Starting phenix.real_space_refine on Sun Aug 9 15:47:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l5d_62829/08_2026/9l5d_62829.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l5d_62829/08_2026/9l5d_62829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l5d_62829/08_2026/9l5d_62829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l5d_62829/08_2026/9l5d_62829.map" model { file = "/net/cci-nas-00/data/ceres_data/9l5d_62829/08_2026/9l5d_62829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l5d_62829/08_2026/9l5d_62829.cif" } resolution = 1.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 192 5.16 5 C 22080 2.51 5 N 5904 2.21 5 O 7512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35688 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3266 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 415, 3238 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 393} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 415, 3238 Classifications: {'peptide': 415} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 393} Chain breaks: 6 bond proxies already assigned to first conformer: 3279 Chain: "S" Number of atoms: 1033 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 119, 992 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 9, 'TRANS': 109} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 119, 989 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 9, 'TRANS': 109} Chain breaks: 1 bond proxies already assigned to first conformer: 975 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "S" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "B" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "D" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "F" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} Chain: "G" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "H" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 117 Classifications: {'water': 117} Link IDs: {None: 116} Chain: "I" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "J" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 117 Classifications: {'water': 117} Link IDs: {None: 116} Chain: "K" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "L" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 117 Classifications: {'water': 117} Link IDs: {None: 116} Chain: "M" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "N" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 117 Classifications: {'water': 117} Link IDs: {None: 116} Chain: "O" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Restraints were copied for chains: B, D, F, H, J, L, N, C, E, G, I, K, M, O Residues with excluded nonbonded symmetry interactions: 64 residue: pdb=" N AVAL A 57 " occ=0.37 ... (12 atoms not shown) pdb=" CG2BVAL A 57 " occ=0.63 residue group: pdb=" N AGLN S 2 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS S 2 " occ=0.50 residue group: pdb=" N ATHR S 22 " occ=0.50 ... (11 atoms not shown) pdb=" OG BSER S 22 " occ=0.50 residue group: pdb=" N ASER S 24 " occ=0.50 ... (11 atoms not shown) pdb=" CG2BVAL S 24 " occ=0.50 residue group: pdb=" N AILE S 34 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU S 34 " occ=0.50 residue group: pdb=" N ASER S 58 " occ=0.50 ... (11 atoms not shown) pdb=" CG2BTHR S 58 " occ=0.50 residue group: pdb=" N AASN S 96 " occ=0.50 ... (10 atoms not shown) pdb=" O BGLY S 96 " occ=0.50 residue: pdb=" N AVAL B 57 " occ=0.37 ... (12 atoms not shown) pdb=" CG2BVAL B 57 " occ=0.63 residue group: pdb=" N AGLN C 2 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS C 2 " occ=0.50 residue group: pdb=" N ATHR C 22 " occ=0.50 ... (11 atoms not shown) pdb=" OG BSER C 22 " occ=0.50 residue group: pdb=" N ASER C 24 " occ=0.50 ... (11 atoms not shown) pdb=" CG2BVAL C 24 " occ=0.50 residue group: pdb=" N AILE C 34 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU C 34 " occ=0.50 ... (remaining 52 not shown) Time building chain proxies: 4.82, per 1000 atoms: 0.14 Number of scatterers: 35688 At special positions: 0 Unit cell: (134.85, 134.85, 126.15, 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 192 16.00 O 7512 8.00 N 5904 7.00 C 22080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG ACYS A 247 " - pdb=" SG ACYS H 247 " distance=2.02 Simple disulfide: pdb=" SG ACYS B 247 " - pdb=" SG ACYS J 247 " distance=2.02 Simple disulfide: pdb=" SG ACYS D 247 " - pdb=" SG ACYS N 247 " distance=2.02 Simple disulfide: pdb=" SG ACYS F 247 " - pdb=" SG ACYS L 247 " distance=2.02 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: 2.57 Conformation dependent library (CDL) restraints added in 2.0 seconds 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 32 sheets defined 48.5% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 69 through 75 removed outlier: 3.754A pdb=" N ASP A 72 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 112 through 122 Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 297 through 303 removed outlier: 3.952A pdb=" N ILE A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.549A pdb=" N LEU A 314 " --> pdb=" O HIS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.761A pdb=" N LEU A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 433 Processing helix chain 'A' and resid 436 through 452 removed outlier: 6.358A pdb=" N ASN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TRP A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'S' and resid 22 through 36 removed outlier: 3.518A pdb=" N GLU S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 94 removed outlier: 4.020A pdb=" N VAL S 83 " --> pdb=" O ASP S 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU S 86 " --> pdb=" O GLN S 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 59 Processing helix chain 'B' and resid 69 through 75 removed outlier: 3.754A pdb=" N ASP B 72 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 112 through 122 Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 213 through 233 Processing helix chain 'B' and resid 246 through 261 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 297 through 303 removed outlier: 3.952A pdb=" N ILE B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.549A pdb=" N LEU B 314 " --> pdb=" O HIS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.761A pdb=" N LEU B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 433 Processing helix chain 'B' and resid 436 through 452 removed outlier: 6.358A pdb=" N ASN B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TRP B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 459 Processing helix chain 'C' and resid 22 through 36 removed outlier: 3.518A pdb=" N GLU C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 94 removed outlier: 4.020A pdb=" N VAL C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 59 Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.754A pdb=" N ASP D 72 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 213 through 233 Processing helix chain 'D' and resid 246 through 261 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 273 through 288 Processing helix chain 'D' and resid 297 through 303 removed outlier: 3.952A pdb=" N ILE D 301 " --> pdb=" O MET D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 322 removed outlier: 3.549A pdb=" N LEU D 314 " --> pdb=" O HIS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 386 through 395 Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.761A pdb=" N LEU D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 433 Processing helix chain 'D' and resid 436 through 452 removed outlier: 6.358A pdb=" N ASN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU D 443 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TRP