136 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR1f 138 " --> pdb=" O VAL1f 122 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL1f 122 " --> pdb=" O THR1f 138 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR1f 140 " --> pdb=" O SER1f 120 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP1f 118 " --> pdb=" O VAL1f 142 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU1f 144 " --> pdb=" O ASN1f 116 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ASN1f 116 " --> pdb=" O GLU1f 144 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU1f 146 " --> pdb=" O LEU1f 114 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU1f 114 " --> pdb=" O LEU1f 146 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL1f 148 " --> pdb=" O TRP1f 112 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP1f 112 " --> pdb=" O VAL1f 148 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN1f 116 " --> pdb=" O LYS1f 95 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LYS1f 95 " --> pdb=" O ASN1f 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1a' and resid 127 through 128 removed outlier: 7.142A pdb=" N THR1f 136 " --> pdb=" O ALA1f 124 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA1f 124 " --> pdb=" O THR1f 136 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR1f 138 " --> pdb=" O VAL1f 122 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL1f 122 " --> pdb=" O THR1f 138 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR1f 140 " --> pdb=" O SER1f 120 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP1f 118 " --> pdb=" O VAL1f 142 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU1f 144 " --> pdb=" O ASN1f 116 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ASN1f 116 " --> pdb=" O GLU1f 144 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU1f 146 " --> pdb=" O LEU1f 114 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU1f 114 " --> pdb=" O LEU1f 146 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL1f 148 " --> pdb=" O TRP1f 112 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP1f 112 " --> pdb=" O VAL1f 148 " (cutoff:3.500A) removed outlier: 28.130A pdb=" N TRP1f 112 " --> pdb=" O ASN1e 45 " (cutoff:3.500A) removed outlier: 25.108A pdb=" N ASN1e 45 " --> pdb=" O TRP1f 112 " (cutoff:3.500A) removed outlier: 21.332A pdb=" N LEU1f 114 " --> pdb=" O GLN1e 43 " (cutoff:3.500A) removed outlier: 18.284A pdb=" N GLN1e 43 " --> pdb=" O LEU1f 114 " (cutoff:3.500A) removed outlier: 15.826A pdb=" N ASN1f 116 " --> pdb=" O ARG1e 41 " (cutoff:3.500A) removed outlier: 11.638A pdb=" N ARG1e 41 " --> pdb=" O ASN1f 116 " (cutoff:3.500A) removed outlier: 12.426A pdb=" N TRP1f 118 " --> pdb=" O VAL1e 39 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N VAL1e 39 " --> pdb=" O TRP1f 118 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER1f 120 " --> pdb=" O GLN1e 37 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLU1e 36 " --> pdb=" O ALA1e 61 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ALA1e 61 " --> pdb=" O GLU1e 36 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP1e 38 " --> pdb=" O GLY1e 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '1f' and resid 127 through 128 removed outlier: 3.837A pdb=" N LYS1e 121 " --> pdb=" O THR1e 140 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL1e 142 " --> pdb=" O CYS1e 119 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N CYS1e 119 " --> pdb=" O VAL1e 142 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLU1e 144 " --> pdb=" O ALA1e 117 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA1e 117 " --> pdb=" O GLU1e 144 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU1e 146 " --> pdb=" O ARG1e 115 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ARG1e 115 " --> pdb=" O LEU1e 146 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL1e 148 " --> pdb=" O ASN1e 113 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN1e 113 " --> pdb=" O VAL1e 148 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ARG1e 111 " --> pdb=" O VAL1e 101 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL1e 101 " --> pdb=" O ARG1e 111 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASN1e 113 " --> pdb=" O ILE1e 99 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE1e 99 " --> pdb=" O ASN1e 113 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ARG1e 115 " --> pdb=" O ALA1e 97 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA1e 97 " --> pdb=" O ARG1e 115 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '1f' and resid 127 through 128 removed outlier: 3.837A pdb=" N LYS1e 121 " --> pdb=" O THR1e 140 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL1e 142 " --> pdb=" O CYS1e 119 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N CYS1e 119 " --> pdb=" O VAL1e 142 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLU1e 144 " --> pdb=" O ALA1e 117 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA1e 117 " --> pdb=" O GLU1e 144 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU1e 146 " --> pdb=" O ARG1e 115 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ARG1e 115 " --> pdb=" O LEU1e 146 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N VAL1e 148 " --> pdb=" O ASN1e 113 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN1e 113 " --> pdb=" O VAL1e 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '1e' and resid 127 through 128 Processing sheet with id=AB3, first strand: chain '1d' and resid 15 through 19 removed outlier: 6.903A pdb=" N ALA1d 97 " --> pdb=" O ARG1d 115 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ARG1d 115 " --> pdb=" O ALA1d 97 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE1d 99 " --> pdb=" O ASN1d 113 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN1d 113 " --> pdb=" O ILE1d 99 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL1d 101 " --> pdb=" O ARG1d 111 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ARG1d 111 " --> pdb=" O VAL1d 101 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU1d 145 " --> pdb=" O ARG1d 115 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ALA1d 117 " --> pdb=" O PHE1d 143 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE1d 143 " --> pdb=" O ALA1d 117 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N CYS1d 119 " --> pdb=" O ILE1d 141 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE1d 141 " --> pdb=" O CYS1d 119 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS1d 121 " --> pdb=" O ILE1d 139 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE1d 139 " --> pdb=" O LYS1d 121 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL1d 123 " --> pdb=" O GLU1d 137 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU1d 137 " --> pdb=" O VAL1d 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '1d' and resid 15 through 19 removed outlier: 6.903A pdb=" N ALA1d 97 " --> pdb=" O ARG1d 115 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ARG1d 115 " --> pdb=" O ALA1d 97 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE1d 99 " --> pdb=" O ASN1d 113 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN1d 113 " --> pdb=" O ILE1d 99 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL1d 101 " --> pdb=" O ARG1d 111 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ARG1d 111 " --> pdb=" O VAL1d 101 " (cutoff:3.500A) removed outlier: 28.108A pdb=" N TRP1d 112 " --> pdb=" O ASN1c 45 " (cutoff:3.500A) removed outlier: 25.049A pdb=" N ASN1c 45 " --> pdb=" O TRP1d 112 " (cutoff:3.500A) removed outlier: 21.270A pdb=" N LEU1d 114 " --> pdb=" O GLN1c 43 " (cutoff:3.500A) removed outlier: 18.264A pdb=" N GLN1c 43 " --> pdb=" O LEU1d 114 " (cutoff:3.500A) removed outlier: 15.718A pdb=" N ASN1d 116 " --> pdb=" O ARG1c 41 " (cutoff:3.500A) removed outlier: 11.514A pdb=" N ARG1c 41 " --> pdb=" O ASN1d 116 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N TRP1d 118 " --> pdb=" O VAL1c 39 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N VAL1c 39 " --> pdb=" O TRP1d 118 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER1d 120 " --> pdb=" O GLN1c 37 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU1c 33 " --> pdb=" O ALA1d 124 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLU1c 36 " --> pdb=" O ALA1c 61 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ALA1c 61 " --> pdb=" O GLU1c 36 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ASP1c 38 " --> pdb=" O GLY1c 59 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '1d' and resid 37 through 45 removed outlier: 4.683A pdb=" N ASP1d 38 " --> pdb=" O GLY1d 59 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '1d' and resid 127 through 128 Processing sheet with id=AB7, first strand: chain '1c' and resid 15 through 19 removed outlier: 5.761A pdb=" N LYS1c 95 " --> pdb=" O ASN1c 116 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN1c 116 " --> pdb=" O LYS1c 95 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU1c 145 " --> pdb=" O ARG1c 115 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '1c' and resid 65 through 71 removed outlier: 7.063A pdb=" N THR1c 136 " --> pdb=" O ALA1c 124 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA1c 124 " --> pdb=" O THR1c 136 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR1c 138 " --> pdb=" O VAL1c 122 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL1c 122 " --> pdb=" O THR1c 138 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR1c 140 " --> pdb=" O SER1c 120 " (cutoff:3.500A) removed outlier: 28.126A pdb=" N TRP1c 112 " --> pdb=" O ASN1b 45 " (cutoff:3.500A) removed outlier: 25.106A pdb=" N ASN1b 45 " --> pdb=" O TRP1c 112 " (cutoff:3.500A) removed outlier: 21.341A pdb=" N LEU1c 114 " --> pdb=" O GLN1b 43 " (cutoff:3.500A) removed outlier: 18.377A pdb=" N GLN1b 43 " --> pdb=" O LEU1c 114 " (cutoff:3.500A) removed outlier: 15.785A pdb=" N ASN1c 116 " --> pdb=" O ARG1b 41 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ARG1b 41 " --> pdb=" O ASN1c 116 " (cutoff:3.500A) removed outlier: 12.380A pdb=" N TRP1c 118 " --> pdb=" O VAL1b 39 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N VAL1b 39 " --> pdb=" O TRP1c 118 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N SER1c 120 " --> pdb=" O GLN1b 37 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLU1b 36 " --> pdb=" O ALA1b 61 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA1b 61 " --> pdb=" O GLU1b 36 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASP1b 38 " --> pdb=" O GLY1b 59 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '2A' and resid 49 through 51 removed outlier: 6.680A pdb=" N ALA2A 34 " --> pdb=" O TYR2A 86 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL2A 88 " --> pdb=" O ALA2A 34 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N PHE2A 36 " --> pdb=" O VAL2A 88 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL2A 33 " --> pdb=" O ILE2A 262 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET2A 264 " --> pdb=" O VAL2A 33 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N SER2A 263 " --> pdb=" O VAL2A 302 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ILE2A 304 " --> pdb=" O SER2A 263 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL2A 265 " --> pdb=" O ILE2A 304 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ASN2A 403 " --> pdb=" O ALA2A 331 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU2A 333 " --> pdb=" O ASN2A 403 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE2A 405 " --> pdb=" O LEU2A 333 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '2A' and resid 348 through 351 removed outlier: 3.529A pdb=" N ASP2A 384 " --> pdb=" O LYS2A 339 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '2A' and resid 489 through 492 removed outlier: 6.267A pdb=" N VAL2A 508 " --> pdb=" O THR0A 184 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ARG0A 186 " --> pdb=" O VAL2A 508 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N CYS2A 510 " --> pdb=" O ARG0A 186 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLY0A 188 " --> pdb=" O CYS2A 510 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE2A 512 " --> pdb=" O GLY0A 188 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '0A' and resid 24 through 26 removed outlier: 6.421A pdb=" N ASP0A 24 " --> pdb=" O VAL0A 43 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ALA0A 45 " --> pdb=" O ASP0A 24 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA0A 26 " --> pdb=" O ALA0A 45 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU0A 47 " --> pdb=" O ALA0A 26 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL0A 43 " --> pdb=" O TRP0A 90 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TRP0A 90 " --> pdb=" O VAL0A 43 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ALA0A 45 " --> pdb=" O THR0A 88 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR0A 88 " --> pdb=" O ALA0A 45 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU0A 47 " --> pdb=" O LEU0A 86 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU0A 86 " --> pdb=" O LEU0A 47 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP0A 49 " --> pdb=" O SER0A 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '0A' and resid 62 through 65 removed outlier: 6.087A pdb=" N VAL0A 62 " --> pdb=" O ARG0A 74 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG0A 74 " --> pdb=" O VAL0A 62 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL0A 64 " --> pdb=" O VAL0A 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '2F' and resid 49 through 51 removed outlier: 6.707A pdb=" N ALA2F 34 " --> pdb=" O TYR2F 86 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL2F 88 " --> pdb=" O ALA2F 34 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N PHE2F 36 " --> pdb=" O VAL2F 88 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL2F 33 " --> pdb=" O SER2F 263 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL2F 265 " --> pdb=" O VAL2F 33 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ALA2F 35 " --> pdb=" O VAL2F 265 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER2F 263 " --> pdb=" O VAL2F 302 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ILE2F 304 " --> pdb=" O SER2F 263 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL2F 265 " --> pdb=" O ILE2F 304 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N ASN2F 403 " --> pdb=" O ALA2F 331 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU2F 333 " --> pdb=" O ASN2F 403 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE2F 405 " --> pdb=" O LEU2F 333 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '2F' and resid 348 through 351 removed outlier: 3.563A pdb=" N ASP2F 384 " --> pdb=" O LYS2F 339 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '2F' and resid 489 through 492 removed outlier: 6.272A pdb=" N VAL2F 508 " --> pdb=" O THR0F 184 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ARG0F 186 " --> pdb=" O VAL2F 508 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N CYS2F 510 " --> pdb=" O ARG0F 186 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '0F' and resid 24 through 26 removed outlier: 6.450A pdb=" N ASP0F 24 " --> pdb=" O VAL0F 43 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA0F 45 " --> pdb=" O ASP0F 24 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA0F 26 " --> pdb=" O ALA0F 45 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU0F 47 " --> pdb=" O ALA0F 26 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL0F 43 " --> pdb=" O TRP0F 90 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TRP0F 90 " --> pdb=" O VAL0F 43 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ALA0F 45 " --> pdb=" O THR0F 88 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N THR0F 88 " --> pdb=" O ALA0F 45 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU0F 47 " --> pdb=" O LEU0F 86 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU0F 86 " --> pdb=" O LEU0F 47 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP0F 49 " --> pdb=" O SER0F 84 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '0F' and resid 62 through 65 removed outlier: 6.066A pdb=" N VAL0F 62 " --> pdb=" O ARG0F 74 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG0F 74 " --> pdb=" O VAL0F 62 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL0F 64 " --> pdb=" O VAL0F 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '2E' and resid 49 through 51 removed outlier: 6.694A pdb=" N ALA2E 34 " --> pdb=" O TYR2E 86 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL2E 88 " --> pdb=" O ALA2E 34 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE2E 36 " --> pdb=" O VAL2E 88 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL2E 33 " --> pdb=" O ILE2E 262 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET2E 264 " --> pdb=" O VAL2E 33 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N SER2E 263 " --> pdb=" O VAL2E 302 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE2E 304 " --> pdb=" O SER2E 263 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL2E 265 " --> pdb=" O ILE2E 304 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASN2E 403 " --> pdb=" O ALA2E 331 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU2E 333 " --> pdb=" O ASN2E 403 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE2E 405 " --> pdb=" O LEU2E 333 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '2E' and resid 348 through 351 removed outlier: 3.549A pdb=" N ASP2E 384 " --> pdb=" O LYS2E 339 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '2E' and resid 489 through 492 Processing sheet with id=AD4, first strand: chain '0E' and resid 24 through 26 removed outlier: 6.439A pdb=" N ASP0E 24 " --> pdb=" O VAL0E 43 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ALA0E 45 " --> pdb=" O ASP0E 24 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA0E 26 " --> pdb=" O ALA0E 45 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU0E 47 " --> pdb=" O ALA0E 26 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL0E 43 " --> pdb=" O TRP0E 90 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TRP0E 90 " --> pdb=" O VAL0E 43 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ALA0E 45 " --> pdb=" O THR0E 88 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR0E 88 " --> pdb=" O ALA0E 45 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU0E 47 " --> pdb=" O LEU0E 86 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU0E 86 " --> pdb=" O LEU0E 47 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP0E 49 " --> pdb=" O SER0E 84 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '0E' and resid 62 through 65 removed outlier: 6.214A pdb=" N VAL0E 62 " --> pdb=" O ARG0E 74 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG0E 74 " --> pdb=" O VAL0E 62 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL0E 64 " --> pdb=" O VAL0E 72 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '2D' and resid 49 through 51 removed outlier: 6.648A pdb=" N ALA2D 34 " --> pdb=" O TYR2D 86 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL2D 88 " --> pdb=" O ALA2D 34 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE2D 36 " --> pdb=" O VAL2D 88 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL2D 33 " --> pdb=" O ILE2D 262 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET2D 264 " --> pdb=" O VAL2D 33 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N SER2D 263 " --> pdb=" O VAL2D 302 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE2D 304 " --> pdb=" O SER2D 263 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL2D 265 " --> pdb=" O ILE2D 304 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N ASN2D 403 " --> pdb=" O ALA2D 331 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU2D 333 " --> pdb=" O ASN2D 403 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE2D 405 " --> pdb=" O LEU2D 333 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '2D' and resid 347 through 351 removed outlier: 3.630A pdb=" N ASP2D 384 " --> pdb=" O LYS2D 339 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '2D' and resid 489 through 492 Processing sheet with id=AD9, first strand: chain '0D' and resid 24 through 26 removed outlier: 6.430A pdb=" N ASP0D 24 " --> pdb=" O VAL0D 43 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA0D 45 " --> pdb=" O ASP0D 24 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA0D 26 " --> pdb=" O ALA0D 45 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU0D 47 " --> pdb=" O ALA0D 26 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL0D 43 " --> pdb=" O TRP0D 90 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TRP0D 90 " --> pdb=" O VAL0D 43 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ALA0D 45 " --> pdb=" O THR0D 88 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR0D 88 " --> pdb=" O ALA0D 45 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU0D 47 " --> pdb=" O LEU0D 86 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU0D 86 " --> pdb=" O LEU0D 47 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP0D 49 " --> pdb=" O SER0D 84 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '0D' and resid 62 through 65 removed outlier: 6.071A pdb=" N VAL0D 62 " --> pdb=" O ARG0D 74 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG0D 74 " --> pdb=" O VAL0D 62 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL0D 64 " --> pdb=" O VAL0D 72 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '2C' and resid 49 through 51 removed outlier: 6.661A pdb=" N ALA2C 34 " --> pdb=" O TYR2C 86 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL2C 88 " --> pdb=" O ALA2C 34 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N PHE2C 36 " --> pdb=" O VAL2C 88 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL2C 90 " --> pdb=" O PHE2C 36 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLY2C 38 " --> pdb=" O VAL2C 90 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL2C 33 " --> pdb=" O SER2C 263 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL2C 265 " --> pdb=" O VAL2C 33 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA2C 35 " --> pdb=" O VAL2C 265 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N SER2C 263 " --> pdb=" O VAL2C 302 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE2C 304 " --> pdb=" O SER2C 263 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL2C 265 " --> pdb=" O ILE2C 304 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ASN2C 403 " --> pdb=" O ALA2C 331 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU2C 333 " --> pdb=" O ASN2C 403 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE2C 405 " --> pdb=" O LEU2C 333 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '2C' and resid 348 through 351 Processing sheet with id=AE4, first strand: chain '2C' and resid 489 through 492 Processing sheet with id=AE5, first strand: chain '0C' and resid 24 through 26 removed outlier: 6.450A pdb=" N ASP0C 24 " --> pdb=" O VAL0C 43 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ALA0C 45 " --> pdb=" O ASP0C 24 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA0C 26 " --> pdb=" O ALA0C 45 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU0C 47 " --> pdb=" O ALA0C 26 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL0C 43 " --> pdb=" O TRP0C 90 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TRP0C 90 " --> pdb=" O VAL0C 43 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ALA0C 45 " --> pdb=" O THR0C 88 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR0C 88 " --> pdb=" O ALA0C 45 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU0C 47 " --> pdb=" O LEU0C 86 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU0C 86 " --> pdb=" O LEU0C 47 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP0C 49 " --> pdb=" O SER0C 84 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '0C' and resid 62 through 65 removed outlier: 6.173A pdb=" N VAL0C 62 " --> pdb=" O ARG0C 74 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG0C 74 " --> pdb=" O VAL0C 62 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL0C 64 " --> pdb=" O VAL0C 72 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '2B' and resid 49 through 51 removed outlier: 6.661A pdb=" N ALA2B 34 " --> pdb=" O TYR2B 86 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL2B 88 " --> pdb=" O ALA2B 34 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N PHE2B 36 " --> pdb=" O VAL2B 88 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL2B 90 " --> pdb=" O PHE2B 36 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLY2B 38 " --> pdb=" O VAL2B 90 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL2B 33 " --> pdb=" O ILE2B 262 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET2B 264 " --> pdb=" O VAL2B 33 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N SER2B 263 " --> pdb=" O VAL2B 302 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE2B 304 " --> pdb=" O SER2B 263 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL2B 265 " --> pdb=" O ILE2B 304 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ASN2B 403 " --> pdb=" O ALA2B 331 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU2B 333 " --> pdb=" O ASN2B 403 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE2B 405 " --> pdb=" O LEU2B 333 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '2B' and resid 348 through 351 removed outlier: 3.552A pdb=" N ASP2B 384 " --> pdb=" O LYS2B 339 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '2B' and resid 489 through 492 removed outlier: 6.204A pdb=" N VAL2B 508 " --> pdb=" O THR0B 184 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ARG0B 186 " --> pdb=" O VAL2B 508 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS2B 510 " --> pdb=" O ARG0B 186 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLY0B 188 " --> pdb=" O CYS2B 510 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE2B 512 " --> pdb=" O GLY0B 188 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '0B' and resid 24 through 26 removed outlier: 6.437A pdb=" N ASP0B 24 " --> pdb=" O VAL0B 43 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA0B 45 " --> pdb=" O ASP0B 24 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ALA0B 26 " --> pdb=" O ALA0B 45 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU0B 47 " --> pdb=" O ALA0B 26 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL0B 43 " --> pdb=" O TRP0B 90 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TRP0B 90 " --> pdb=" O VAL0B 43 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ALA0B 45 " --> pdb=" O THR0B 88 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N THR0B 88 " --> pdb=" O ALA0B 45 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LEU0B 47 " --> pdb=" O LEU0B 86 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU0B 86 " --> pdb=" O LEU0B 47 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP0B 49 " --> pdb=" O SER0B 84 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '0B' and resid 62 through 65 removed outlier: 6.234A pdb=" N VAL0B 62 " --> pdb=" O ARG0B 74 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG0B 74 " --> pdb=" O VAL0B 62 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL0B 64 " --> pdb=" O VAL0B 72 " (cutoff:3.500A) 1333 hydrogen bonds defined for protein. 3744 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: 8.08 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 5574 1.27 - 1.41: 8436 1.41 - 1.55: 19554 1.55 - 1.68: 18 1.68 - 1.82: 186 Bond restraints: 33768 Sorted by residual: bond pdb=" C GLN1a 44 " pdb=" O GLN1a 44 " ideal model delta sigma weight residual 1.234 1.137 0.097 1.18e-02 7.18e+03 6.72e+01 bond pdb=" C ASN1a 45 " pdb=" O ASN1a 45 " ideal model delta sigma weight residual 1.234 1.135 0.099 1.23e-02 6.61e+03 6.49e+01 bond pdb=" C ARG1f 70 " pdb=" O ARG1f 70 " ideal model delta sigma weight residual 1.234 1.152 0.082 1.28e-02 6.10e+03 4.15e+01 bond pdb=" C GLN1a 43 " pdb=" O GLN1a 43 " ideal model delta sigma weight residual 1.236 1.159 0.077 1.21e-02 6.83e+03 4.02e+01 bond pdb=" C MET1f 57 " pdb=" O MET1f 57 " ideal model delta sigma weight residual 1.238 1.157 0.081 1.28e-02 6.10e+03 4.00e+01 ... (remaining 33763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 45370 2.61 - 5.23: 555 5.23 - 7.84: 63 7.84 - 10.46: 18 10.46 - 13.07: 8 Bond angle restraints: 46014 Sorted by residual: angle pdb=" N GLY1a 47 " pdb=" CA GLY1a 47 " pdb=" C GLY1a 47 " ideal model delta sigma weight residual 112.50 125.57 -13.07 1.16e+00 7.43e-01 1.27e+02 angle pdb=" C MET1b 57 " pdb=" N PRO1b 58 " pdb=" CA PRO1b 58 " ideal model delta sigma weight residual 119.76 130.62 -10.86 1.00e+00 1.00e+00 1.18e+02 angle pdb=" C MET1e 57 " pdb=" N PRO1e 58 " pdb=" CA PRO1e 58 " ideal model delta sigma weight residual 119.76 130.39 -10.63 1.00e+00 1.00e+00 1.13e+02 angle pdb=" C MET1a 57 " pdb=" N PRO1a 58 " pdb=" CA PRO1a 58 " ideal model delta sigma weight residual 119.78 128.27 -8.49 1.03e+00 9.43e-01 6.80e+01 angle pdb=" C MET1d 57 " pdb=" N PRO1d 58 " pdb=" CA PRO1d 58 " ideal model delta sigma weight residual 119.84 129.71 -9.87 1.25e+00 6.40e-01 6.24e+01 ... (remaining 46009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 17469 17.96 - 35.93: 1989 35.93 - 53.89: 534 53.89 - 71.85: 107 71.85 - 89.81: 19 Dihedral angle restraints: 20118 sinusoidal: 7950 harmonic: 12168 Sorted by residual: dihedral pdb=" C GLN1a 34 " pdb=" N GLN1a 34 " pdb=" CA GLN1a 34 " pdb=" CB GLN1a 34 " ideal model delta harmonic sigma weight residual -122.60 -108.98 -13.62 0 2.50e+00 1.60e-01 2.97e+01 dihedral pdb=" C GLN1a 43 " pdb=" N GLN1a 43 " pdb=" CA GLN1a 43 " pdb=" CB GLN1a 43 " ideal model delta harmonic sigma weight residual -122.60 -110.25 -12.35 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" C GLN1a 44 " pdb=" N GLN1a 44 " pdb=" CA GLN1a 44 " pdb=" CB GLN1a 44 " ideal model delta harmonic sigma weight residual -122.60 -110.47 -12.13 0 2.50e+00 1.60e-01 2.36e+01 ... (remaining 20115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4537 0.088 - 0.175: 506 0.175 - 0.263: 21 0.263 - 0.350: 4 0.350 - 0.438: 2 Chirality restraints: 5070 Sorted by residual: chirality pdb=" CA THR1a 48 " pdb=" N THR1a 48 " pdb=" C THR1a 48 " pdb=" CB THR1a 48 " both_signs ideal model delta sigma weight residual False 2.53 2.09 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA THR1a 49 " pdb=" N THR1a 49 " pdb=" C THR1a 49 " pdb=" CB THR1a 49 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA PRO1b 58 " pdb=" N PRO1b 58 " pdb=" C PRO1b 58 " pdb=" CB PRO1b 58 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 5067 not shown) Planarity restraints: 6072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA1b 61 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ALA1b 61 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA1b 61 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS1b 62 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY1d 130 