D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 459 Processing helix chain 'E' and resid 22 through 36 removed outlier: 3.518A pdb=" N GLU E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 94 removed outlier: 4.020A pdb=" N VAL E 83 " --> pdb=" O ASP E 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU E 86 " --> pdb=" O GLN E 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 59 Processing helix chain 'F' and resid 69 through 75 removed outlier: 3.754A pdb=" N ASP F 72 " --> pdb=" O VAL F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 112 through 122 Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 154 through 163 Processing helix chain 'F' and resid 181 through 195 Processing helix chain 'F' and resid 213 through 233 Processing helix chain 'F' and resid 246 through 261 Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 297 through 303 removed outlier: 3.952A pdb=" N ILE F 301 " --> pdb=" O MET F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 322 removed outlier: 3.549A pdb=" N LEU F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 351 Processing helix chain 'F' and resid 357 through 361 Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 386 through 395 Processing helix chain 'F' and resid 403 through 408 removed outlier: 3.761A pdb=" N LEU F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 433 Processing helix chain 'F' and resid 436 through 452 removed outlier: 6.358A pdb=" N ASN F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU F 443 " --> pdb=" O VAL F 439 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TRP F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 459 Processing helix chain 'G' and resid 22 through 36 removed outlier: 3.518A pdb=" N GLU G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 94 removed outlier: 4.020A pdb=" N VAL G 83 " --> pdb=" O ASP G 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 59 Processing helix chain 'H' and resid 69 through 75 removed outlier: 3.754A pdb=" N ASP H 72 " --> pdb=" O VAL H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 108 Processing helix chain 'H' and resid 112 through 122 Processing helix chain 'H' and resid 123 through 127 Processing helix chain 'H' and resid 141 through 146 Processing helix chain 'H' and resid 154 through 163 Processing helix chain 'H' and resid 181 through 195 Processing helix chain 'H' and resid 213 through 233 Processing helix chain 'H' and resid 246 through 261 Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'H' and resid 273 through 288 Processing helix chain 'H' and resid 297 through 303 removed outlier: 3.952A pdb=" N ILE H 301 " --> pdb=" O MET H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 322 removed outlier: 3.549A pdb=" N LEU H 314 " --> pdb=" O HIS H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 351 Processing helix chain 'H' and resid 357 through 361 Processing helix chain 'H' and resid 383 through 385 No H-bonds generated for 'chain 'H' and resid 383 through 385' Processing helix chain 'H' and resid 386 through 395 Processing helix chain 'H' and resid 403 through 408 removed outlier: 3.761A pdb=" N LEU H 407 " --> pdb=" O GLY H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 433 Processing helix chain 'H' and resid 436 through 452 removed outlier: 6.358A pdb=" N ASN H 442 " --> pdb=" O ALA H 438 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU H 443 " --> pdb=" O VAL H 439 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TRP H 451 " --> pdb=" O GLU H 447 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 459 Processing helix chain 'I' and resid 22 through 36 removed outlier: 3.518A pdb=" N GLU I 29 " --> pdb=" O GLU I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 94 removed outlier: 4.020A pdb=" N VAL I 83 " --> pdb=" O ASP I 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 59 Processing helix chain 'J' and resid 69 through 75 removed outlier: 3.754A pdb=" N ASP J 72 " --> pdb=" O VAL J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 112 through 122 Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 141 through 146 Processing helix chain 'J' and resid 154 through 163 Processing helix chain 'J' and resid 181 through 195 Processing helix chain 'J' and resid 213 through 233 Processing helix chain 'J' and resid 246 through 261 Processing helix chain 'J' and resid 269 through 273 Processing helix chain 'J' and resid 273 through 288 Processing helix chain 'J' and resid 297 through 303 removed outlier: 3.952A pdb=" N ILE J 301 " --> pdb=" O MET J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 322 removed outlier: 3.549A pdb=" N LEU J 314 " --> pdb=" O HIS J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 351 Processing helix chain 'J' and resid 357 through 361 Processing helix chain 'J' and resid 383 through 385 No H-bonds generated for 'chain 'J' and resid 383 through 385' Processing helix chain 'J' and resid 386 through 395 Processing helix chain 'J' and resid 403 through 408 removed outlier: 3.761A pdb=" N LEU J 407 " --> pdb=" O GLY J 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 412 through 433 Processing helix chain 'J' and resid 436 through 452 removed outlier: 6.358A pdb=" N ASN J 442 " --> pdb=" O ALA J 438 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU J 443 " --> pdb=" O VAL J 439 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TRP J 451 " --> pdb=" O GLU J 447 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 459 Processing helix chain 'K' and resid 22 through 36 removed outlier: 3.518A pdb=" N GLU K 29 " --> pdb=" O GLU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 94 removed outlier: 4.020A pdb=" N VAL K 83 " --> pdb=" O ASP K 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU K 86 " --> pdb=" O GLN K 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 59 Processing helix chain 'L' and resid 69 through 75 removed outlier: 3.754A pdb=" N ASP L 72 " --> pdb=" O VAL L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'L' and resid 112 through 122 Processing helix chain 'L' and resid 123 through 127 Processing helix chain 'L' and resid 141 through 146 Processing helix chain 'L' and resid 154 through 163 Processing helix chain 'L' and resid 181 through 195 Processing helix chain 'L' and resid 213 through 233 Processing helix chain 'L' and resid 246 through 261 Processing helix chain 'L' and resid 269 through 273 Processing helix chain 'L' and resid 273 through 288 Processing helix chain 'L' and resid 297 through 303 removed outlier: 3.952A pdb=" N ILE L 301 " --> pdb=" O MET L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 322 removed outlier: 3.549A pdb=" N LEU L 314 " --> pdb=" O HIS L 310 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 351 Processing helix chain 'L' and resid 357 through 361 Processing helix chain 'L' and resid 383 through 385 No H-bonds generated for 'chain 'L' and resid 383 through 385' Processing helix chain 'L' and resid 386 through 395 Processing helix chain 'L' and resid 403 through 408 removed outlier: 3.761A pdb=" N LEU L 407 " --> pdb=" O GLY L 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 433 Processing helix chain 'L' and resid 436 through 452 removed outlier: 6.358A pdb=" N ASN L 442 " --> pdb=" O ALA L 438 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU L 443 " --> pdb=" O VAL L 439 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TRP L 451 " --> pdb=" O GLU L 447 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 459 Processing helix chain 'M' and resid 22 through 36 removed outlier: 3.518A pdb=" N GLU M 29 " --> pdb=" O GLU M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 94 removed outlier: 4.020A pdb=" N VAL M 83 " --> pdb=" O ASP M 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU M 86 " --> pdb=" O GLN M 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 59 Processing helix chain 'N' and resid 69 through 75 removed outlier: 3.754A pdb=" N ASP N 72 " --> pdb=" O VAL N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 108 Processing helix chain 'N' and resid 112 through 122 Processing helix chain 'N' and resid 123 through 127 Processing helix chain 'N' and resid 141 through 146 Processing helix chain 'N' and resid 154 through 163 Processing helix chain 'N' and resid 181 through 195 Processing helix chain 'N' and resid 213 through 233 Processing helix chain 'N' and resid 246 through 261 Processing helix chain 'N' and resid 269 through 273 Processing helix chain 'N' and resid 273 through 288 Processing helix chain 'N' and resid 297 through 303 removed outlier: 3.952A pdb=" N ILE N 301 " --> pdb=" O MET N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 322 removed outlier: 3.549A pdb=" N LEU N 314 " --> pdb=" O HIS N 310 " (cutoff:3.500A) Processing helix chain 'N' and resid 339 through 351 Processing helix chain 'N' and resid 357 through 361 Processing helix chain 'N' and resid 383 through 385 No H-bonds generated for 'chain 'N' and resid 383 through 385' Processing helix chain 'N' and resid 386 through 395 Processing helix chain 'N' and resid 403 through 408 removed outlier: 3.761A pdb=" N LEU N 407 " --> pdb=" O GLY N 403 " (cutoff:3.500A) Processing helix chain 'N' and resid 412 through 433 Processing helix chain 'N' and resid 436 through 452 removed outlier: 6.358A pdb=" N ASN N 442 " --> pdb=" O ALA N 438 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU N 443 " --> pdb=" O VAL N 439 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TRP N 451 " --> pdb=" O GLU N 447 " (cutoff:3.500A) Processing helix chain 'N' and resid 452 through 459 Processing helix chain 'O' and resid 22 through 36 removed outlier: 3.518A pdb=" N GLU O 29 " --> pdb=" O GLU O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 94 removed outlier: 4.020A pdb=" N VAL O 83 " --> pdb=" O ASP O 79 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU O 86 " --> pdb=" O GLN O 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 5.622A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 173 removed outlier: 6.439A pdb=" N LEU A 170 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS A 201 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS A 172 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR A 200 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN A 241 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N HIS A 238 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET A 266 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU A 240 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASP A 268 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 265 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N HIS A 294 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS A 267 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 326 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA A 378 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 169 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE A 402 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY A 171 " --> pdb=" O PHE A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA4, first strand: chain 'S' and resid 68 through 70 removed outlier: 4.564A pdb=" N VAL S 42 " --> pdb=" O TRP S 70 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE S 99 " --> pdb=" O ALA S 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 83 through 89 removed outlier: 5.622A pdb=" N CYS B 84 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 102 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS B 86 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 37 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B 138 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA B 39 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 173 removed outlier: 6.439A pdb=" N LEU B 170 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS B 201 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS B 172 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR B 200 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN B 241 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N HIS B 238 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET B 266 " --> pdb=" O HIS B 238 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B 240 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASP B 268 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL B 265 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N HIS B 294 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS B 267 " --> pdb=" O HIS B 294 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 326 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN B 401 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA B 378 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU B 169 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE B 402 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY B 171 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AA8, first strand: chain 'C' and resid 68 through 70 removed outlier: 4.564A pdb=" N VAL C 42 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 99 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 83 through 89 removed outlier: 5.622A pdb=" N CYS D 84 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA D 102 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS D 86 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU D 37 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU D 138 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA D 39 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 173 removed outlier: 6.439A pdb=" N LEU D 170 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS D 201 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS D 172 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR D 200 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN D 241 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N HIS D 238 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET D 266 " --> pdb=" O HIS D 238 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU D 240 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASP D 268 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL D 265 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N HIS D 294 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS D 267 " --> pdb=" O HIS D 294 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE D 326 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN D 401 " --> pdb=" O PRO D 376 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA D 378 " --> pdb=" O GLN D 401 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU D 169 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE D 402 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY D 171 " --> pdb=" O PHE D 402 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AB3, first strand: chain 'E' and resid 68 through 70 removed outlier: 4.564A pdb=" N VAL E 42 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 99 " --> pdb=" O ALA E 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 83 through 89 removed outlier: 5.622A pdb=" N CYS F 84 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA F 102 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS F 86 " --> pdb=" O TYR F 100 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU F 37 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU F 138 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA F 39 " --> pdb=" O GLU F 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 169 through 173 removed outlier: 6.439A pdb=" N LEU F 170 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS F 201 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS F 172 " --> pdb=" O LYS F 201 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR F 200 " --> pdb=" O TYR F 239 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN F 241 " --> pdb=" O THR F 200 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N HIS F 238 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET F 266 " --> pdb=" O HIS F 238 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU F 240 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASP F 268 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL F 265 " --> pdb=" O HIS F 292 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N HIS F 294 " --> pdb=" O VAL F 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS F 267 " --> pdb=" O HIS F 294 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE F 326 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN F 401 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA F 378 " --> pdb=" O GLN F 401 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU F 169 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE F 402 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY F 171 " --> pdb=" O PHE F 402 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AB7, first strand: chain 'G' and resid 68 through 70 removed outlier: 4.564A pdb=" N VAL G 42 " --> pdb=" O TRP G 70 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE G 99 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 83 through 89 removed outlier: 5.622A pdb=" N CYS H 84 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA H 102 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS H 86 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU H 37 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU H 138 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA H 39 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 169 through 173 removed outlier: 6.439A pdb=" N LEU H 170 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS H 201 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS H 172 " --> pdb=" O LYS H 201 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR H 200 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN H 241 " --> pdb=" O THR H 200 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N HIS H 238 " --> pdb=" O ILE H 264 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET H 266 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU H 240 " --> pdb=" O MET H 266 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASP H 268 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL H 265 " --> pdb=" O HIS H 292 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N HIS H 294 " --> pdb=" O VAL H 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS H 267 " --> pdb=" O HIS H 294 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE H 326 " --> pdb=" O VAL H 377 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN H 401 " --> pdb=" O PRO H 376 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA H 378 " --> pdb=" O GLN H 401 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU H 169 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE H 402 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY H 171 " --> pdb=" O PHE H 402 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 353 through 354 Processing sheet with id=AC2, first strand: chain 'I' and resid 68 through 70 removed outlier: 4.564A pdb=" N VAL I 42 " --> pdb=" O TRP I 70 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE I 99 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 83 through 89 removed outlier: 5.622A pdb=" N CYS J 84 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA J 102 " --> pdb=" O CYS J 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS J 86 " --> pdb=" O TYR J 100 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU J 37 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU J 138 " --> pdb=" O LEU J 37 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA J 39 " --> pdb=" O GLU J 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 169 through 173 removed outlier: 6.439A pdb=" N LEU J 170 " --> pdb=" O PHE J 199 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS J 201 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS J 172 " --> pdb=" O LYS J 201 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR J 200 " --> pdb=" O TYR J 239 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN J 241 " --> pdb=" O THR J 200 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N HIS J 238 " --> pdb=" O ILE J 264 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET J 266 " --> pdb=" O HIS J 238 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU J 240 " --> pdb=" O MET J 266 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASP J 268 " --> pdb=" O LEU J 240 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL J 265 " --> pdb=" O HIS J 292 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N HIS J 294 " --> pdb=" O VAL J 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS J 267 " --> pdb=" O HIS J 294 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE J 326 " --> pdb=" O VAL J 377 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN J 401 " --> pdb=" O PRO J 376 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA J 378 " --> pdb=" O GLN J 401 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU J 169 " --> pdb=" O LEU J 400 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE J 402 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY J 171 " --> pdb=" O PHE J 402 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 353 through 354 Processing sheet with id=AC6, first strand: chain 'K' and resid 68 through 70 removed outlier: 4.564A pdb=" N VAL K 42 " --> pdb=" O TRP K 70 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE K 99 " --> pdb=" O ALA K 117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 83 through 89 removed outlier: 5.622A pdb=" N CYS L 84 " --> pdb=" O ALA L 102 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA L 102 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS L 86 " --> pdb=" O TYR L 100 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU L 37 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU L 138 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA L 39 " --> pdb=" O GLU L 136 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 169 through 173 removed outlier: 6.439A pdb=" N LEU L 170 " --> pdb=" O PHE L 199 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS L 201 " --> pdb=" O LEU L 170 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS L 172 " --> pdb=" O LYS L 201 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR L 200 " --> pdb=" O TYR L 239 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN L 241 " --> pdb=" O THR L 200 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N HIS L 238 " --> pdb=" O ILE L 264 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET L 266 " --> pdb=" O HIS L 238 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU L 240 " --> pdb=" O MET L 266 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASP L 268 " --> pdb=" O LEU L 240 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL L 265 " --> pdb=" O HIS L 292 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N HIS L 294 " --> pdb=" O VAL L 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS L 267 " --> pdb=" O HIS L 294 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE L 326 " --> pdb=" O VAL L 377 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN L 401 " --> pdb=" O PRO L 376 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA L 378 " --> pdb=" O GLN L 401 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU L 169 " --> pdb=" O LEU L 400 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE L 402 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY L 171 " --> pdb=" O PHE L 402 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 353 through 354 Processing sheet with id=AD1, first strand: chain 'M' and resid 68 through 70 removed outlier: 4.564A pdb=" N VAL M 42 " --> pdb=" O TRP M 70 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE M 99 " --> pdb=" O ALA M 117 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 83 through 89 removed outlier: 5.622A pdb=" N CYS N 84 " --> pdb=" O ALA N 102 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA N 102 " --> pdb=" O CYS N 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS N 86 " --> pdb=" O TYR N 100 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU N 37 " --> pdb=" O LEU N 138 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU N 138 " --> pdb=" O LEU N 37 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA N 39 " --> pdb=" O GLU N 136 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 169 through 173 removed outlier: 6.439A pdb=" N LEU N 170 " --> pdb=" O PHE N 199 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS N 201 " --> pdb=" O LEU N 170 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS N 172 " --> pdb=" O LYS N 201 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR N 200 " --> pdb=" O TYR N 239 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN N 241 " --> pdb=" O THR N 200 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N HIS N 238 " --> pdb=" O ILE N 264 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET N 266 " --> pdb=" O HIS N 238 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU N 240 " --> pdb=" O MET N 266 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASP N 268 " --> pdb=" O LEU N 240 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL N 265 " --> pdb=" O HIS N 292 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N HIS N 294 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS N 267 " --> pdb=" O HIS N 294 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE N 326 " --> pdb=" O VAL N 377 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN N 401 " --> pdb=" O PRO N 376 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA N 378 " --> pdb=" O GLN N 401 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU N 169 " --> pdb=" O LEU N 400 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N PHE N 402 " --> pdb=" O LEU N 169 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY N 171 " --> pdb=" O PHE N 402 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 353 through 354 Processing sheet with id=AD5, first strand: chain 'O' and resid 68 through 70 removed outlier: 4.564A pdb=" N VAL O 42 " --> pdb=" O TRP O 70 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE O 99 " --> pdb=" O ALA O 117 " (cutoff:3.500A) 1632 hydrogen bonds defined for protein. 4464 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: 7.27 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5752 1.31 - 1.44: 9768 1.44 - 1.56: 19624 1.56 - 1.69: 8 1.69 - 1.81: 248 Bond restraints: 35400 Sorted by residual: bond pdb=" C PHE A 127 " pdb=" O PHE A 127 " ideal model delta sigma weight residual 1.234 1.188 0.047 1.20e-02 6.94e+03 1.51e+01 bond pdb=" C PHE J 127 " pdb=" O PHE J 127 " ideal model delta sigma weight residual 1.234 1.188 0.047 1.20e-02 6.94e+03 1.51e+01 bond pdb=" C PHE B 127 " pdb=" O PHE B 127 " ideal model delta sigma weight residual 1.234 1.188 0.047 1.20e-02 6.94e+03 1.51e+01 bond pdb=" C PHE H 127 " pdb=" O PHE H 127 " ideal model delta sigma weight residual 1.234 1.188 0.047 1.20e-02 6.94e+03 1.51e+01 bond pdb=" C PHE L 127 " pdb=" O PHE L 127 " ideal model delta sigma weight residual 1.234 1.188 0.047 1.20e-02 6.94e+03 1.51e+01 ... (remaining 35395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 38544 1.88 - 3.77: 8008 3.77 - 5.65: 1336 5.65 - 7.53: 200 7.53 - 9.42: 24 Bond angle restraints: 48112 Sorted by residual: angle pdb=" CA PHE N 345 " pdb=" CB PHE N 345 " pdb=" CG PHE N 345 " ideal model delta sigma weight residual 113.80 120.32 -6.52 1.00e+00 1.00e+00 4.25e+01 angle pdb=" CA PHE H 345 " pdb=" CB PHE H 345 " pdb=" CG PHE H 345 " ideal model delta sigma weight residual 113.80 120.32 -6.52 1.00e+00 1.00e+00 4.25e+01 angle pdb=" CA PHE J 345 " pdb=" CB PHE J 345 " pdb=" CG PHE J 345 " ideal model delta sigma weight residual 113.80 120.32 -6.52 1.00e+00 1.00e+00 4.25e+01 angle pdb=" CA PHE L 345 " pdb=" CB PHE L 345 " pdb=" CG PHE L 345 " ideal model delta sigma weight residual 113.80 120.32 -6.52 1.00e+00 1.00e+00 4.25e+01 angle pdb=" CA PHE D 345 " pdb=" CB PHE D 345 " pdb=" CG PHE D 345 " ideal model delta sigma weight residual 113.80 120.32 -6.52 1.00e+00 1.00e+00 4.25e+01 ... (remaining 48107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 18960 16.46 - 32.91: 1528 32.91 - 49.37: 244 49.37 - 65.82: 104 65.82 - 82.28: 40 Dihedral angle restraints: 20876 sinusoidal: 8340 harmonic: 12536 Sorted by residual: dihedral pdb=" CB ACYS B 247 " pdb=" SG ACYS B 247 " pdb=" SG ACYS J 247 " pdb=" CB ACYS J 247 " ideal model delta sinusoidal sigma weight residual -86.00 -41.36 -44.64 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CB ACYS D 247 " pdb=" SG ACYS D 247 " pdb=" SG ACYS N 247 " pdb=" CB ACYS N 247 " ideal model delta sinusoidal sigma weight residual -86.00 -41.36 -44.64 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CB ACYS F 247 " pdb=" SG ACYS F 247 " pdb=" SG ACYS L 247 " pdb=" CB ACYS L 247 " ideal model delta sinusoidal sigma weight residual -86.00 -41.36 -44.64 1 1.00e+01 1.00e-02 2.77e+01 ... (remaining 20873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2712 0.056 - 0.111: 1456 0.111 - 0.167: 824 0.167 - 0.223: 88 0.223 - 0.278: 48 Chirality restraints: 5128 Sorted by residual: chirality pdb=" CA GLU I 25 " pdb=" N GLU I 25 " pdb=" C GLU I 25 " pdb=" CB GLU I 25 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA GLU S 25 " pdb=" N GLU S 25 " pdb=" C GLU S 25 " pdb=" CB GLU S 25 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA GLU K 25 " pdb=" N GLU K 25 " pdb=" C GLU K 25 " pdb=" CB GLU K 25 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 5125 not shown) Planarity restraints: 6240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 61 " -0.046 2.00e-02 2.50e+03 2.83e-02 1.61e+01 pdb=" CG TYR C 61 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR C 61 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR C 61 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR C 61 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR C 61 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 61 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR C 61 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 61 " 0.046 2.00e-02 2.50e+03 2.83e-02 1.61e+01 pdb=" CG TYR G 61 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR G 61 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR G 61 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR G 61 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR G 61 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR G 61 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR G 61 