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C GLY1d 130 " 0.056 2.00e-02 2.50e+03 pdb=" O GLY1d 130 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP1d 131 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN1a 107 " -0.054 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO1a 108 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO1a 108 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO1a 108 " -0.044 5.00e-02 4.00e+02 ... (remaining 6069 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5217 2.76 - 3.30: 29056 3.30 - 3.83: 53300 3.83 - 4.37: 61143 4.37 - 4.90: 110953 Nonbonded interactions: 259669 Sorted by model distance: nonbonded pdb=" OE1 GLN2A 288 " pdb=" OH TYR2A 326 " model vdw 2.230 3.040 nonbonded pdb=" O GLN2A 311 " pdb=" OH TYR2A 335 " model vdw 2.251 3.040 nonbonded pdb=" O GLN2D 311 " pdb=" OH TYR2D 335 " model vdw 2.256 3.040 nonbonded pdb=" OE2 GLU1f 69 " pdb=" OG1 THR1f 136 " model vdw 2.259 3.040 nonbonded pdb=" O ALA2C 331 " pdb=" OG1 THR2C 420 " model vdw 2.287 3.040 ... (remaining 259664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0A' selection = chain '0B' selection = chain '0C' selection = chain '0D' selection = chain '0E' selection = chain '0F' } ncs_group { reference = chain '1a' selection = chain '1b' selection = chain '1c' selection = chain '1d' selection = chain '1e' selection = chain '1f' } ncs_group { reference = chain '2A' selection = chain '2B' selection = chain '2C' selection = chain '2D' selection = chain '2E' selection = chain '2F' } 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: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.140 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 : 0.005 0.101 33768 Z= 0.324 Angle : 0.668 13.072 46014 Z= 0.409 Chirality : 0.049 0.438 5070 Planarity : 0.005 0.126 6072 Dihedral : 16.325 89.815 12318 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.69 % Allowed : 22.92 % Favored : 76.39 % Cbeta Deviations : 0.28 % 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 aren not related in a simple way. whole: 0.68 (0.13), residues: 4188 helix: 1.74 (0.15), residues: 1164 sheet: 0.43 (0.17), residues: 1146 loop : -0.29 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG2A 276 TYR 0.011 0.001 TYR0C 170 PHE 0.016 0.001 PHE1e 143 TRP 0.012 0.001 TRP1a 118 HIS 0.006 0.001 HIS0E 98 Details of bonding type rmsd covalent geometry : bond 0.00504 (33768) covalent geometry : angle 0.66786 (46014) hydrogen bonds : bond 0.14566 ( 1302) hydrogen bonds : angle 6.15360 ( 3744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 465 time to evaluate : 1.279 Fit side-chains REVERT: 1a 41 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8162 (mtp-110) REVERT: 1a 46 GLN cc_start: 0.9382 (OUTLIER) cc_final: 0.7991 (tp40) REVERT: 1f 90 MET cc_start: 0.9110 (mmm) cc_final: 0.8871 (mmp) REVERT: 1b 14 ASN cc_start: 0.8278 (t0) cc_final: 0.8038 (t0) REVERT: 1b 70 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8959 (ttp-170) REVERT: 2A 384 ASP cc_start: 0.8061 (t0) cc_final: 0.7815 (m-30) REVERT: 2A 489 TYR cc_start: 0.8528 (p90) cc_final: 0.8135 (p90) REVERT: 2F 378 VAL cc_start: 0.9001 (t) cc_final: 0.8695 (p) REVERT: 2E 298 MET cc_start: 0.8490 (mmm) cc_final: 0.8272 (mmm) REVERT: 2D 366 SER cc_start: 0.8622 (m) cc_final: 0.8412 (m) REVERT: 2D 484 SER cc_start: 0.8947 (m) cc_final: 0.8644 (p) REVERT: 2B 298 MET cc_start: 0.8421 (mmm) cc_final: 0.8205 (mmm) outliers start: 24 outliers final: 14 residues processed: 486 average time/residue: 0.1992 time to fit residues: 158.1442 Evaluate side-chains 375 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 358 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1a residue 33 LEU Chi-restraints excluded: chain 1a residue 34 GLN Chi-restraints excluded: chain 1a residue 41 ARG Chi-restraints excluded: chain 1a residue 46 GLN Chi-restraints excluded: chain 1a residue 48 THR Chi-restraints excluded: chain 1a residue 51 ARG Chi-restraints excluded: chain 1a residue 54 VAL Chi-restraints excluded: chain 1f residue 57 MET Chi-restraints excluded: chain 1f residue 63 ASP Chi-restraints excluded: chain 1d residue 63 ASP Chi-restraints excluded: chain 1c residue 27 LEU Chi-restraints excluded: chain 1c residue 57 MET Chi-restraints excluded: chain 1c residue 63 ASP Chi-restraints excluded: chain 1b residue 70 ARG Chi-restraints excluded: chain 0D residue 18 LEU Chi-restraints excluded: chain 0C residue 3 HIS Chi-restraints excluded: chain 0C residue 4 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1a 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1a 52 ASN 1a 67 GLN 1e 28 ASN 1e 67 GLN 1d 28 ASN 1d 37 GLN 1b 28 ASN 1b 32 ASN 2F 473 ASN 2E 72 HIS 2D 72 HIS 2D 498 ASN ** 2C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2C 473 ASN ** 2B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113728 restraints weight = 47820.788| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.81 r_work: 0.3216 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 33768 Z= 0.270 Angle : 0.618 9.652 46014 Z= 0.321 Chirality : 0.048 0.175 5070 Planarity : 0.005 0.051 6072 Dihedral : 4.929 86.949 4717 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.95 % Allowed : 20.75 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.13), residues: 4188 helix: 1.28 (0.15), residues: 1236 sheet: 0.34 (0.17), residues: 1044 loop : -0.69 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG2B 276 TYR 0.024 0.002 TYR1a 42 PHE 0.019 0.002 PHE2C 481 TRP 0.016 0.001 TRP1c 118 HIS 0.005 0.001 HIS0E 58 Details of bonding type rmsd covalent geometry : bond 0.00667 (33768) covalent geometry : angle 0.61847 (46014) hydrogen bonds : bond 0.04132 ( 1302) hydrogen bonds : angle 4.71365 ( 3744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 372 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: 1f 20 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8521 (t70) REVERT: 1e 90 MET cc_start: 0.8839 (mmm) cc_final: 0.8485 (mmt) REVERT: 1d 72 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8225 (mtt) REVERT: 1c 20 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8725 (t70) REVERT: 1b 131 ASP cc_start: 0.8306 (t0) cc_final: 0.7955 (t0) REVERT: 2A 363 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8265 (ttm170) REVERT: 2A 384 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: 2A 391 ARG cc_start: 0.5963 (ttt180) cc_final: 0.4994 (ttm170) REVERT: 2A 489 TYR cc_start: 0.8602 (p90) cc_final: 0.8330 (p90) REVERT: 2F 22 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6865 (pm20) REVERT: 2F 314 ARG cc_start: 0.7942 (ptt90) cc_final: 0.7599 (mtm-85) REVERT: 0F 132 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8226 (ttp) REVERT: 0E 1 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.5625 (mtt) REVERT: 0E 180 THR cc_start: 0.8982 (p) cc_final: 0.8717 (m) REVERT: 2D 51 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8538 (p) REVERT: 2D 391 ARG cc_start: 0.5920 (ttt180) cc_final: 0.5010 (ttm170) REVERT: 2D 498 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8932 (p0) REVERT: 0D 67 GLN cc_start: 0.6607 (pm20) cc_final: 0.6225 (pp30) REVERT: 2C 22 GLU cc_start: 0.7457 (mt-10) cc_final: 0.6856 (pm20) REVERT: 2C 366 SER cc_start: 0.8935 (m) cc_final: 0.8663 (t) REVERT: 2C 496 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7464 (mp0) REVERT: 0C 79 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8322 (ptm160) REVERT: 0C 160 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8318 (t0) REVERT: 2B 22 GLU cc_start: 0.6760 (pm20) cc_final: 0.6518 (pm20) REVERT: 2B 391 ARG cc_start: 0.6410 (ttt180) cc_final: 0.5492 (ttm170) REVERT: 0B 181 GLU cc_start: 0.8580 (mt-10) cc_final: 0.7828 (tt0) outliers start: 171 outliers final: 118 residues processed: 518 average time/residue: 0.1795 time to fit residues: 154.2696 Evaluate side-chains 465 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 336 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1a residue 9 VAL Chi-restraints excluded: chain 1a residue 11 VAL Chi-restraints excluded: chain 1a residue 33 LEU Chi-restraints excluded: chain 1a residue 34 GLN Chi-restraints excluded: chain 1a residue 54 VAL Chi-restraints excluded: chain 1a residue 65 SER Chi-restraints excluded: chain 1a residue 73 SER Chi-restraints excluded: chain 1a residue 79 THR Chi-restraints excluded: chain 1a residue 118 TRP Chi-restraints excluded: chain 1f residue 9 VAL Chi-restraints excluded: chain 1f residue 11 VAL Chi-restraints excluded: chain 1f residue 20 ASP Chi-restraints excluded: chain 1f residue 57 MET Chi-restraints excluded: chain 1f residue 60 VAL Chi-restraints excluded: chain 1f residue 79 THR Chi-restraints excluded: chain 1f residue 100 ILE Chi-restraints excluded: chain 1f residue 126 THR Chi-restraints excluded: chain 1e residue 33 LEU Chi-restraints excluded: chain 1e residue 79 THR Chi-restraints excluded: chain 1e residue 100 ILE Chi-restraints excluded: chain 1e residue 101 VAL Chi-restraints excluded: chain 1e residue 126 THR Chi-restraints excluded: chain 1d residue 9 VAL Chi-restraints excluded: chain 1d residue 11 VAL Chi-restraints excluded: chain 1d residue 54 VAL Chi-restraints excluded: chain 1d residue 72 MET Chi-restraints excluded: chain 1d residue 73 SER Chi-restraints excluded: chain 1d residue 143 PHE Chi-restraints excluded: chain 1d residue 147 VAL Chi-restraints excluded: chain 1c residue 9 VAL Chi-restraints excluded: chain 1c residue 17 ILE Chi-restraints excluded: chain 1c residue 20 ASP Chi-restraints excluded: chain 1c residue 57 MET Chi-restraints excluded: chain 1c residue 79 THR Chi-restraints excluded: chain 1c residue 100 ILE Chi-restraints excluded: chain 1c residue 143 PHE Chi-restraints excluded: chain 1b residue 9 VAL Chi-restraints excluded: chain 1b residue 33 LEU Chi-restraints excluded: chain 1b residue 54 VAL Chi-restraints excluded: chain 1b residue 79 THR Chi-restraints excluded: chain 1b residue 100 ILE Chi-restraints excluded: chain 1b residue 101 VAL Chi-restraints excluded: chain 2A residue 33 VAL Chi-restraints excluded: chain 2A residue 363 ARG Chi-restraints excluded: chain 2A residue 384 ASP Chi-restraints excluded: chain 2A residue 387 LEU Chi-restraints excluded: chain 2A residue 390 THR Chi-restraints excluded: chain 2A residue 407 SER Chi-restraints excluded: chain 0A residue 18 LEU Chi-restraints excluded: chain 0A residue 31 THR Chi-restraints excluded: chain 0A residue 71 VAL Chi-restraints excluded: chain 0A residue 158 SER Chi-restraints excluded: chain 2F residue 33 VAL Chi-restraints excluded: chain 2F residue 39 LEU Chi-restraints excluded: chain 2F residue 267 VAL Chi-restraints excluded: chain 2F residue 297 LEU Chi-restraints excluded: chain 2F residue 387 LEU Chi-restraints excluded: chain 2F residue 407 SER Chi-restraints excluded: chain 2F residue 459 LEU Chi-restraints excluded: chain 2F residue 492 LYS Chi-restraints excluded: chain 2F residue 498 ASN Chi-restraints excluded: chain 0F residue 8 VAL Chi-restraints excluded: chain 0F residue 9 LEU Chi-restraints excluded: chain 0F residue 31 THR Chi-restraints excluded: chain 0F residue 48 TYR Chi-restraints excluded: chain 0F residue 71 VAL Chi-restraints excluded: chain 0F residue 132 MET Chi-restraints excluded: chain 0F residue 158 SER Chi-restraints excluded: chain 0F residue 160 ASP Chi-restraints excluded: chain 2E residue 33 VAL Chi-restraints excluded: chain 2E residue 39 LEU Chi-restraints excluded: chain 2E residue 267 VAL Chi-restraints excluded: chain 2E residue 387 LEU Chi-restraints excluded: chain 2E residue 390 THR Chi-restraints excluded: chain 2E residue 407 SER Chi-restraints excluded: chain 0E residue 1 MET Chi-restraints excluded: chain 0E residue 18 LEU Chi-restraints excluded: chain 0E residue 54 VAL Chi-restraints excluded: chain 0E residue 71 VAL Chi-restraints excluded: chain 0E residue 105 LEU Chi-restraints excluded: chain 0E residue 133 THR Chi-restraints excluded: chain 2D residue 33 VAL Chi-restraints excluded: chain 2D residue 51 VAL Chi-restraints excluded: chain 2D residue 387 LEU Chi-restraints excluded: chain 2D residue 407 SER Chi-restraints excluded: chain 2D residue 498 ASN Chi-restraints excluded: chain 2D residue 508 VAL Chi-restraints excluded: chain 2D residue 509 VAL Chi-restraints excluded: chain 0D residue 18 LEU Chi-restraints excluded: chain 0D residue 31 THR Chi-restraints excluded: chain 0D residue 71 VAL Chi-restraints excluded: chain 0D residue 93 THR Chi-restraints excluded: chain 0D residue 158 SER Chi-restraints excluded: chain 2C residue 33 VAL Chi-restraints excluded: chain 2C residue 39 LEU Chi-restraints excluded: chain 2C residue 267 VAL Chi-restraints excluded: chain 2C residue 297 LEU Chi-restraints excluded: chain 2C residue 370 VAL Chi-restraints excluded: chain 2C residue 386 GLU Chi-restraints excluded: chain 2C residue 387 LEU Chi-restraints excluded: chain 2C residue 445 ILE Chi-restraints excluded: chain 2C residue 459 LEU Chi-restraints excluded: chain 2C residue 498 ASN Chi-restraints excluded: chain 0C residue 3 HIS Chi-restraints excluded: chain 0C residue 8 VAL Chi-restraints excluded: chain 0C residue 31 THR Chi-restraints excluded: chain 0C residue 54 VAL Chi-restraints excluded: chain 0C residue 71 VAL Chi-restraints excluded: chain 0C residue 79 ARG Chi-restraints excluded: chain 0C residue 133 THR Chi-restraints excluded: chain 0C residue 158 SER Chi-restraints excluded: chain 0C residue 160 ASP Chi-restraints excluded: chain 0C residue 187 ILE Chi-restraints excluded: chain 2B residue 33 VAL Chi-restraints excluded: chain 2B residue 39 LEU Chi-restraints excluded: chain 2B residue 267 VAL Chi-restraints excluded: chain 2B residue 281 LEU Chi-restraints excluded: chain 2B residue 323 THR Chi-restraints excluded: chain 2B residue 387 LEU Chi-restraints excluded: chain 2B residue 508 VAL Chi-restraints excluded: chain 0B residue 8 VAL Chi-restraints excluded: chain 0B residue 9 LEU Chi-restraints excluded: chain 0B residue 18 LEU Chi-restraints excluded: chain 0B residue 54 VAL Chi-restraints excluded: chain 0B residue 71 VAL Chi-restraints excluded: chain 0B residue 79 ARG Chi-restraints excluded: chain 0B residue 105 LEU Chi-restraints excluded: chain 0B residue 170 TYR Chi-restraints excluded: chain 0B residue 185 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 76 optimal weight: 7.9990 chunk 377 optimal weight: 0.0670 chunk 409 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 243 optimal weight: 0.0000 chunk 315 optimal weight: 5.9990 chunk 264 optimal weight: 0.8980 chunk 249 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0E 205 HIS 2D 72 HIS 2D 498 ASN 2B 72 HIS 0B 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119223 restraints weight = 47032.096| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.78 r_work: 0.3283 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 33768 Z= 0.090 Angle : 0.475 7.669 46014 Z= 0.242 Chirality : 0.043 0.154 5070 Planarity : 0.004 0.051 6072 Dihedral : 4.100 55.924 4690 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.07 % Allowed : 23.12 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.13), residues: 4188 helix: 1.68 (0.15), residues: 1200 sheet: 0.30 (0.16), residues: 1140 loop : -0.45 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG2F 276 TYR 0.027 0.001 TYR0C 170 PHE 0.019 0.001 PHE2D 481 TRP 0.011 0.001 TRP1a 118 HIS 0.016 0.001 HIS0B 205 Details of