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 61 " -0.046 2.00e-02 2.50e+03 2.83e-02 1.61e+01 pdb=" CG TYR K 61 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR K 61 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR K 61 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR K 61 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR K 61 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR K 61 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR K 61 " -0.039 2.00e-02 2.50e+03 ... (remaining 6237 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 216 2.42 - 3.04: 23160 3.04 - 3.66: 62812 3.66 - 4.28: 103584 4.28 - 4.90: 161244 Nonbonded interactions: 351016 Sorted by model distance: nonbonded pdb=" O GLN N 366 " pdb=" O HOH N 601 " model vdw 1.796 3.040 nonbonded pdb=" O GLN J 366 " pdb=" O HOH J 601 " model vdw 1.796 3.040 nonbonded pdb=" O GLN A 366 " pdb=" O HOH A 601 " model vdw 1.796 3.040 nonbonded pdb=" O GLN F 366 " pdb=" O HOH F 601 " model vdw 1.796 3.040 nonbonded pdb=" O GLN H 366 " pdb=" O HOH H 601 " model vdw 1.796 3.040 ... (remaining 351011 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'S' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 29.140 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 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 : 0.010 0.063 35404 Z= 0.609 Angle : 1.577 9.419 48120 Z= 1.042 Chirality : 0.080 0.278 5128 Planarity : 0.013 0.149 6240 Dihedral : 13.380 82.280 12896 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.68 % Favored : 95.93 % Rotamer: Outliers : 1.32 % Allowed : 4.42 % Favored : 94.26 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.10), residues: 4320 helix: -1.23 (0.10), residues: 1800 sheet: -0.81 (0.16), residues: 680 loop : -1.65 (0.12), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.004 ARG J 194 TYR 0.046 0.008 TYR O 61 PHE 0.033 0.007 PHE L 345 TRP 0.027 0.006 TRP F 368 HIS 0.025 0.006 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00961 / 0.61 (35400) covalent geometry : angle 1.57278 / 1.04 (48112) SS BOND : bond 0.01403 / 0.70 ( 4) SS BOND : angle 8.91899 / 5.60 ( 8) hydrogen bonds : bond 0.16615 / 10.87 ( 1632) hydrogen bonds : angle 8.74087 / 6.20 ( 4464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 502 time to evaluate : 1.196 Fit side-chains REVERT: A 116 MET cc_start: 0.5598 (ttp) cc_final: 0.5360 (ttp) REVERT: A 127 PHE cc_start: 0.4411 (OUTLIER) cc_final: 0.3841 (m-10) REVERT: A 339 ARG cc_start: 0.4646 (mtp180) cc_final: 0.4038 (tmt90) REVERT: S 36 ASN cc_start: 0.6438 (m-40) cc_final: 0.5842 (m110) REVERT: S 82 GLN cc_start: 0.6061 (mt0) cc_final: 0.5793 (mt0) REVERT: S 92 LYS cc_start: 0.6522 (tttt) cc_final: 0.6075 (ttmt) REVERT: B 116 MET cc_start: 0.5574 (ttp) cc_final: 0.5354 (ttp) REVERT: B 127 PHE cc_start: 0.4400 (OUTLIER) cc_final: 0.3823 (m-10) REVERT: B 339 ARG cc_start: 0.4631 (mtp180) cc_final: 0.4026 (tmt90) REVERT: B 392 GLU cc_start: 0.5287 (tm-30) cc_final: 0.4672 (tm-30) REVERT: C 36 ASN cc_start: 0.6462 (m-40) cc_final: 0.5871 (m110) REVERT: C 82 GLN cc_start: 0.6131 (mt0) cc_final: 0.5871 (mt0) REVERT: C 92 LYS cc_start: 0.6582 (tttt) cc_final: 0.6132 (ttmt) REVERT: D 116 MET cc_start: 0.5539 (ttp) cc_final: 0.5322 (ttp) REVERT: D 127 PHE cc_start: 0.4423 (OUTLIER) cc_final: 0.3855 (m-10) REVERT: D 339 ARG cc_start: 0.4627 (mtp180) cc_final: 0.4029 (tmt90) REVERT: D 392 GLU cc_start: 0.5274 (tm-30) cc_final: 0.4660 (tm-30) REVERT: E 9 LYS cc_start: 0.6826 (mmtp) cc_final: 0.6537 (mmtp) REVERT: E 36 ASN cc_start: 0.6386 (m-40) cc_final: 0.5795 (m110) REVERT: E 82 GLN cc_start: 0.6152 (mt0) cc_final: 0.5885 (mt0) REVERT: E 92 LYS cc_start: 0.6523 (tttt) cc_final: 0.6075 (ttmt) REVERT: F 116 MET cc_start: 0.5584 (ttp) cc_final: 0.5345 (ttp) REVERT: F 127 PHE cc_start: 0.4437 (OUTLIER) cc_final: 0.3865 (m-10) REVERT: F 339 ARG cc_start: 0.4658 (mtp180) cc_final: 0.4051 (tmt90) REVERT: F 392 GLU cc_start: 0.5307 (tm-30) cc_final: 0.4691 (tm-30) REVERT: G 36 ASN cc_start: 0.6346 (m-40) cc_final: 0.5759 (m110) REVERT: G 82 GLN cc_start: 0.6105 (mt0) cc_final: 0.5837 (mt0) REVERT: G 92 LYS cc_start: 0.6486 (tttt) cc_final: 0.6036 (ttmt) REVERT: H 116 MET cc_start: 0.5567 (ttp) cc_final: 0.5329 (ttp) REVERT: H 127 PHE cc_start: 0.4383 (OUTLIER) cc_final: 0.3804 (m-10) REVERT: H 339 ARG cc_start: 0.4556 (mtp180) cc_final: 0.3945 (tmt90) REVERT: I 36 ASN cc_start: 0.6509 (m-40) cc_final: 0.5916 (m110) REVERT: I 82 GLN cc_start: 0.6064 (mt0) cc_final: 0.5805 (mt0) REVERT: I 92 LYS cc_start: 0.6395 (tttt) cc_final: 0.5959 (ttmt) REVERT: J 116 MET cc_start: 0.5619 (ttp) cc_final: 0.5380 (ttp) REVERT: J 127 PHE cc_start: 0.4381 (OUTLIER) cc_final: 0.3803 (m-10) REVERT: J 339 ARG cc_start: 0.4612 (mtp180) cc_final: 0.4002 (tmt90) REVERT: J 392 GLU cc_start: 0.5305 (tm-30) cc_final: 0.4686 (tm-30) REVERT: K 36 ASN cc_start: 0.6452 (m-40) cc_final: 0.5855 (m110) REVERT: K 82 GLN cc_start: 0.6019 (mt0) cc_final: 0.5754 (mt0) REVERT: K 92 LYS cc_start: 0.6354 (tttt) cc_final: 0.5917 (ttmt) REVERT: L 107 LEU cc_start: 0.5665 (mt) cc_final: 0.4883 (tp) REVERT: L 116 MET cc_start: 0.5554 (ttp) cc_final: 0.5335 (ttp) REVERT: L 127 PHE cc_start: 0.4385 (OUTLIER) cc_final: 0.3814 (m-10) REVERT: L 339 ARG cc_start: 0.4617 (mtp180) cc_final: 0.4008 (tmt90) REVERT: L 392 GLU cc_start: 0.5304 (tm-30) cc_final: 0.4685 (tm-30) REVERT: M 9 LYS cc_start: 0.6837 (mmtp) cc_final: 0.6547 (mmtp) REVERT: M 36 ASN cc_start: 0.6438 (m-40) cc_final: 0.5844 (m110) REVERT: M 92 LYS cc_start: 0.6370 (tttt) cc_final: 0.5934 (ttmt) REVERT: N 116 MET cc_start: 0.5597 (ttp) cc_final: 0.5358 (ttp) REVERT: N 127 PHE cc_start: 0.4421 (OUTLIER) cc_final: 0.3851 (m-10) REVERT: N 339 ARG cc_start: 0.4674 (mtp180) cc_final: 0.4072 (tmt90) REVERT: O 9 LYS cc_start: 0.6816 (mmtp) cc_final: 0.6528 (mmtp) REVERT: O 82 GLN cc_start: 0.6051 (mt0) cc_final: 0.5793 (mt0) REVERT: O 92 LYS cc_start: 0.6323 (tttt) cc_final: 0.5886 (ttmt) outliers start: 48 outliers final: 12 residues processed: 534 average time/residue: 0.7839 time to fit residues: 497.7333 Evaluate side-chains 468 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 448 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 142 PRO Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 142 PRO Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 142 PRO Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 142 PRO Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 142 PRO Chi-restraints excluded: chain J residue 127 PHE Chi-restraints excluded: chain J residue 142 PRO Chi-restraints excluded: chain L residue 127 PHE Chi-restraints excluded: chain L residue 142 PRO Chi-restraints excluded: chain L residue 445 ILE Chi-restraints excluded: chain N residue 127 PHE Chi-restraints excluded: chain N residue 142 PRO Chi-restraints excluded: chain N residue 445 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.240720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.223755 restraints weight = 1121164.122| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 8.17 r_work: 0.3747 rms_B_bonded: 6.21 restraints_weight: 2.0000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (7 function evaluations) r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35404 Z= 0.140 Angle : 0.642 7.922 48120 Z= 0.338 Chirality : 0.045 0.160 5128 Planarity : 0.005 0.035 6240 Dihedral : 5.850 44.956 4864 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.91 % Allowed : 6.54 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.12), residues: 4320 helix: 0.92 (0.12), residues: 1768 sheet: -0.46 (0.17), residues: 680 loop : -0.41 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 217 TYR 0.013 0.002 TYR J 239 PHE 0.027 0.002 PHE J 345 TRP 0.006 0.001 TRP L 214 HIS 0.010 0.001 HIS H 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (35400) covalent geometry : angle 0.64117 / 0.34 (48112) SS BOND : bond 0.00890 / 0.45 ( 4) SS BOND : angle 2.92051 / 1.83 ( 8) hydrogen bonds : bond 0.04192 / 2.72 ( 1632) hydrogen bonds : angle 6.38120 / 4.54 ( 4464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 524 time to evaluate : 1.354 Fit side-chains REVERT: B 356 LYS cc_start: 0.5735 (ttmm) cc_final: 0.5502 (ttmt) REVERT: F 356 LYS cc_start: 0.5651 (ttmm) cc_final: 0.5425 (ttmt) REVERT: I 36 ASN cc_start: 0.7467 (m-40) cc_final: 0.7259 (m110) REVERT: L 356 LYS cc_start: 0.5606 (ttmm) cc_final: 0.5392 (ttmt) REVERT: N 356 LYS cc_start: 0.5786 (ttmm) cc_final: 0.5572 (ttmt) outliers start: 33 outliers final: 0 residues processed: 529 average time/residue: 0.7719 time to fit residues: 485.5518 Evaluate side-chains 469 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 258 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 386 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 316 optimal weight: 9.9990 chunk 409 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 36 ASN S 82 GLN C 36 ASN E 36 ASN G 36 ASN K 36 ASN M 36 ASN M 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.226262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.196638 restraints weight = 116855.939| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.71 r_work: 0.3812 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work: 0.3652 rms_B_bonded: 4.54 restraints_weight: 0.1250 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (14 function evaluations) r_final: 0.3632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35404 Z= 0.176 Angle : 0.676 8.542 48120 Z= 0.357 Chirality : 0.045 0.159 5128 Planarity : 0.005 0.041 6240 Dihedral : 5.219 22.960 4816 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.30 % Allowed : 9.16 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.12), residues: 4320 helix: 1.36 (0.12), residues: 1768 sheet: -0.64 (0.16), residues: 776 loop : 0.01 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 41 TYR 0.018 0.002 TYR G 61 PHE 0.025 0.003 PHE D 345 TRP 0.005 0.001 TRP F 214 HIS 0.010 0.002 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (35400) covalent geometry : angle 0.67507 / 0.36 (48112) SS BOND : bond 0.00928 / 0.46 ( 4) SS BOND : angle 2.84161 / 1.78 ( 8) hydrogen bonds : bond 0.04502 / 2.92 ( 1632) hydrogen bonds : angle 6.26491 / 4.46 ( 4464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 510 time to evaluate : 1.347 Fit side-chains REVERT: A 407 LEU cc_start: 0.4819 (OUTLIER) cc_final: 0.4457 (mt) REVERT: B 407 LEU cc_start: 0.4809 (OUTLIER) cc_final: 0.4455 (mt) REVERT: H 407 LEU cc_start: 0.4782 (OUTLIER) cc_final: 0.4424 (mt) REVERT: I 92 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7673 (ttmt) REVERT: J 407 LEU cc_start: 0.4767 (OUTLIER) cc_final: 0.4410 (mt) REVERT: K 92 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7672 (ttmt) REVERT: L 407 LEU cc_start: 0.4793 (OUTLIER) cc_final: 0.4441 (mt) outliers start: 11 outliers final: 3 residues processed: 515 average time/residue: 0.7141 time to fit residues: 440.6109 Evaluate side-chains 501 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 491 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain J residue 445 ILE Chi-restraints excluded: chain K residue 92 LYS Chi-restraints excluded: chain L residue 407 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 96 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 372 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 286 optimal weight: 8.9990 chunk 392 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN S 36 ASN S 82 GLN C 36 ASN C 82 GLN E 36 ASN E 82 GLN G 36 ASN G 82 GLN H 304 GLN ** H 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN K 36 ASN K 82 GLN M 36 ASN M 82 GLN O 82 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.224375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.194153 restraints weight = 113871.037| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.60 r_work: 0.3756 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (16 function evaluations) r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 35404 Z= 0.288 Angle : 0.833 8.981 48120 Z= 0.442 Chirality : 0.050 0.187 5128 Planarity : 0.007 0.053 6240 Dihedral : 5.523 23.932 4816 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.91 % Allowed : 9.24 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.12), residues: 4320 helix: 1.20 (0.11), residues: 1752 sheet: -0.60 (0.17), residues: 640 loop : -0.29 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 253 TYR 0.029 0.004 TYR E 61 PHE 0.033 0.004 PHE J 311 TRP 0.010 0.003 TRP G 38 HIS 0.016 0.003 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.29 (35400) covalent geometry : angle 0.83199 / 0.44 (48112) SS BOND : bond 0.00977 / 0.49 ( 4) SS BOND : angle 3.67179 / 2.31 ( 8) hydrogen bonds : bond 0.05561 / 3.61 ( 1632) hydrogen bonds : angle 6.69741 / 4.77 ( 4464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 485 time to evaluate : 1.229 Fit side-chains REVERT: A 407 LEU cc_start: 0.4890 (OUTLIER) cc_final: 0.4532 (mt) REVERT: B 407 LEU cc_start: 0.4897 (OUTLIER) cc_final: 0.4546 (mt) REVERT: G 36 ASN cc_start: 0.7736 (m-40) cc_final: 0.7532 (m110) REVERT: H 407 LEU cc_start: 0.4871 (OUTLIER) cc_final: 0.4501 (mt) REVERT: I 92 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7675 (ttmt) REVERT: J 407 LEU cc_start: 0.4838 (OUTLIER) cc_final: 0.4474 (mt) REVERT: K 92 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7631 (ttmt) REVERT: L 407 LEU cc_start: 0.4869 (OUTLIER) cc_final: 0.4516 (mt) outliers start: 33 outliers final: 11 residues processed: 501 average time/residue: 0.7089 time to fit residues: 423.3120 Evaluate side-chains 473 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 455 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 445 ILE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 172 CYS Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain K residue 92 LYS Chi-restraints excluded: chain L residue 172 CYS Chi-restraints excluded: chain L residue 407 LEU Chi-restraints excluded: chain N residue 172 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 340 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 392 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 337 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 ASN B 304 GLN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN C 82 GLN D 304 GLN ** D 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN F 304 GLN G 82 GLN H 304 GLN ** H 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN J 304 GLN ** J 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN L 304 GLN ** L 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 ASN M 82 GLN N 304 GLN ** N 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.227010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.197124 restraints weight = 125765.923| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.81 r_work: 0.3814 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work: 0.3647 rms_B_bonded: 4.94 restraints_weight: 0.1250 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35404 Z= 0.170 Angle : 0.671 9.606 48120 Z= 0.353 Chirality : 0.045 0.166 5128 Planarity : 0.005 0.045 6240 Dihedral : 5.196 22.982 4816 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.33 % Allowed : 9.99 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.12), residues: 4320 helix: 1.52 (0.12), residues: 1768 sheet: -0.74 (0.17), residues: 