bonding type rmsd covalent geometry : bond 0.00199 (33768) covalent geometry : angle 0.47504 (46014) hydrogen bonds : bond 0.02909 ( 1302) hydrogen bonds : angle 4.42403 ( 3744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 362 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: 1c 121 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8741 (ttmt) REVERT: 2A 22 GLU cc_start: 0.7097 (pm20) cc_final: 0.6760 (pm20) REVERT: 2A 489 TYR cc_start: 0.8371 (p90) cc_final: 0.8092 (p90) REVERT: 2F 22 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6853 (pm20) REVERT: 0F 132 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8135 (ttp) REVERT: 0E 1 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.5349 (mtt) REVERT: 2D 363 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.7958 (ttm170) REVERT: 2D 489 TYR cc_start: 0.8484 (p90) cc_final: 0.8136 (p90) REVERT: 0D 67 GLN cc_start: 0.6422 (pm20) cc_final: 0.6194 (pp30) REVERT: 2C 22 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6846 (pm20) REVERT: 2C 366 SER cc_start: 0.8851 (m) cc_final: 0.8594 (t) REVERT: 0C 160 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8232 (t0) REVERT: 0B 83 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7753 (mt) outliers start: 106 outliers final: 74 residues processed: 444 average time/residue: 0.1888 time to fit residues: 139.5960 Evaluate side-chains 415 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 335 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1a residue 33 LEU Chi-restraints excluded: chain 1a residue 34 GLN Chi-restraints excluded: chain 1a residue 57 MET Chi-restraints excluded: chain 1a residue 65 SER Chi-restraints excluded: chain 1a residue 73 SER Chi-restraints excluded: chain 1a residue 100 ILE Chi-restraints excluded: chain 1a residue 118 TRP Chi-restraints excluded: chain 1f residue 9 VAL Chi-restraints excluded: chain 1f residue 54 VAL Chi-restraints excluded: chain 1f residue 79 THR Chi-restraints excluded: chain 1e residue 33 LEU Chi-restraints excluded: chain 1e residue 73 SER Chi-restraints excluded: chain 1e residue 79 THR Chi-restraints excluded: chain 1e residue 100 ILE Chi-restraints excluded: chain 1d residue 57 MET Chi-restraints excluded: chain 1d residue 65 SER Chi-restraints excluded: chain 1d residue 73 SER Chi-restraints excluded: chain 1c residue 54 VAL Chi-restraints excluded: chain 1c residue 100 ILE Chi-restraints excluded: chain 1c residue 121 LYS Chi-restraints excluded: chain 1c residue 143 PHE Chi-restraints excluded: chain 1b residue 9 VAL Chi-restraints excluded: chain 1b residue 33 LEU Chi-restraints excluded: chain 1b residue 79 THR Chi-restraints excluded: chain 1b residue 100 ILE Chi-restraints excluded: chain 1b residue 101 VAL Chi-restraints excluded: chain 2A residue 33 VAL Chi-restraints excluded: chain 2A residue 267 VAL Chi-restraints excluded: chain 2A residue 407 SER Chi-restraints excluded: chain 2A residue 498 ASN Chi-restraints excluded: chain 0A residue 8 VAL Chi-restraints excluded: chain 0A residue 18 LEU Chi-restraints excluded: chain 0A residue 71 VAL Chi-restraints excluded: chain 0A residue 196 MET Chi-restraints excluded: chain 2F residue 407 SER Chi-restraints excluded: chain 2F residue 445 ILE Chi-restraints excluded: chain 2F residue 459 LEU Chi-restraints excluded: chain 2F residue 498 ASN Chi-restraints excluded: chain 0F residue 71 VAL Chi-restraints excluded: chain 0F residue 132 MET Chi-restraints excluded: chain 2E residue 33 VAL Chi-restraints excluded: chain 2E residue 39 LEU Chi-restraints excluded: chain 2E residue 267 VAL Chi-restraints excluded: chain 2E residue 366 SER Chi-restraints excluded: chain 2E residue 407 SER Chi-restraints excluded: chain 0E residue 1 MET Chi-restraints excluded: chain 0E residue 18 LEU Chi-restraints excluded: chain 0E residue 71 VAL Chi-restraints excluded: chain 0E residue 93 THR Chi-restraints excluded: chain 0E residue 160 ASP Chi-restraints excluded: chain 0E residue 170 TYR Chi-restraints excluded: chain 0E residue 193 ASP Chi-restraints excluded: chain 2D residue 33 VAL Chi-restraints excluded: chain 2D residue 267 VAL Chi-restraints excluded: chain 2D residue 363 ARG Chi-restraints excluded: chain 2D residue 407 SER Chi-restraints excluded: chain 2D residue 509 VAL Chi-restraints excluded: chain 0D residue 71 VAL Chi-restraints excluded: chain 0D residue 184 THR Chi-restraints excluded: chain 2C residue 39 LEU Chi-restraints excluded: chain 2C residue 267 VAL Chi-restraints excluded: chain 2C residue 370 VAL Chi-restraints excluded: chain 2C residue 386 GLU Chi-restraints excluded: chain 2C residue 498 ASN Chi-restraints excluded: chain 0C residue 1 MET Chi-restraints excluded: chain 0C residue 3 HIS Chi-restraints excluded: chain 0C residue 71 VAL Chi-restraints excluded: chain 0C residue 160 ASP Chi-restraints excluded: chain 2B residue 33 VAL Chi-restraints excluded: chain 2B residue 39 LEU Chi-restraints excluded: chain 2B residue 267 VAL Chi-restraints excluded: chain 2B residue 366 SER Chi-restraints excluded: chain 2B residue 508 VAL Chi-restraints excluded: chain 0B residue 8 VAL Chi-restraints excluded: chain 0B residue 18 LEU Chi-restraints excluded: chain 0B residue 71 VAL Chi-restraints excluded: chain 0B residue 83 LEU Chi-restraints excluded: chain 0B residue 170 TYR Chi-restraints excluded: chain 0B residue 185 VAL Chi-restraints excluded: chain 0B residue 193 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 85 optimal weight: 4.9990 chunk 407 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1a 28 ASN 1a 37 GLN ** 1a 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1d 32 ASN 2A 458 ASN ** 2F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2F 458 ASN ** 2E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0E 205 HIS 2D 72 HIS 2D 457 HIS ** 2C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2C 458 ASN ** 2B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2B 458 ASN 0B 205 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.131605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111992 restraints weight = 47438.656| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.80 r_work: 0.3182 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 33768 Z= 0.265 Angle : 0.597 8.758 46014 Z= 0.308 Chirality : 0.048 0.171 5070 Planarity : 0.005 0.047 6072 Dihedral : 4.392 50.978 4681 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.30 % Allowed : 21.85 % Favored : 72.86 % 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 aren not related in a simple way. whole: 0.13 (0.13), residues: 4188 helix: 1.27 (0.15), residues: 1236 sheet: 0.28 (0.17), residues: 1038 loop : -0.77 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG1f 89 TYR 0.017 0.002 TYR0C 117 PHE 0.024 0.002 PHE2B 481 TRP 0.017 0.001 TRP1f 118 HIS 0.009 0.001 HIS0B 205 Details of bonding type rmsd covalent geometry : bond 0.00649 (33768) covalent geometry : angle 0.59660 (46014) hydrogen bonds : bond 0.04127 ( 1302) hydrogen bonds : angle 4.56830 ( 3744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 333 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: 1f 20 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8577 (t70) REVERT: 1e 90 MET cc_start: 0.8970 (mmm) cc_final: 0.8583 (mmp) REVERT: 1d 8 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.5961 (t0) REVERT: 1d 72 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8211 (mtt) REVERT: 1c 20 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8705 (t70) REVERT: 1b 14 ASN cc_start: 0.8553 (t0) cc_final: 0.8272 (t0) REVERT: 1b 131 ASP cc_start: 0.8437 (t0) cc_final: 0.8116 (t0) REVERT: 2A 22 GLU cc_start: 0.7102 (pm20) cc_final: 0.6821 (pm20) REVERT: 2A 384 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7823 (m-30) REVERT: 2A 391 ARG cc_start: 0.6131 (ttt180) cc_final: 0.5185 (ttm-80) REVERT: 2F 51 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8639 (p) REVERT: 0F 132 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8233 (ttp) REVERT: 2E 366 SER cc_start: 0.8716 (m) cc_final: 0.8083 (t) REVERT: 2D 22 GLU cc_start: 0.7083 (pm20) cc_final: 0.6774 (pm20) REVERT: 0D 67 GLN cc_start: 0.6509 (pm20) cc_final: 0.6264 (pp30) REVERT: 2C 51 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8610 (p) REVERT: 2C 366 SER cc_start: 0.8903 (m) cc_final: 0.8649 (t) REVERT: 2C 496 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7496 (mp0) REVERT: 0C 160 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8308 (t0) REVERT: 2B 366 SER cc_start: 0.8695 (m) cc_final: 0.8048 (t) REVERT: 0B 83 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7919 (mt) REVERT: 0B 181 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8050 (tt0) outliers start: 183 outliers final: 144 residues processed: 488 average time/residue: 0.1840 time to fit residues: 151.3158 Evaluate side-chains 474 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 320 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1a residue 9 VAL Chi-restraints excluded: chain 1a residue 11 VAL Chi-restraints excluded: chain 1a residue 17 ILE Chi-restraints excluded: chain 1a residue 29 SER Chi-restraints excluded: chain 1a residue 33 LEU Chi-restraints excluded: chain 1a residue 34 GLN Chi-restraints excluded: chain 1a residue 36 GLU Chi-restraints excluded: chain 1a residue 54 VAL Chi-restraints excluded: chain 1a residue 57 MET Chi-restraints excluded: chain 1a residue 79 THR Chi-restraints excluded: chain 1a residue 100 ILE Chi-restraints excluded: chain 1a residue 118 TRP Chi-restraints excluded: chain 1f residue 9 VAL Chi-restraints excluded: chain 1f residue 11 VAL Chi-restraints excluded: chain 1f residue 20 ASP Chi-restraints excluded: chain 1f residue 53 ASN Chi-restraints excluded: chain 1f residue 54 VAL Chi-restraints excluded: chain 1f residue 79 THR Chi-restraints excluded: chain 1f residue 92 THR Chi-restraints excluded: chain 1f residue 100 ILE Chi-restraints excluded: chain 1f residue 126 THR Chi-restraints excluded: chain 1e residue 8 ASP Chi-restraints excluded: chain 1e residue 33 LEU Chi-restraints excluded: chain 1e residue 54 VAL Chi-restraints excluded: chain 1e residue 56 LEU Chi-restraints excluded: chain 1e residue 79 THR Chi-restraints excluded: chain 1e residue 101 VAL Chi-restraints excluded: chain 1e residue 126 THR Chi-restraints excluded: chain 1d residue 8 ASP Chi-restraints excluded: chain 1d residue 9 VAL Chi-restraints excluded: chain 1d residue 11 VAL Chi-restraints excluded: chain 1d residue 57 MET Chi-restraints excluded: chain 1d residue 65 SER Chi-restraints excluded: chain 1d residue 72 MET Chi-restraints excluded: chain 1d residue 100 ILE Chi-restraints excluded: chain 1d residue 126 THR Chi-restraints excluded: chain 1d residue 147 VAL Chi-restraints excluded: chain 1c residue 9 VAL Chi-restraints excluded: chain 1c residue 11 VAL Chi-restraints excluded: chain 1c residue 20 ASP Chi-restraints excluded: chain 1c residue 53 ASN Chi-restraints excluded: chain 1c residue 54 VAL Chi-restraints excluded: chain 1c residue 79 THR Chi-restraints excluded: chain 1c residue 92 THR Chi-restraints excluded: chain 1c residue 100 ILE Chi-restraints excluded: chain 1c residue 121 LYS Chi-restraints excluded: chain 1c residue 126 THR Chi-restraints excluded: chain 1c residue 143 PHE Chi-restraints excluded: chain 1b residue 9 VAL Chi-restraints excluded: chain 1b residue 11 VAL Chi-restraints excluded: chain 1b residue 33 LEU Chi-restraints excluded: chain 1b residue 56 LEU Chi-restraints excluded: chain 1b residue 79 THR Chi-restraints excluded: chain 1b residue 101 VAL Chi-restraints excluded: chain 2A residue 33 VAL Chi-restraints excluded: chain 2A residue 267 VAL Chi-restraints excluded: chain 2A residue 384 ASP Chi-restraints excluded: chain 2A residue 387 LEU Chi-restraints excluded: chain 2A residue 390 THR Chi-restraints excluded: chain 2A residue 407 SER Chi-restraints excluded: chain 2A residue 498 ASN Chi-restraints excluded: chain 0A residue 8 VAL Chi-restraints excluded: chain 0A residue 18 LEU Chi-restraints excluded: chain 0A residue 19 THR Chi-restraints excluded: chain 0A residue 31 THR Chi-restraints excluded: chain 0A residue 64 VAL Chi-restraints excluded: chain 0A residue 71 VAL Chi-restraints excluded: chain 0A residue 93 THR Chi-restraints excluded: chain 0A residue 158 SER Chi-restraints excluded: chain 0A residue 196 MET Chi-restraints excluded: chain 2F residue 33 VAL Chi-restraints excluded: chain 2F residue 39 LEU Chi-restraints excluded: chain 2F residue 51 VAL Chi-restraints excluded: chain 2F residue 267 VAL Chi-restraints excluded: chain 2F residue 281 LEU Chi-restraints excluded: chain 2F residue 297 LEU Chi-restraints excluded: chain 2F residue 378 VAL Chi-restraints excluded: chain 2F residue 387 LEU Chi-restraints excluded: chain 2F residue 407 SER Chi-restraints excluded: chain 2F residue 445 ILE Chi-restraints excluded: chain 2F residue 459 LEU Chi-restraints excluded: chain 2F residue 498 ASN Chi-restraints excluded: chain 0F residue 8 VAL Chi-restraints excluded: chain 0F residue 31 THR Chi-restraints excluded: chain 0F residue 48 TYR Chi-restraints excluded: chain 0F residue 71 VAL Chi-restraints excluded: chain 0F residue 132 MET Chi-restraints excluded: chain 0F residue 158 SER Chi-restraints excluded: chain 0F residue 160 ASP Chi-restraints excluded: chain 2E residue 33 VAL Chi-restraints excluded: chain 2E residue 39 LEU Chi-restraints excluded: chain 2E residue 267 VAL Chi-restraints excluded: chain 2E residue 387 LEU Chi-restraints excluded: chain 2E residue 390 THR Chi-restraints excluded: chain 2E residue 407 SER Chi-restraints excluded: chain 0E residue 18 LEU Chi-restraints excluded: chain 0E residue 71 VAL Chi-restraints excluded: chain 0E residue 93 THR Chi-restraints excluded: chain 0E residue 133 THR Chi-restraints excluded: chain 0E residue 160 ASP Chi-restraints excluded: chain 0E residue 185 VAL Chi-restraints excluded: chain 0E residue 193 ASP Chi-restraints excluded: chain 2D residue 33 VAL Chi-restraints excluded: chain 2D residue 267 VAL Chi-restraints excluded: chain 2D residue 370 VAL Chi-restraints excluded: chain 2D residue 387 LEU Chi-restraints excluded: chain 2D residue 390 THR Chi-restraints excluded: chain 2D residue 407 SER Chi-restraints excluded: chain 2D residue 445 ILE Chi-restraints excluded: chain 2D residue 509 VAL Chi-restraints excluded: chain 0D residue 64 VAL Chi-restraints excluded: chain 0D residue 71 VAL Chi-restraints excluded: chain 0D residue 93 THR Chi-restraints excluded: chain 0D residue 158 SER Chi-restraints excluded: chain 0D residue 184 THR Chi-restraints excluded: chain 2C residue 33 VAL Chi-restraints excluded: chain 2C residue 39 LEU Chi-restraints excluded: chain 2C residue 51 VAL Chi-restraints excluded: chain 2C residue 267 VAL Chi-restraints excluded: chain 2C residue 297 LEU Chi-restraints excluded: chain 2C residue 370 VAL Chi-restraints excluded: chain 2C residue 386 GLU Chi-restraints excluded: chain 2C residue 387 LEU Chi-restraints excluded: chain 2C residue 445 ILE Chi-restraints excluded: chain 2C residue 459 LEU Chi-restraints excluded: chain 2C residue 498 ASN Chi-restraints excluded: chain 0C residue 3 HIS Chi-restraints excluded: chain 0C residue 31 THR Chi-restraints excluded: chain 0C residue 54 VAL Chi-restraints excluded: chain 0C residue 71 VAL Chi-restraints excluded: chain 0C residue 79 ARG Chi-restraints excluded: chain 0C residue 93 THR Chi-restraints excluded: chain 0C residue 133 THR Chi-restraints excluded: chain 0C residue 158 SER Chi-restraints excluded: chain 0C residue 160 ASP Chi-restraints excluded: chain 0C residue 185 VAL Chi-restraints excluded: chain 2B residue 33 VAL Chi-restraints excluded: chain 2B residue 39 LEU Chi-restraints excluded: chain 2B residue 46 ASN Chi-restraints excluded: chain 2B residue 267 VAL Chi-restraints excluded: chain 2B residue 281 LEU Chi-restraints excluded: chain 2B residue 323 THR Chi-restraints excluded: chain 2B residue 387 LEU Chi-restraints excluded: chain 2B residue 508 VAL Chi-restraints excluded: chain 0B residue 8 VAL Chi-restraints excluded: chain 0B residue 9 LEU Chi-restraints excluded: chain 0B residue 18 LEU Chi-restraints excluded: chain 0B residue 48 TYR Chi-restraints excluded: chain 0B residue 71 VAL Chi-restraints excluded: chain 0B residue 83 LEU Chi-restraints excluded: chain 0B residue 134 VAL Chi-restraints excluded: chain 0B residue 170 TYR Chi-restraints excluded: chain 0B residue 185 VAL Chi-restraints excluded: chain 0B residue 193 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 281 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 376 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 354 optimal weight: 10.0000 chunk 241 optimal weight: 4.9990 chunk 311 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 209 optimal weight: 0.0170 chunk 159 optimal weight: 2.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0E 205 HIS ** 2C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2C 364 ASN ** 2B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0B 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115705 restraints weight = 47257.324| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.82 r_work: 0.3211 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33768 Z= 0.119 Angle : 0.494 8.466 46014 Z= 0.252 Chirality : 0.044 0.159 5070 Planarity : 0.004 0.047 6072 Dihedral : 4.091 47.693 4681 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.08 % Allowed : 23.15 % Favored : 72.77 % 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 aren not related in a simple way. whole: 0.29 (0.13), residues: 4188 helix: 1.45 (0.15), residues: 1230 sheet: 0.30 (0.17), residues: 1038 loop : -0.67 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG2E 276 TYR 0.013 0.001 TYR0F 117 PHE 0.024 0.001 PHE2B 481 TRP 0.011 0.001 TRP1a 118 HIS 0.010 0.001 HIS0B 205 Details of bonding type rmsd covalent geometry : bond 0.00283 (33768) covalent geometry : angle 0.49435 (46014) hydrogen bonds : bond 0.03084 ( 1302) hydrogen bonds : angle 4.40482 ( 3744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 344 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1a 33 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8746 (pp) REVERT: 1f 20 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8503 (t70) REVERT: 1e 90 MET cc_start: 0.8865 (mmm) cc_final: 0.8583 (mmm) REVERT: 1d 8 ASP cc_start: 0.6624 (OUTLIER) cc_final: 0.5970 (t0) REVERT: 1c 20 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8664 (t70) REVERT: 1c 121 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8802 (ttmt) REVERT: 1b 14 ASN cc_start: 0.8539 (t0) cc_final: 0.8264 (t0) REVERT: 2A 22 GLU cc_start: 0.7087 (pm20) cc_final: 0.6825 (pm20) REVERT: 2A 384 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: 2A 496 GLU cc_start: 0.6275 (tt0) cc_final: 0.5997 (tt0) REVERT: 0F 132 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8193 (ttp) REVERT: 2E 366 SER cc_start: 0.8662 (m) cc_final: 0.8062 (t) REVERT: 2D 22 GLU cc_start: 0.7134 (pm20) cc_final: 0.6805 (pm20) REVERT: 2D 363 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8016 (ttm170) REVERT: 2D 489 TYR cc_start: 0.8607 (p90) cc_final: 0.8166 (p90) REVERT: 2C 366 SER cc_start: 0.8897 (m) cc_final: 0.8681 (t) REVERT: 0C 105 LEU cc_start: 0.8969 (tp) cc_final: 0.8708 (tp) REVERT: 0C 160 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8356 (t0) REVERT: 2B 366 SER cc_start: 0.8647 (m) cc_final: 0.8040 (t) REVERT: 0B 83 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7829 (mt) REVERT: 0B 181 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8035 (tt0) outliers start: 141 outliers final: 113 residues processed: 467 average time/residue: 0.1745 time to fit residues: 135.9504 Evaluate side-chains 449 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 326 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1a residue 9 VAL Chi-restraints excluded: chain 1a residue 11 VAL Chi-restraints excluded: chain 1a residue 33 LEU Chi-restraints excluded: chain 1a residue 34 GLN Chi-restraints excluded: chain 1a residue 57 MET Chi-restraints excluded: chain 1a residue 65 SER Chi-restraints excluded: chain 1a residue 100 ILE Chi-restraints excluded: chain 1a residue 118 TRP Chi-restraints excluded: chain 1a residue 126 THR Chi-restraints excluded: chain 1f residue 9 VAL Chi-restraints excluded: chain 1f residue 20 ASP Chi-restraints excluded: chain 1f residue 54 VAL Chi-restraints excluded: chain 1f residue 79 THR Chi-restraints excluded: chain 1f residue 100 ILE Chi-restraints excluded: chain 1e residue 8 ASP Chi-restraints excluded: chain 1e residue 33 LEU Chi-restraints excluded: chain 1e residue 54 VAL Chi-restraints excluded: chain 1e residue 56 LEU Chi-restraints excluded: chain 1e residue 73 SER Chi-restraints excluded: chain 1e residue 79 THR Chi-restraints excluded: chain 1e residue 92 THR Chi-restraints excluded: chain 1e residue 100 ILE Chi-restraints excluded: chain 1e residue 101 VAL Chi-restraints excluded: chain 1d residue 8 ASP Chi-restraints excluded: chain 1d residue 9 VAL Chi-restraints excluded: chain 1d residue 54 VAL Chi-restraints excluded: chain 1d residue 57 MET Chi-restraints excluded: chain 1d residue 65 SER Chi-restraints excluded: chain 1d residue 72 MET Chi-restraints excluded: chain 1d residue 73 SER Chi-restraints excluded: chain 1d residue 126 THR Chi-restraints excluded: chain 1c residue 8 ASP Chi-restraints excluded: chain 1c residue 20 ASP Chi-restraints excluded: chain 1c residue 54 VAL Chi-restraints excluded: chain 1c residue 79 THR Chi-restraints excluded: chain 1c residue 100 ILE Chi-restraints excluded: chain 1c residue 121 LYS Chi-restraints excluded: chain 1c residue 126 THR Chi-restraints excluded: chain 1c residue 143 PHE Chi-restraints excluded: chain 1b residue 9 VAL Chi-restraints excluded: chain 1b residue 33 LEU Chi-restraints excluded: chain 1b residue 54 VAL Chi-restraints excluded: chain 1b residue 56 LEU Chi-restraints excluded: chain 1b residue 73 SER Chi-restraints excluded: chain 1b residue 79 THR Chi-restraints excluded: chain 1b residue 100 ILE Chi-restraints excluded: chain 1b residue 101 VAL Chi-restraints excluded: chain 2A residue 33 VAL Chi-restraints excluded: chain 2A residue 39 LEU Chi-restraints excluded: chain 2A residue 267 VAL Chi-restraints excluded: chain 2A residue 384 ASP Chi-restraints excluded: chain 2A residue 407 SER Chi-restraints excluded: chain 2A residue 498 ASN Chi-restraints excluded: chain 0A residue 8 VAL Chi-restraints excluded: chain 0A residue 18 LEU Chi-restraints excluded: chain 0A residue 48 TYR Chi-restraints excluded: chain 0A residue 71 VAL Chi-restraints excluded: chain 0A residue 93 THR Chi-restraints excluded: chain 0A residue 196 MET Chi-restraints excluded: chain 2F residue 39 LEU Chi-restraints excluded: chain 2F residue 267 VAL Chi-restraints excluded: chain 2F residue 378 VAL Chi-restraints excluded: chain 2F residue 407 SER Chi-restraints excluded: chain 2F residue 445 ILE Chi-restraints excluded: chain 2F residue 459 LEU Chi-restraints excluded: chain 2F residue 498 ASN Chi-restraints excluded: chain 0F residue 8 VAL Chi-restraints excluded: chain 0F residue 9 LEU Chi-restraints excluded: chain 0F residue 54 VAL Chi-restraints excluded: chain 0F residue 71 VAL Chi-restraints excluded: chain 0F residue 93 THR Chi-restraints excluded: chain 0F residue 132 MET Chi-restraints excluded: chain 2E residue 33 VAL Chi-restraints excluded: chain 2E residue 39 LEU Chi-restraints excluded: chain 2E residue 267 VAL Chi-restraints excluded: chain 2E residue 407 SER Chi-restraints excluded: chain 0E residue 18 LEU Chi-restraints excluded: chain 0E residue 71 VAL Chi-restraints excluded: chain 0E residue 93 THR Chi-restraints excluded: chain 0E residue 160 ASP Chi-restraints excluded: chain 0E residue 170 TYR Chi-restraints excluded: chain 0E residue 193 ASP Chi-restraints excluded: chain 2D residue 33 VAL Chi-restraints excluded: chain 2D residue 267 VAL Chi-restraints excluded: chain 2D residue 363 ARG Chi-restraints excluded: chain 2D residue 370 VAL Chi-restraints excluded: chain 2D residue 390 THR Chi-restraints excluded: chain 2D residue 407 SER Chi-restraints excluded: chain 0D residue 8 VAL Chi-restraints excluded: chain 0D residue 31 THR Chi-restraints excluded: chain 0D residue 71 VAL Chi-restraints excluded: chain 0D residue 184 THR Chi-restraints excluded: chain 2C residue 33 VAL Chi-restraints excluded: chain 2C residue 39 LEU Chi-restraints excluded: chain 2C residue 267 VAL Chi-restraints excluded: chain 2C residue 281 LEU Chi-restraints excluded: chain 2C residue 370 VAL Chi-restraints excluded: chain 2C residue 386 GLU Chi-restraints excluded: chain 2C residue 387 LEU Chi-restraints excluded: chain 2C residue 459 LEU Chi-restraints excluded: chain 2C residue 498 ASN Chi-restraints excluded: chain 2C residue 502 SER Chi-restraints excluded: chain 0C residue 3 HIS Chi-restraints excluded: chain 0C residue 8 VAL Chi-restraints excluded: chain 0C residue 54 VAL Chi-restraints excluded: chain 0C residue 71 VAL Chi-restraints excluded: chain 0C residue 160 ASP Chi-restraints excluded: chain 2B residue 33 VAL Chi-restraints excluded: chain 2B residue 39 LEU Chi-restraints excluded: chain 2B residue 267 VAL Chi-restraints excluded: chain 2B residue 281 LEU Chi-restraints excluded: chain 2B residue 323 THR Chi-restraints excluded: chain 2B residue 387 LEU Chi-restraints excluded: chain 2B residue 509 VAL Chi-restraints excluded: chain 0B residue 8 VAL Chi-restraints excluded: chain 0B residue 18 LEU Chi-restraints excluded: chain 0B residue 71 VAL Chi-restraints excluded: chain 0B residue 79 ARG Chi-restraints excluded: chain 0B residue 83 LEU Chi-restraints excluded: chain 0B residue 93 THR Chi-restraints excluded: chain 0B residue 105 LEU Chi-restraints excluded: chain 0B residue 170 TYR Chi-restraints excluded: chain 0B residue 185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 277 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 chunk 371 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1a 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0E 205 HIS ** 2C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0B 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114678 restraints weight = 47282.806| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.79 r_work: 0.3217 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33768 Z= 0.155 Angle : 0.514 11.280 46014 Z= 0.260 Chirality : 0.045 0.161 5070 Planarity : 0.004 0.050 6072 Dihedral : 4.093 46.323 4681 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.83 % Allowed : 22.37 % Favored : 72.80 % 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 aren not related in a simple way. whole: 0.26 (0.13), residues: 4188 helix: 1.48 (0.15), residues: 1230 sheet: 0.24 (0.17), residues: 1038 loop : -0.69 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG2D 276 TYR 0.013 0.001 TYR0F 117 PHE 0.025 0.001 PHE2E 481 TRP 0.010 0.001 TRP1c 118 HIS 0.010 0.001 HIS0B 205 Details of bonding type rmsd covalent geometry : bond 0.00380 (33768) covalent geometry : angle 0.51416 (46014) hydrogen bonds : bond 0.03235 ( 1302) hydrogen bonds : angle 4.34845 ( 3744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 343 time to evaluate : 1.397 Fit side-chains REVERT: 1a 33 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8792 (pp) REVERT: 1f 20 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8538 (t70) REVERT: 1e 90 MET cc_start: 0.8871 (mmm) cc_final: 0.8601 (mmm) REVERT: 1d 72 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8163 (mtt) REVERT: 1c 20 ASP cc_start: 0.8966 (OUTLIER) cc_final: 0.8698 (t70) REVERT: 1b 14 ASN cc_start: 0.8566 (t0) cc_final: 0.8292 (t0) REVERT: 1b 90 MET cc_start: 0.8851 (mmm) cc_final: 0.8592 (mmt) REVERT: 2A 22 GLU cc_start: 0.7114 (pm20) cc_final: 0.6852 (pm20) REVERT: 2A 384 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: 2A 496 GLU cc_start: 0.6460 (tt0) cc_final: 0.6116 (tt0) REVERT: 0A 48 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.6067 (t80) REVERT: 2F 366 SER cc_start: 0.8651 (m) cc_final: 0.8262 (t) REVERT: 0F 132 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8204 (ttp) REVERT: 2E 366 SER cc_start: 0.8691 (m) cc_final: 0.8192 (t) REVERT: 0E 83 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.7896 (mt) REVERT: 2D 22 GLU cc_start: 0.7200 (pm20) cc_final: 0.6889 (pm20) REVERT: 2D 39 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8089 (mt) REVERT: 2D 51 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8526 (p) REVERT: 2D 363 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8108 (ttm170) REVERT: 2D 489 TYR cc_start: 0.8658 (p90) cc_final: 0.8197 (p90) REVERT: 0C 83 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7774 (mt) REVERT: 0C 105 LEU cc_start: 0.8976 (tp) cc_final: 0.8756 (tp) REVERT: 0C 160 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8366 (t0) REVERT: 2B 22 GLU cc_start: 0.6894 (pm20) cc_final: 0.6618 (pm20) REVERT: 2B 366 SER cc_start: 0.8683 (m) cc_final: 0.8182 (t) REVERT: 0B 83 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7890 (mt) REVERT: 0B 181 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8078 (tt0) outliers start: 167 outliers final: 139 residues processed: 487 average time/residue: 0.1928 time to fit residues: 156.0738 Evaluate side-chains 480 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 327 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1a residue 9 VAL Chi-restraints excluded: chain 1a residue 11 VAL Chi-restraints excluded: chain 1a residue 29 SER Chi-restraints excluded: chain 1a residue 33 LEU Chi-restraints excluded: chain 1a residue 34 GLN Chi-restraints excluded: chain 1a residue 54 VAL Chi-restraints excluded: chain 1a residue 57 MET Chi-restraints excluded: chain 1a residue 65 SER Chi-restraints excluded: chain 1a residue 79 THR Chi-restraints excluded: chain 1a residue 92 THR Chi-restraints excluded: chain 1a residue 100 ILE Chi-restraints excluded: chain 1a residue 118 TRP Chi-restraints excluded: chain 1a residue 126 THR Chi-restraints excluded: chain 1a residue 133 ASN Chi-restraints excluded: chain 1f residue 9 VAL Chi-restraints excluded: chain 1f residue 11 VAL Chi-restraints excluded: chain 1f residue 20 ASP Chi-restraints excluded: chain 1f residue 54 VAL Chi-restraints excluded: chain 1f residue 79 THR Chi-restraints excluded: chain 1f residue 92 THR Chi-restraints excluded: chain 1f residue 100 ILE Chi-restraints excluded: chain 1f residue 126 THR Chi-restraints excluded: chain 1e residue 8 ASP Chi-restraints excluded: chain 1e residue 33 LEU Chi-restraints excluded: chain 1e residue 54 VAL Chi-restraints excluded: chain 1e residue 56 LEU Chi-restraints excluded: chain 1e residue 79 THR Chi-restraints excluded: chain 1e residue 92 THR Chi-restraints excluded: chain 1e residue 100 ILE Chi-restraints excluded: chain 1e residue 101 VAL Chi-restraints excluded: chain 1e residue 126 THR Chi-restraints excluded: chain 1d residue 8 ASP Chi-restraints excluded: chain 1d residue 9 VAL Chi-restraints excluded: chain 1d residue 11 VAL Chi-restraints excluded: chain 1d residue 54 VAL Chi-restraints excluded: chain 1d residue 57 MET Chi-restraints excluded: chain 1d residue 65 SER Chi-restraints excluded: chain 1d residue 72 MET Chi-restraints excluded: chain 1d residue 100 ILE Chi-restraints excluded: chain 1d residue 126 THR Chi-restraints excluded: chain 1d residue 147 VAL Chi-restraints excluded: chain 1c residue 9 VAL Chi-restraints excluded: chain 1c residue 11 VAL Chi-restraints excluded: chain 1c residue 20 ASP Chi-restraints excluded: chain 1c residue 53 ASN Chi-restraints excluded: chain 1c residue 54 VAL Chi-restraints excluded: chain 1c residue 79 THR Chi-restraints excluded: chain 1c residue 100 ILE Chi-restraints excluded: chain 1c residue 126 THR Chi-restraints excluded: chain 1c residue 143 PHE Chi-restraints excluded: chain 1b residue 9 VAL Chi-restraints excluded: chain 1b residue 11 VAL Chi-restraints excluded: chain 1b residue 33 LEU Chi-restraints excluded: chain 1b residue 54 VAL Chi-restraints excluded: chain 1b residue 56 LEU Chi-restraints excluded: chain 1b residue 79 THR Chi-restraints excluded: chain 1b residue 92 THR Chi-restraints excluded: chain 1b residue 100 ILE Chi-restraints excluded: chain 1b residue 101 VAL Chi-restraints excluded: chain 2A residue 33 VAL Chi-restraints excluded: chain 2A residue 39 LEU Chi-restraints excluded: chain 2A residue 267 VAL Chi-restraints excluded: chain 2A residue 384 ASP Chi-restraints excluded: chain 2A residue 387 LEU Chi-restraints excluded: chain 2A residue 407 SER Chi-restraints excluded: chain 2A residue 498 ASN Chi-restraints excluded: chain 0A residue 8 VAL Chi-restraints excluded: chain 0A residue 18 LEU Chi-restraints excluded: chain 0A residue 48 TYR Chi-restraints excluded: chain 0A residue 71 VAL Chi-restraints excluded: chain 0A residue 93 THR Chi-restraints excluded: chain 0A residue 132 MET Chi-restraints excluded: chain 0A residue 158 SER Chi-restraints excluded: chain 0A residue 196 MET Chi-restraints excluded: chain 2F residue 32 SER Chi-restraints excluded: chain 2F residue 39 LEU Chi-restraints excluded: chain 2F residue 267 VAL Chi-restraints excluded: chain 2F residue 378 VAL Chi-restraints excluded: chain 2F residue 387 LEU Chi-restraints excluded: chain 2F residue 407 SER Chi-restraints excluded: chain 2F residue 445 ILE Chi-restraints excluded: chain 2F residue 459 LEU Chi-restraints excluded: chain 2F residue 492 LYS Chi-restraints excluded: chain 2F residue 498 ASN Chi-restraints excluded: chain 0F residue 8 VAL Chi-restraints excluded: chain 0F residue 31 THR Chi-restraints excluded: chain 0F residue 54 VAL Chi-restraints excluded: chain 0F residue 71 VAL Chi-restraints excluded: chain 0F residue 93 THR Chi-restraints excluded: chain 0F residue 132 MET Chi-restraints excluded: chain 2E residue 33 VAL Chi-restraints excluded: chain 2E residue 39 LEU Chi-restraints excluded: chain 2E residue 267 VAL Chi-restraints excluded: chain 2E residue 390 THR Chi-restraints excluded: chain 2E residue 407 SER Chi-restraints excluded: chain 0E residue 18 LEU Chi-restraints excluded: chain 0E residue 54 VAL Chi-restraints excluded: chain 0E residue 71 VAL Chi-restraints excluded: chain 0E residue 83 LEU Chi-restraints excluded: chain 0E residue 93 THR Chi-restraints excluded: chain 0E residue 105 LEU Chi-restraints excluded: chain 0E residue 133 THR Chi-restraints excluded: chain 0E residue 160 ASP Chi-restraints excluded: chain 0E residue 193 ASP Chi-restraints excluded: chain 2D residue 33 VAL Chi-restraints excluded: chain 2D residue 39 LEU Chi-restraints excluded: chain 2D residue 51 VAL Chi-restraints excluded: chain 2D residue 267 VAL Chi-restraints excluded: chain 2D residue 363 ARG Chi-restraints excluded: chain 2D residue 370 VAL Chi-restraints excluded: chain 2D residue 390 THR Chi-restraints excluded: chain 2D residue 407 SER Chi-restraints excluded: chain 2D residue 445 ILE Chi-restraints excluded: chain 0D residue 8 VAL Chi-restraints excluded: chain 0D residue 31 THR Chi-restraints excluded: chain 0D residue 71 VAL Chi-restraints excluded: chain 0D residue 132 MET Chi-restraints excluded: chain 0D residue 184 THR Chi-restraints excluded: chain 2C residue 33 VAL Chi-restraints excluded: chain 2C residue 39 LEU Chi-restraints excluded: chain 2C residue 267 VAL Chi-restraints excluded: chain 2C residue 281 LEU Chi-restraints excluded: chain 2C residue 370 VAL Chi-restraints excluded: chain 2C residue 386 GLU Chi-restraints excluded: chain 2C residue 387 LEU Chi-restraints excluded: chain 2C residue 459 LEU Chi-restraints excluded: chain 2C residue 498 ASN Chi-restraints excluded: chain 2C residue 502 SER Chi-restraints excluded: chain 0C residue 3 HIS Chi-restraints excluded: chain 0C residue 8 VAL Chi-restraints excluded: chain 0C residue 54 VAL Chi-restraints excluded: chain 0C residue 71 VAL Chi-restraints excluded: chain 0C residue 83 LEU Chi-restraints excluded: chain 0C residue 93 THR Chi-restraints excluded: chain 0C residue 160 ASP Chi-restraints excluded: chain 2B residue 33 VAL Chi-restraints excluded: chain 2B residue 39 LEU Chi-restraints excluded: chain 2B residue 46 ASN Chi-restraints excluded: chain 2B residue 267 VAL Chi-restraints excluded: chain 2B residue 281 LEU Chi-restraints excluded: chain 2B residue 323 THR Chi-restraints excluded: chain 2B residue 387 LEU Chi-restraints excluded: chain 2B residue 508 VAL Chi-restraints excluded: chain 0B residue 8 VAL Chi-restraints excluded: chain 0B residue 9 LEU Chi-restraints excluded: chain 0B residue 18 LEU Chi-restraints excluded: chain 0B residue 71 VAL Chi-restraints excluded: chain 0B residue 83 LEU Chi-restraints excluded: chain 0B residue 93 THR Chi-restraints excluded: chain 0B residue 105 LEU Chi-restraints excluded: chain 0B residue 170 TYR Chi-restraints excluded: chain 0B residue 185 VAL Chi-restraints excluded: chain 0B residue 193 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 123 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 148 optimal weight: 0.5980 chunk 407 optimal weight: 0.9980 chunk 366 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 128 optimal weight: 5.9990 chunk 399 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 223 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1a 32 ASN 1a 46 GLN ** 2F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0E 205 HIS ** 2C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0B 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117945 restraints weight = 47289.233| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.80 r_work: 0.3274 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33768 Z= 0.090 Angle : 0.475 8.629 46014 Z= 0.237 Chirality : 0.043 0.151 5070 Planarity : 0.004 0.050 6072 Dihedral : 3.836 44.766 4681 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.79 % Allowed : 23.67 % Favored : 72.54 % 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 aren not related in a simple way. whole: 0.41 (0.13), residues: 4188 helix: 1.67 (0.15), residues: 1230 sheet: 0.13 (0.17), residues: 1086 loop : -0.53 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG2D 276 TYR 0.013 0.001 TYR0F 117 PHE 0.027 0.001 PHE2B 481 TRP 0.012 0.001 TRP1a 118 HIS 0.010 0.001 HIS0B 205 Details of bonding type rmsd covalent geometry : bond 0.00207 (33768) covalent geometry : angle 0.47470 (46014) hydrogen bonds : bond 0.02579 ( 1302) hydrogen bonds : angle 4.20323 ( 3744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 356 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: 1a 33 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8842 (pp) REVERT: 1a 46 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7164 (tp-100) REVERT: 1f 20 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8520 (t70) REVERT: 1e 90 MET cc_start: 0.8729 (mmm) cc_final: 0.8459 (mmm) REVERT: 1c 20 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8621 (t70) REVERT: 1c 121 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8309 (ttmt) REVERT: 1b 14 ASN cc_start: 0.8543 (t0) cc_final: 0.8265 (t0) REVERT: 2A 22 GLU cc_start: 0.7053 (pm20) cc_final: 0.6844 (pm20) REVERT: 2A 384 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7753 (m-30) REVERT: 2A 496 GLU cc_start: 0.6408 (tt0) cc_final: 0.6093 (tt0) REVERT: 2E 366 SER cc_start: 0.8626 (m) cc_final: 0.8178 (t) REVERT: 0E 1 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.5418 (mtt) REVERT: 0E 83 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7871 (mt) REVERT: 2D 22 GLU cc_start: 0.7055 (pm20) cc_final: 0.6826 (pm20) REVERT: 2D 39 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8003 (mt) REVERT: 2D 363 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8129 (ttm170) REVERT: 2D 489 TYR cc_start: 0.8557 (p90) cc_final: 0.8131 (p90) REVERT: 0C 83 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7750 (mt) REVERT: 0C 105 LEU cc_start: 0.8958 (tp) cc_final: 0.8754 (tp) REVERT: 2B 366 SER cc_start: 0.8617 (m) cc_final: 0.8167 (t) REVERT: 0B 83 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7798 (mt) REVERT: 0B 181 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8018 (tt0) outliers start: 131 outliers final: 103 residues processed: 470 average time/residue: 0.1927 time to fit residues: 151.5366 Evaluate side-chains 454 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 339 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1a residue 9 VAL Chi-restraints excluded: chain 1a residue 11 VAL Chi-restraints excluded: chain 1a residue 29 SER Chi-restraints excluded: chain 1a residue 33 LEU Chi-restraints excluded: chain 1a residue 34 GLN Chi-restraints excluded: chain 1a residue 46 GLN Chi-restraints excluded: chain 1a residue 57 MET Chi-restraints excluded: chain 1a residue 100 ILE Chi-restraints excluded: chain 1a residue 118 TRP Chi-restraints excluded: chain 1a residue 126 THR Chi-restraints excluded: chain 1f residue 9 VAL Chi-restraints excluded: chain 1f residue 11 VAL Chi-restraints excluded: chain 1f residue 20 ASP Chi-restraints excluded: chain 1f residue 54 VAL Chi-restraints excluded: chain 1f residue 79 THR Chi-restraints excluded: chain 1f residue 92 THR Chi-restraints excluded: chain 1f residue 100 ILE Chi-restraints excluded: chain 1e residue 8 ASP Chi-restraints excluded: chain 1e residue 33 LEU Chi-restraints excluded: chain 1e residue 54 VAL Chi-restraints excluded: chain 1e residue 56 LEU Chi-restraints excluded: chain 1e residue 79 THR Chi-restraints excluded: chain 1e residue 100 ILE Chi-restraints excluded: chain 1e residue 101 VAL Chi-restraints excluded: chain 1d residue 8 ASP Chi-restraints excluded: chain 1d residue 9 VAL Chi-restraints excluded: chain 1d residue 54 VAL Chi-restraints excluded: chain 1d residue 65 SER Chi-restraints excluded: chain 1d residue 67 GLN Chi-restraints excluded: chain 1d residue 72 MET Chi-restraints excluded: chain 1d residue 73 SER Chi-restraints excluded: chain 1d residue 100 ILE Chi-restraints excluded: chain 1d residue 126 THR Chi-restraints excluded: chain 1c residue 8 ASP Chi-restraints excluded: chain 1c residue 9 VAL Chi-restraints excluded: chain 1c residue 20 ASP Chi-restraints excluded: chain 1c residue 54 VAL Chi-restraints excluded: chain 1c residue 79 THR Chi-restraints excluded: chain 1c residue 100 ILE Chi-restraints excluded: chain 1c residue 121 LYS Chi-restraints excluded: chain 1c residue 126 THR Chi-restraints excluded: chain 1c residue 143 PHE Chi-restraints excluded: chain 1b residue 9 VAL Chi-restraints excluded: chain 1b residue 33 LEU Chi-restraints excluded: chain 1b residue 54 VAL Chi-restraints excluded: chain 1b residue 56 LEU Chi-restraints excluded: chain 1b residue 79 THR Chi-restraints excluded: chain 1b residue 92 THR Chi-restraints excluded: chain 1b residue 100 ILE Chi-restraints excluded: chain 1b residue 101 VAL Chi-restraints excluded: chain 2A residue 33 VAL Chi-restraints excluded: chain 2A residue 39 LEU Chi-restraints excluded: chain 2A residue 267 VAL Chi-restraints excluded: chain 2A residue 384 ASP Chi-restraints excluded: chain 2A residue 407 SER Chi-restraints excluded: chain 2A residue 498 ASN Chi-restraints excluded: chain 0A residue 8 VAL Chi-restraints excluded: chain 0A residue 18 LEU Chi-restraints excluded: chain 0A residue 48 TYR Chi-restraints excluded: chain 0A residue 71 VAL Chi-restraints excluded: chain 0A residue 93 THR Chi-restraints excluded: chain 0A residue 132 MET Chi-restraints excluded: chain 2F residue 32 SER Chi-restraints excluded: chain 2F residue 39 LEU Chi-restraints excluded: chain 2F residue 267 VAL Chi-restraints excluded: chain 2F residue 378 VAL Chi-restraints excluded: chain 2F residue 407 SER Chi-restraints excluded: chain 2F residue 445 ILE Chi-restraints excluded: chain 2F residue 459 LEU Chi-restraints excluded: chain 2F residue 498 ASN Chi-restraints excluded: chain 0F residue 8 VAL Chi-restraints excluded: chain 0F residue 71 VAL Chi-restraints excluded: chain 0F residue 93 THR Chi-restraints excluded: chain 2E residue 33 VAL Chi-restraints excluded: chain 2E residue 39 LEU Chi-restraints excluded: chain 2E residue 267 VAL Chi-restraints excluded: chain 2E residue 407 SER Chi-restraints excluded: chain 0E residue 1 MET Chi-restraints excluded: chain 0E residue 18 LEU Chi-restraints excluded: chain 0E residue 54 VAL Chi-restraints excluded: chain 0E residue 71 VAL Chi-restraints excluded: chain 0E residue 83 LEU Chi-restraints excluded: chain 0E residue 93 THR Chi-restraints excluded: chain 0E residue 160 ASP Chi-restraints excluded: chain 0E residue 170 TYR Chi-restraints excluded: chain 2D residue 33 VAL Chi-restraints excluded: chain 2D residue 39 LEU Chi-restraints excluded: chain 2D residue 267 VAL Chi-restraints excluded: chain 2D residue 363 ARG Chi-restraints excluded: chain 2D residue 407 SER Chi-restraints excluded: chain 0D residue 8 VAL Chi-restraints excluded: chain 0D residue 71 VAL Chi-restraints excluded: chain 0D residue 184 THR Chi-restraints excluded: chain 2C residue 39 LEU Chi-restraints excluded: chain 2C residue 267 VAL Chi-restraints excluded: chain 2C residue 370 VAL Chi-restraints excluded: chain 2C residue 459 LEU Chi-restraints excluded: chain 2C residue 498 ASN Chi-restraints excluded: chain 2C residue 502 SER Chi-restraints excluded: chain 0C residue 3 HIS Chi-restraints excluded: chain 0C residue 71 VAL Chi-restraints excluded: chain 0C residue 83 LEU Chi-restraints excluded: chain 0C residue 93 THR Chi-restraints excluded: chain 2B residue 33 VAL Chi-restraints excluded: chain 2B residue 39 LEU Chi-restraints excluded: chain 2B residue 267 VAL Chi-restraints excluded: chain 2B residue 323 THR Chi-restraints excluded: chain 0B residue 8 VAL Chi-restraints excluded: chain 0B residue 18 LEU Chi-restraints excluded: chain 0B residue 71 VAL Chi-restraints excluded: chain 0B residue 83 LEU Chi-restraints excluded: chain 0B residue 93 THR Chi-restraints excluded: chain 0B residue 170 TYR Chi-restraints excluded: chain 0B residue 185 VAL Chi-restraints excluded: chain 0B residue 193 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 172 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 416 optimal weight: 0.9990 chunk 384 optimal weight: 0.0070 chunk 164 optimal weight: 10.0000 chunk 360 optimal weight: 0.0040 chunk 203 optimal weight: 10.0000 overall best weight: 2.0016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1a 32 ASN ** 1a 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1d 32 ASN ** 2F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0E 205 HIS ** 2C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0C 205 HIS ** 2B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0B 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115882 restraints weight = 47159.517| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.80 r_work: 0.3247 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33768 Z= 0.136 Angle : 0.497 9.108 46014 Z= 0.248 Chirality : 0.044 0.158 5070 Planarity : 0.004 0.064 6072 Dihedral : 3.892 45.381 4681 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.25 % Allowed : 23.64 % Favored : 72.11 % 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 aren not related in a simple way. whole: 0.42 (0.13), residues: 4188 helix: 1.65 (0.15), residues: 1230 sheet: 0.17 (0.17), residues: 1074 loop : -0.53 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG2A 276 TYR 0.012 0.001 TYR0D 48 PHE 0.027 0.001 PHE2E 481 TRP 0.010 0.001 TRP1a 118 HIS 0.011 0.001 HIS0C 205 Details of bonding type rmsd covalent geometry : bond 0.00330 (33768) covalent geometry : angle 0.49679 (46014) hydrogen bonds : bond 0.02907 ( 1302) hydrogen bonds : angle 4.18466 ( 3744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 341 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: 1a 33 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8853 (pp) REVERT: 1f 20 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8543 (t70) REVERT: 1e 90 MET cc_start: 0.8840 (mmm) cc_final: 0.8555 (mmp) REVERT: 1c 20 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8636 (t70) REVERT: 1b 14 ASN cc_start: 0.8533 (t0) cc_final: 0.8251 (t0) REVERT: 1b 131 ASP cc_start: 0.8386 (t0) cc_final: 0.8052 (t0) REVERT: 2A 22 GLU cc_start: 0.7019 (pm20) cc_final: 0.6813 (pm20) REVERT: 2A 384 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: 2A 496 GLU cc_start: 0.6527 (tt0) cc_final: 0.6205 (tt0) REVERT: 2F 366 SER cc_start: 0.8650 (m) cc_final: 0.8321 (t) REVERT: 2E 366 SER cc_start: 0.8788 (m) cc_final: 0.8252 (t) REVERT: 0E 1 MET cc_start: 0.6519 (OUTLIER) cc_final: 0.5535 (mtt) REVERT: 0E 83 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7889 (mt) REVERT: 2D 22 GLU cc_start: 0.7094 (pm20) cc_final: 0.6805 (pm20) REVERT: 2D 39 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8070 (mt) REVERT: 2D 363 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8104 (ttm170) REVERT: 2D 489 TYR cc_start: 0.8612 (p90) cc_final: 0.8177 (p90) REVERT: 0C 83 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7744 (mt) REVERT: 2B 22 GLU cc_start: 0.6881 (pm20) cc_final: 0.6598 (pm20) REVERT: 2B 366 SER cc_start: 0.8774 (m) cc_final: 0.8261 (t) REVERT: 0B 83 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7820 (mt) REVERT: 0B 181 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8052 (tt0) outliers start: 147 outliers final: 125 residues processed: 469 average time/residue: 0.1806 time to fit residues: 141.7248 Evaluate side-chains 466 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 331 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1a residue 9 VAL Chi-restraints excluded: chain 1a residue 11 VAL Chi-restraints excluded: chain 1a residue 29 SER Chi-restraints excluded: chain 1a residue 33 LEU Chi-restraints excluded: chain 1a residue 54 VAL Chi-restraints excluded: chain 1a residue 57 MET Chi-restraints excluded: chain 1a residue 65 SER Chi-restraints excluded: chain 1a residue 79 THR Chi-restraints excluded: chain 1a residue 100 ILE Chi-restraints excluded: chain 1a residue 118 TRP Chi-restraints excluded: chain 1a residue 126 THR Chi-restraints excluded: chain 1f residue 9 VAL Chi-restraints excluded: chain 1f residue 11 VAL Chi-restraints excluded: chain 1f residue 20 ASP Chi-restraints excluded: chain 1f residue 26 TYR Chi-restraints excluded: chain 1f residue 54 VAL Chi-restraints excluded: chain 1f residue 79 THR Chi-restraints excluded: chain 1f residue 92 THR Chi-restraints excluded: chain 1f residue 100 ILE Chi-restraints excluded: chain 1f residue 126 THR Chi-restraints excluded: chain 1e residue 8 ASP Chi-restraints excluded: chain 1e residue 33 LEU Chi-restraints excluded: chain 1e residue 54 VAL Chi-restraints excluded: chain 1e residue 56 LEU Chi-restraints excluded: chain 1e residue 73 SER Chi-restraints excluded: chain 1e residue 79 THR Chi-restraints excluded: chain 1e residue 100 ILE Chi-restraints excluded: chain 1e residue 101 VAL Chi-restraints excluded: chain 1e residue 126 THR Chi-restraints excluded: chain 1d residue 8 ASP Chi-restraints excluded: chain 1d residue 9 VAL Chi-restraints excluded: chain 1d residue 54 VAL Chi-restraints excluded: chain 1d residue 67 GLN Chi-restraints excluded: chain 1d residue 72 MET Chi-restraints excluded: chain 1d residue 73 SER Chi-restraints excluded: chain 1d residue 100 ILE Chi-restraints excluded: chain 1d residue 126 THR Chi-restraints excluded: chain 1c residue 8 ASP Chi-restraints excluded: chain 1c residue 9 VAL Chi-restraints excluded: chain 1c residue 11 VAL Chi-restraints excluded: chain 1c residue 20 ASP Chi-restraints excluded: chain 1c residue 54 VAL Chi-restraints excluded: chain 1c residue 79 THR Chi-restraints excluded: chain 1c residue 100 ILE Chi-restraints excluded: chain 1c residue 126 THR Chi-restraints excluded: chain 1c residue 143 PHE Chi-restraints excluded: chain 1b residue 9 VAL Chi-restraints excluded: chain 1b residue 33 LEU Chi-restraints excluded: chain 1b residue 54 VAL Chi-restraints excluded: chain 1b residue 56 LEU Chi-restraints excluded: chain 1b residue 73 SER Chi-restraints excluded: chain 1b residue 79 THR Chi-restraints excluded: chain 1b residue 92 THR Chi-restraints excluded: chain 1b residue 100 ILE Chi-restraints excluded: chain 1b residue 101 VAL Chi-restraints excluded: chain 1b residue 126 THR Chi-restraints excluded: chain 2A residue 33 VAL Chi-restraints excluded: chain 2A residue 39 LEU Chi-restraints excluded: chain 2A residue 267 VAL Chi-restraints excluded: chain 2A residue 384 ASP Chi-restraints excluded: chain 2A residue 387 LEU Chi-restraints excluded: chain 2A residue 407 SER Chi-restraints excluded: chain 2A residue 498 ASN Chi-restraints excluded: chain 0A residue 8 VAL Chi-restraints excluded: chain 0A residue 18 LEU Chi-restraints excluded: chain 0A residue 48 TYR Chi-restraints excluded: chain 0A residue 71 VAL Chi-restraints excluded: chain 0A residue 93 THR Chi-restraints excluded: chain 0A residue 132 MET Chi-restraints excluded: chain 0A residue 196 MET Chi-restraints excluded: chain 2F residue 32 SER Chi-restraints excluded: chain 2F residue 39 LEU Chi-restraints excluded: chain 2F residue 267 VAL Chi-restraints excluded: chain 2F residue 378 VAL Chi-restraints excluded: chain 2F residue 407 SER Chi-restraints excluded: chain 2F residue 445 ILE Chi-restraints excluded: chain 2F residue 459 LEU Chi-restraints excluded: chain 2F residue 498 ASN Chi-restraints excluded: chain 0F residue 8 VAL Chi-restraints excluded: chain 0F residue 54 VAL Chi-restraints excluded: chain 0F residue 71 VAL Chi-restraints excluded: chain 0F residue 93 THR Chi-restraints excluded: chain 2E residue 33 VAL Chi-restraints excluded: chain 2E residue 39 LEU Chi-restraints excluded: chain 2E residue 267 VAL Chi-restraints excluded: chain 2E residue 387 LEU Chi-restraints excluded: chain 2E residue 407 SER Chi-restraints excluded: chain 0E residue 1 MET Chi-restraints excluded: chain 0E residue 18 LEU Chi-restraints excluded: chain 0E residue 54 VAL Chi-restraints excluded: chain 0E residue 71 VAL Chi-restraints excluded: chain 0E residue 83 LEU Chi-restraints excluded: chain 0E residue 93 THR Chi-restraints excluded: chain 0E residue 105 LEU Chi-restraints excluded: chain 0E residue 160 ASP Chi-restraints excluded: chain 0E residue 170 TYR Chi-restraints excluded: chain 2D residue 33 VAL Chi-restraints excluded: chain 2D residue 39 LEU Chi-restraints excluded: chain 2D residue 267 VAL Chi-restraints excluded: chain 2D residue 363 ARG Chi-restraints excluded: chain 2D residue 370 VAL Chi-restraints excluded: chain 2D residue 387 LEU Chi-restraints excluded: chain 2D residue 407 SER Chi-restraints excluded: chain 0D residue 8 VAL Chi-restraints excluded: chain 0D residue 71 VAL Chi-restraints excluded: chain 0D residue 79 ARG Chi-restraints excluded: chain 0D residue 132 MET Chi-restraints excluded: chain 0D residue 184 THR Chi-restraints excluded: chain 2C residue 33 VAL Chi-restraints excluded: chain 2C residue 39 LEU Chi-restraints excluded: chain 2C residue 267 VAL Chi-restraints excluded: chain 2C residue 370 VAL Chi-restraints excluded: chain 2C residue 459 LEU Chi-restraints excluded: chain 2C residue 498 ASN Chi-restraints excluded: chain 2C residue 502 SER Chi-restraints excluded: chain 0C residue 3 HIS Chi-restraints excluded: chain 0C residue 54 VAL Chi-restraints excluded: chain 0C residue 71 VAL Chi-restraints excluded: chain 0C residue 79 ARG Chi-restraints excluded: chain 0C residue 83 LEU Chi-restraints excluded: chain 0C residue 93 THR Chi-restraints excluded: chain 2B residue 33 VAL Chi-restraints excluded: chain 2B residue 39 LEU Chi-restraints excluded: chain 2B residue 267 VAL Chi-restraints excluded: chain 2B residue 323 THR Chi-restraints excluded: chain 2B residue 508 VAL Chi-restraints excluded: chain 0B residue 8 VAL Chi-restraints excluded: chain 0B residue 18 LEU Chi-restraints excluded: chain 0B residue 54 VAL Chi-restraints excluded: chain 0B residue 71 VAL Chi-restraints excluded: chain 0B residue 83 LEU Chi-restraints excluded: chain 0B residue 93 THR Chi-restraints excluded: chain 0B residue 170 TYR Chi-restraints excluded: chain 0B residue 185 VAL Chi-restraints excluded: chain 0B residue 193 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 374 optimal weight: 7.9990 chunk 328 optimal weight: 5.9990 chunk 286 optimal weight: 0.7980 chunk 373 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 130 optimal weight: 0.0670 chunk 301 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1a 32 ASN ** 2F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0E 205 HIS ** 2C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0C 205 HIS ** 2B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0B 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116372 restraints weight = 47217.289| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.80 r_work: 0.3248 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33768 Z= 0.116 Angle : 0.494 8.779 46014 Z= 0.246 Chirality : 0.044 0.157 5070 Planarity : 0.004 0.061 6072 Dihedral : 3.815 44.142 4678 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.28 % Allowed : 23.78 % Favored : 71.93 % 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 aren not related in a simple way. whole: 0.39 (0.13), residues: 4188 helix: 1.68 (0.15), residues: 1230 sheet: 0.11 (0.17), residues: 1086 loop : -0.55 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG2B 276 TYR 0.012 0.001 TYR0F 117 PHE 0.027 0.001 PHE2E 481 TRP 0.011 0.001 TRP1a 118 HIS 0.010 0.001 HIS0B 205 Details of bonding type rmsd covalent geometry : bond 0.00280 (33768) covalent geometry : angle 0.49425 (46014) hydrogen bonds : bond 0.02799 ( 1302) hydrogen bonds : angle 4.17468 ( 3744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 337 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: 1a 33 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8849 (pp) REVERT: 1f 20 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8532 (t70) REVERT: 1e 90 MET cc_start: 0.8812 (mmm) cc_final: 0.8509 (mmt) REVERT: 1c 20 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8532 (t70) REVERT: 1c 121 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8601 (ttmt) REVERT: 2A 384 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: 2A 496 GLU cc_start: 0.6567 (tt0) cc_final: 0.6265 (tt0) REVERT: 2F 366 SER cc_start: 0.8630 (m) cc_final: 0.8303 (t) REVERT: 2E 22 GLU cc_start: 0.6899 (pm20) cc_final: 0.6590 (pm20) REVERT: 2E 366 SER cc_start: 0.8776 (m) cc_final: 0.8272 (t) REVERT: 0E 1 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.5487 (mtt) REVERT: 0E 83 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7886 (mt) REVERT: 2D 22 GLU cc_start: 0.7072 (pm20) cc_final: 0.6841 (pm20) REVERT: 2D 39 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8090 (mt) REVERT: 2D 363 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8095 (ttm170) REVERT: 2D 489 TYR cc_start: 0.8599 (p90) cc_final: 0.8166 (p90) REVERT: 0C 83 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7740 (mt) REVERT: 2B 22 GLU cc_start: 0.6838 (pm20) cc_final: 0.6580 (pm20) REVERT: 2B 366 SER cc_start: 0.8801 (m) cc_final: 0.8292 (t) REVERT: 0B 83 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7842 (mt) REVERT: 0B 181 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8052 (tt0) outliers start: 148 outliers final: 133 residues processed: 463 average time/residue: 0.1760 time to fit residues: 136.2932 Evaluate side-chains 475 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 331 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1a residue 9 VAL Chi-restraints excluded: chain 1a residue 11 VAL Chi-restraints excluded: chain 1a residue 29 SER Chi-restraints excluded: chain 1a residue 33 LEU Chi-restraints excluded: chain 1a residue 57 MET Chi-restraints excluded: chain 1a residue 65 SER Chi-restraints excluded: chain 1a residue 100 ILE Chi-restraints excluded: chain 1a residue 118 TRP Chi-restraints excluded: chain 1a residue 126 THR Chi-restraints excluded: chain 1a residue 133 ASN Chi-restraints excluded: chain 1f residue 9 VAL Chi-restraints excluded: chain 1f residue 11 VAL Chi-restraints excluded: chain 1f residue 20 ASP Chi-restraints excluded: chain 1f residue 54 VAL Chi-restraints excluded: chain 1f residue 79 THR Chi-restraints excluded: chain 1f residue 92 THR Chi-restraints excluded: chain 1f residue 100 ILE Chi-restraints excluded: chain 1f residue 102 MET Chi-restraints excluded: chain 1f residue 126 THR Chi-restraints excluded: chain 1e residue 8 ASP Chi-restraints excluded: chain 1e residue 33 LEU Chi-restraints excluded: chain 1e residue 54 VAL Chi-restraints excluded: chain 1e residue 56 LEU Chi-restraints excluded: chain 1e residue 73 SER Chi-restraints excluded: chain 1e residue 79 THR Chi-restraints excluded: chain 1e residue 92 THR Chi-restraints excluded: chain 1e residue 100 ILE Chi-restraints excluded: chain 1e residue 101 VAL Chi-restraints excluded: chain 1e residue 126 THR Chi-restraints excluded: chain 1d residue 8 ASP Chi-restraints excluded: chain 1d residue 9 VAL Chi-restraints excluded: chain 1d residue 54 VAL Chi-restraints excluded: chain 1d residue 67 GLN Chi-restraints excluded: chain 1d residue 72 MET Chi-restraints excluded: chain 1d residue 73 SER Chi-restraints excluded: chain 1d residue 100 ILE Chi-restraints excluded: chain 1d residue 126 THR Chi-restraints excluded: chain 1c residue 8 ASP Chi-restraints excluded: chain 1c residue 9 VAL Chi-restraints excluded: chain 1c residue 20 ASP Chi-restraints excluded: chain 1c residue 54 VAL Chi-restraints excluded: chain 1c residue 79 THR Chi-restraints excluded: chain 1c residue 100 ILE Chi-restraints excluded: chain 1c residue 121 LYS Chi-restraints excluded: chain 1c residue 126 THR Chi-restraints excluded: chain 1c residue 143 PHE Chi-restraints excluded: chain 1b residue 8 ASP Chi-restraints excluded: chain 1b residue 9 VAL Chi-restraints excluded: chain 1b residue 33 LEU Chi-restraints excluded: chain 1b residue 54 VAL Chi-restraints excluded: chain 1b residue 56 LEU Chi-restraints excluded: chain 1b residue 73 SER Chi-restraints excluded: chain 1b residue 79 THR Chi-restraints excluded: chain 1b residue 92 THR Chi-restraints excluded: chain 1b residue 100 ILE Chi-restraints excluded: chain 1b residue 101 VAL Chi-restraints excluded: chain 1b residue 126 THR Chi-restraints excluded: chain 2A residue 33 VAL Chi-restraints excluded: chain 2A residue 39 LEU Chi-restraints excluded: chain 2A residue 267 VAL Chi-restraints excluded: chain 2A residue 384 ASP Chi-restraints excluded: chain 2A residue 387 LEU Chi-restraints excluded: chain 2A residue 407 SER Chi-restraints excluded: chain 2A residue 498 ASN Chi-restraints excluded: chain 0A residue 8 VAL Chi-restraints excluded: chain 0A residue 18 LEU Chi-restraints excluded: chain 0A residue 48 TYR Chi-restraints excluded: chain 0A residue 71 VAL Chi-restraints excluded: chain 0A residue 93 THR Chi-restraints excluded: chain 0A residue 132 MET Chi-restraints excluded: chain 0A residue 196 MET Chi-restraints excluded: chain 2F residue 32 SER Chi-restraints excluded: chain 2F residue 39 LEU Chi-restraints excluded: chain 2F residue 267 VAL Chi-restraints excluded: chain 2F residue 378 VAL Chi-restraints excluded: chain 2F residue 387 LEU Chi-restraints excluded: chain 2F residue 407 SER Chi-restraints excluded: chain 2F residue 445 ILE Chi-restraints excluded: chain 2F residue 459 LEU Chi-restraints excluded: chain 2F residue 498 ASN Chi-restraints excluded: chain 0F residue 8 VAL Chi-restraints excluded: chain 0F residue 54 VAL Chi-restraints excluded: chain 0F residue 71 VAL Chi-restraints excluded: chain 0F residue 93 THR Chi-restraints excluded: chain 2E residue 33 VAL Chi-restraints excluded: chain 2E residue 39 LEU Chi-restraints excluded: chain 2E residue 267 VAL Chi-restraints excluded: chain 2E residue 387 LEU Chi-restraints excluded: chain 2E residue 407 SER Chi-restraints excluded: chain 0E residue 1 MET Chi-restraints excluded: chain 0E residue 8 VAL Chi-restraints excluded: chain 0E residue 18 LEU Chi-restraints excluded: chain 0E residue 54 VAL Chi-restraints excluded: chain 0E residue 71 VAL Chi-restraints excluded: chain 0E residue 83 LEU Chi-restraints excluded: chain 0E residue 93 THR Chi-restraints excluded: chain 0E residue 105 LEU Chi-restraints excluded: chain 0E residue 160 ASP Chi-restraints excluded: chain 0E residue 170 TYR Chi-restraints excluded: chain 0E residue 193 ASP Chi-restraints excluded: chain 2D residue 33 VAL Chi-restraints excluded: chain 2D residue 39 LEU Chi-restraints excluded: chain 2D residue 267 VAL Chi-restraints excluded: chain 2D residue 363 ARG Chi-restraints excluded: chain 2D residue 370 VAL Chi-restraints excluded: chain 2D residue 387 LEU Chi-restraints excluded: chain 2D residue 407 SER Chi-restraints excluded: chain 0D residue 8 VAL Chi-restraints excluded: chain 0D residue 71 VAL Chi-restraints excluded: chain 0D residue 93 THR Chi-restraints excluded: chain 0D residue 132 MET Chi-restraints excluded: chain 0D residue 184 THR Chi-restraints excluded: chain 2C residue 33 VAL Chi-restraints excluded: chain 2C residue 39 LEU Chi-restraints excluded: chain 2C residue 267 VAL Chi-restraints excluded: chain 2C residue 297 LEU Chi-restraints excluded: chain 2C residue 370 VAL Chi-restraints excluded: chain 2C residue 459 LEU Chi-restraints excluded: chain 2C residue 498 ASN Chi-restraints excluded: chain 2C residue 502 SER Chi-restraints excluded: chain 0C residue 3 HIS Chi-restraints excluded: chain 0C residue 8 VAL Chi-restraints excluded: chain 0C residue 54 VAL Chi-restraints excluded: chain 0C residue 71 VAL Chi-restraints excluded: chain 0C residue 79 ARG Chi-restraints excluded: chain 0C residue 83 LEU Chi-restraints excluded: chain 0C residue 93 THR Chi-restraints excluded: chain 2B residue 33 VAL Chi-restraints excluded: chain 2B residue 39 LEU Chi-restraints excluded: chain 2B residue 267 VAL Chi-restraints excluded: chain 2B residue 323 THR Chi-restraints excluded: chain 2B residue 508 VAL Chi-restraints excluded: chain 0B residue 8 VAL Chi-restraints excluded: chain 0B residue 18 LEU Chi-restraints excluded: chain 0B residue 54 VAL Chi-restraints excluded: chain 0B residue 71 VAL Chi-restraints excluded: chain 0B residue 79 ARG Chi-restraints excluded: chain 0B residue 83 LEU Chi-restraints excluded: chain 0B residue 93 THR Chi-restraints excluded: chain 0B residue 105 LEU Chi-restraints excluded: chain 0B residue 134 VAL Chi-restraints excluded: chain 0B residue 170 TYR Chi-restraints excluded: chain 0B residue 185 VAL Chi-restraints excluded: chain 0B residue 193 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 413 optimal weight: 9.9990 chunk 384 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 418 optimal weight: 0.0870 chunk 207 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 308 optimal weight: 0.0570 chunk 190 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 150 optimal weight: 9.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1a 32 ASN 1a 46 GLN ** 2F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0E 205 HIS ** 2C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0C 113 GLN 0C 205 HIS ** 2B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0B 205 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.120313 restraints weight = 47473.863| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.81 r_work: 0.3293 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33768 Z= 0.080 Angle : 0.475 9.004 46014 Z= 0.234 Chirality : 0.043 0.149 5070 Planarity : 0.004 0.057 6072 Dihedral : 3.605 43.041 4678 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.44 % Allowed : 24.62 % Favored : 71.93 % 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 aren not related in a simple way. whole: 0.56 (0.13), residues: 4188 helix: 1.94 (0.16), residues: 1194 sheet: 0.15 (0.16), residues: 1152 loop : -0.47 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG2E 276 TYR 0.012 0.001 TYR0F 117 PHE 0.027 0.001 PHE2E 481 TRP 0.012 0.001 TRP1a 118 HIS 0.011 0.001 HIS0E 205 Details of bonding type rmsd covalent geometry : bond 0.00182 (33768) covalent geometry : angle 0.47453 (46014) hydrogen bonds : bond 0.02317 ( 1302) hydrogen bonds : angle 4.04531 ( 3744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 370 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: 1a 33 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8884 (pp) REVERT: 1a 46 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7139 (tp-100) REVERT: 1e 90 MET cc_start: 0.8752 (mmm) cc_final: 0.8188 (mmp) REVERT: 1c 121 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8329 (ttmt) REVERT: 2A 384 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7787 (m-30) REVERT: 2A 496 GLU cc_start: 0.6607 (tt0) cc_final: 0.6303 (tt0) REVERT: 2F 32 SER cc_start: 0.7231 (OUTLIER) cc_final: 0.6852 (t) REVERT: 2F 366 SER cc_start: 0.8532 (m) cc_final: 0.8213 (t) REVERT: 2F 452 PHE cc_start: 0.8320 (m-80) cc_final: 0.8081 (m-80) REVERT: 2E 366 SER cc_start: 0.8693 (m) cc_final: 0.8230 (t) REVERT: 0E 1 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.5275 (mtt) REVERT: 0E 83 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7905 (mt) REVERT: 2D 22 GLU cc_start: 0.6979 (pm20) cc_final: 0.6776 (pm20) REVERT: 2D 39 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8066 (mt) REVERT: 2D 366 SER cc_start: 0.8735 (m) cc_final: 0.8498 (t) REVERT: 2D 489 TYR cc_start: 0.8487 (p90) cc_final: 0.8081 (p90) REVERT: 0C 83 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7743 (mt) REVERT: 0C 105 LEU cc_start: 0.8944 (tp) cc_final: 0.8697 (tp) REVERT: 2B 366 SER cc_start: 0.8722 (m) cc_final: 0.8262 (t) REVERT: 0B 83 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7829 (mt) REVERT: 0B 181 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8017 (tt0) outliers start: 119 outliers final: 97 residues processed: 471 average time/residue: 0.1893 time to fit residues: 149.1272 Evaluate side-chains 455 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 348 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1a residue 9 VAL Chi-restraints excluded: chain 1a residue 33 LEU Chi-restraints excluded: chain 1a residue 46 GLN Chi-restraints excluded: chain 1a residue 100 ILE Chi-restraints excluded: chain 1a residue 118 TRP Chi-restraints excluded: chain 1a residue 133 ASN Chi-restraints excluded: chain 1f residue 9 VAL Chi-restraints excluded: chain 1f residue 11 VAL Chi-restraints excluded: chain 1f residue 54 VAL Chi-restraints excluded: chain 1f residue 79 THR Chi-restraints excluded: chain 1f residue 100 ILE Chi-restraints excluded: chain 1f residue 102 MET Chi-restraints excluded: chain 1f residue 126 THR Chi-restraints excluded: chain 1e residue 33 LEU Chi-restraints excluded: chain 1e residue 54 VAL Chi-restraints excluded: chain 1e residue 56 LEU Chi-restraints excluded: chain 1e residue 79 THR Chi-restraints excluded: chain 1e residue 100 ILE Chi-restraints excluded: chain 1e residue 101 VAL Chi-restraints excluded: chain 1d residue 8 ASP Chi-restraints excluded: chain 1d residue 9 VAL Chi-restraints excluded: chain 1d residue 54 VAL Chi-restraints excluded: chain 1d residue 67 GLN Chi-restraints excluded: chain 1d residue 72 MET Chi-restraints excluded: chain 1d residue 73 SER Chi-restraints excluded: chain 1d residue 100 ILE Chi-restraints excluded: chain 1c residue 8 ASP Chi-restraints excluded: chain 1c residue 9 VAL Chi-restraints excluded: chain 1c residue 11 VAL Chi-restraints excluded: chain 1c residue 54 VAL Chi-restraints excluded: chain 1c residue 79 THR Chi-restraints excluded: chain 1c residue 100 ILE Chi-restraints excluded: chain 1c residue 121 LYS Chi-restraints excluded: chain 1c residue 126 THR Chi-restraints excluded: chain 1c residue 143 PHE Chi-restraints excluded: chain 1b residue 33 LEU Chi-restraints excluded: chain 1b residue 54 VAL Chi-restraints excluded: chain 1b residue 56 LEU Chi-restraints excluded: chain 1b residue 73 SER Chi-restraints excluded: chain 1b residue 79 THR Chi-restraints excluded: chain 1b residue 92 THR Chi-restraints excluded: chain 1b residue 100 ILE Chi-restraints excluded: chain 1b residue 101 VAL Chi-restraints excluded: chain 1b residue 126 THR Chi-restraints excluded: chain 2A residue 39 LEU Chi-restraints excluded: chain 2A residue 267 VAL Chi-restraints excluded: chain 2A residue 384 ASP Chi-restraints excluded: chain 2A residue 407 SER Chi-restraints excluded: chain 2A residue 498 ASN Chi-restraints excluded: chain 0A residue 8 VAL Chi-restraints excluded: chain 0A residue 18 LEU Chi-restraints excluded: chain 0A residue 48 TYR Chi-restraints excluded: chain 0A residue 93 THR Chi-restraints excluded: chain 0A residue 132 MET Chi-restraints excluded: chain 2F residue 32 SER Chi-restraints excluded: chain 2F residue 267 VAL Chi-restraints excluded: chain 2F residue 378 VAL Chi-restraints excluded: chain 2F residue 407 SER Chi-restraints excluded: chain 2F residue 498 ASN Chi-restraints excluded: chain 0F residue 8 VAL Chi-restraints excluded: chain 0F residue 54 VAL Chi-restraints excluded: chain 0F residue 71 VAL Chi-restraints excluded: chain 0F residue 93 THR Chi-restraints excluded: chain 2E residue 33 VAL Chi-restraints excluded: chain 2E residue 267 VAL Chi-restraints excluded: chain 2E residue 407 SER Chi-restraints excluded: chain 0E residue 1 MET Chi-restraints excluded: chain 0E residue 8 VAL Chi-restraints excluded: chain 0E residue 18 LEU Chi-restraints excluded: chain 0E residue 71 VAL Chi-restraints excluded: chain 0E residue 83 LEU Chi-restraints excluded: chain 0E residue 93 THR Chi-restraints excluded: chain 0E residue 105 LEU Chi-restraints excluded: chain 0E residue 160 ASP Chi-restraints excluded: chain 0E residue 170 TYR Chi-restraints excluded: chain 2D residue 39 LEU Chi-restraints excluded: chain 2D residue 370 VAL Chi-restraints excluded: chain 2D residue 387 LEU Chi-restraints excluded: chain 2D residue 407 SER Chi-restraints excluded: chain 0D residue 8 VAL Chi-restraints excluded: chain 0D residue 71 VAL Chi-restraints excluded: chain 0D residue 79 ARG Chi-restraints excluded: chain 0D residue 93 THR Chi-restraints excluded: chain 0D residue 184 THR Chi-restraints excluded: chain 2C residue 267 VAL Chi-restraints excluded: chain 2C residue 370 VAL Chi-restraints excluded: chain 2C residue 459 LEU Chi-restraints excluded: chain 2C residue 498 ASN Chi-restraints excluded: chain 0C residue 3 HIS Chi-restraints excluded: chain 0C residue 8 VAL Chi-restraints excluded: chain 0C residue 54 VAL Chi-restraints excluded: chain 0C residue 71 VAL Chi-restraints excluded: chain 0C residue 83 LEU Chi-restraints excluded: chain 0C residue 93 THR Chi-restraints excluded: chain 2B residue 33 VAL Chi-restraints excluded: chain 2B residue 39 LEU Chi-restraints excluded: chain 2B residue 267 VAL Chi-restraints excluded: chain 2B residue 323 THR Chi-restraints excluded: chain 0B residue 8 VAL Chi-restraints excluded: chain 0B residue 18 LEU Chi-restraints excluded: chain 0B residue 71 VAL Chi-restraints excluded: chain 0B residue 83 LEU Chi-restraints excluded: chain 0B residue 93 THR Chi-restraints excluded: chain 0B residue 105 LEU Chi-restraints excluded: chain 0B residue 134 VAL Chi-restraints excluded: chain 0B residue 170 TYR Chi-restraints excluded: chain 0B residue 193 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 225 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 419 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 317 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1a 46 GLN 1b 37 GLN ** 2F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0E 205 HIS ** 2C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0C 205 HIS ** 2B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0B 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119529 restraints weight = 47431.398| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.80 r_work: 0.3287 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 33768 Z= 0.175 Angle : 0.620 59.199 46014 Z= 0.335 Chirality : 0.047 0.883 5070 Planarity : 0.004 0.054 6072 Dihedral : 3.617 43.067 4678 Min Nonbonded Distance : 1.457 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.53 % Allowed : 24.80 % Favored : 71.67 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: 0.53 (0.13), residues: 4188 helix: 1.87 (0.16), residues: 1194 sheet: 0.16 (0.16), residues: 1152 loop : -0.47 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG2E 276 TYR 0.011 0.001 TYR0F 117 PHE 0.026 0.001 PHE2E 481 TRP 0.012 0.001 TRP1a 118 HIS 0.010 0.001 HIS0E 205 Details of bonding type rmsd covalent geometry : bond 0.00379 (33768) covalent geometry : angle 0.61981 (46014) hydrogen bonds : bond 0.02453 ( 1302) hydrogen bonds : angle 4.03523 ( 3744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7523.12 seconds wall clock time: 129 minutes 11.00 seconds (7751.00 seconds total)