640 loop : -0.06 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 41 TYR 0.017 0.002 TYR O 61 PHE 0.022 0.002 PHE N 345 TRP 0.006 0.001 TRP E 4 HIS 0.014 0.002 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (35400) covalent geometry : angle 0.66980 / 0.35 (48112) SS BOND : bond 0.00954 / 0.48 ( 4) SS BOND : angle 2.74684 / 1.72 ( 8) hydrogen bonds : bond 0.04404 / 2.85 ( 1632) hydrogen bonds : angle 6.24742 / 4.44 ( 4464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 506 time to evaluate : 1.343 Fit side-chains REVERT: A 407 LEU cc_start: 0.4858 (OUTLIER) cc_final: 0.4526 (mt) REVERT: B 407 LEU cc_start: 0.4839 (OUTLIER) cc_final: 0.4511 (mt) REVERT: D 392 GLU cc_start: 0.6761 (tm-30) cc_final: 0.6492 (tm-30) REVERT: G 36 ASN cc_start: 0.7774 (m-40) cc_final: 0.7560 (m110) REVERT: H 407 LEU cc_start: 0.4832 (OUTLIER) cc_final: 0.4503 (mt) REVERT: I 92 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7675 (ttmt) REVERT: J 407 LEU cc_start: 0.4798 (OUTLIER) cc_final: 0.4472 (mt) REVERT: K 92 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7657 (ttmt) REVERT: L 407 LEU cc_start: 0.4813 (OUTLIER) cc_final: 0.4487 (mt) outliers start: 12 outliers final: 6 residues processed: 514 average time/residue: 0.7341 time to fit residues: 452.8615 Evaluate side-chains 498 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 485 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain H residue 445 ILE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain J residue 445 ILE Chi-restraints excluded: chain K residue 92 LYS Chi-restraints excluded: chain L residue 407 LEU Chi-restraints excluded: chain N residue 172 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 318 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 383 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 355 optimal weight: 8.9990 chunk 106 optimal weight: 30.0000 chunk 264 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN S 36 ASN B 304 GLN C 36 ASN D 304 GLN E 36 ASN F 304 GLN H 304 GLN J 304 GLN L 304 GLN M 36 ASN M 96 ASN A N 304 GLN O 96 ASN A Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.223762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.193678 restraints weight = 113592.046| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.62 r_work: 0.3759 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work: 0.3626 rms_B_bonded: 3.87 restraints_weight: 0.1250 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 35404 Z= 0.325 Angle : 0.883 10.671 48120 Z= 0.468 Chirality : 0.052 0.197 5128 Planarity : 0.007 0.063 6240 Dihedral : 5.557 24.268 4816 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.83 % Allowed : 10.10 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.12), residues: 4320 helix: 1.12 (0.11), residues: 1752 sheet: -0.80 (0.17), residues: 688 loop : -0.20 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 253 TYR 0.033 0.004 TYR M 61 PHE 0.034 0.004 PHE B 311 TRP 0.010 0.003 TRP M 38 HIS 0.017 0.003 HIS N 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.32 (35400) covalent geometry : angle 0.88177 / 0.47 (48112) SS BOND : bond 0.01010 / 0.51 ( 4) SS BOND : angle 4.02294 / 2.53 ( 8) hydrogen bonds : bond 0.05798 / 3.76 ( 1632) hydrogen bonds : angle 6.75631 / 4.81 ( 4464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 462 time to evaluate : 1.268 Fit side-chains REVERT: A 117 PHE cc_start: 0.7966 (m-80) cc_final: 0.7764 (m-80) REVERT: A 407 LEU cc_start: 0.4903 (OUTLIER) cc_final: 0.4569 (mt) REVERT: S 123 PHE cc_start: 0.7664 (t80) cc_final: 0.7415 (t80) REVERT: B 304 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7303 (mm110) REVERT: B 407 LEU cc_start: 0.4900 (OUTLIER) cc_final: 0.4571 (mt) REVERT: E 123 PHE cc_start: 0.7666 (t80) cc_final: 0.7459 (t80) REVERT: F 304 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7410 (mm110) REVERT: G 123 PHE cc_start: 0.7649 (t80) cc_final: 0.7401 (t80) REVERT: H 407 LEU cc_start: 0.4891 (OUTLIER) cc_final: 0.4552 (mt) REVERT: I 92 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7693 (ttmt) REVERT: J 117 PHE cc_start: 0.7978 (m-80) cc_final: 0.7758 (m-80) REVERT: J 304 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7319 (mm110) REVERT: J 407 LEU cc_start: 0.4852 (OUTLIER) cc_final: 0.4511 (mt) REVERT: K 92 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7678 (ttmt) REVERT: K 123 PHE cc_start: 0.7607 (t80) cc_final: 0.7387 (t80) REVERT: L 407 LEU cc_start: 0.4859 (OUTLIER) cc_final: 0.4533 (mt) REVERT: M 123 PHE cc_start: 0.7596 (t80) cc_final: 0.7317 (t80) REVERT: N 304 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7401 (mm110) REVERT: O 123 PHE cc_start: 0.7577 (t80) cc_final: 0.7293 (t80) outliers start: 30 outliers final: 13 residues processed: 475 average time/residue: 0.7461 time to fit residues: 421.4183 Evaluate side-chains 465 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 445 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 172 CYS Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain J residue 445 ILE Chi-restraints excluded: chain K residue 92 LYS Chi-restraints excluded: chain L residue 172 CYS Chi-restraints excluded: chain L residue 305 LYS Chi-restraints excluded: chain L residue 407 LEU Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 305 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 369 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 395 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 318 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 chunk 292 optimal weight: 0.6980 chunk 376 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 ASN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN D 304 GLN E 36 ASN H 304 GLN ** H 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 304 GLN ** L 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 ASN O 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.229797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.200861 restraints weight = 119925.518| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.74 r_work: 0.3857 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work: 0.3712 rms_B_bonded: 4.22 restraints_weight: 0.1250 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 39 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (15 function evaluations) r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35404 Z= 0.133 Angle : 0.626 11.217 48120 Z= 0.328 Chirality : 0.044 0.163 5128 Planarity : 0.005 0.042 6240 Dihedral : 5.037 21.992 4816 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.61 % Allowed : 11.04 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.12), residues: 4320 helix: 1.68 (0.12), residues: 1768 sheet: -0.96 (0.17), residues: 584 loop : -0.00 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 41 TYR 0.011 0.002 TYR N 283 PHE 0.021 0.002 PHE N 345 TRP 0.008 0.001 TRP G 4 HIS 0.010 0.001 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (35400) covalent geometry : angle 0.62524 / 0.33 (48112) SS BOND : bond 0.00967 / 0.48 ( 4) SS BOND : angle 2.53097 / 1.59 ( 8) hydrogen bonds : bond 0.03894 / 2.52 ( 1632) hydrogen bonds : angle 6.06829 / 4.31 ( 4464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 507 time to evaluate : 1.372 Fit side-chains REVERT: S 123 PHE cc_start: 0.7625 (t80) cc_final: 0.7412 (t80) REVERT: B 392 GLU cc_start: 0.6803 (tm-30) cc_final: 0.6561 (tm-30) REVERT: D 392 GLU cc_start: 0.6780 (tm-30) cc_final: 0.6540 (tm-30) REVERT: F 392 GLU cc_start: 0.6787 (tm-30) cc_final: 0.6535 (tm-30) REVERT: G 123 PHE cc_start: 0.7612 (t80) cc_final: 0.7398 (t80) REVERT: I 92 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7656 (ttmt) REVERT: J 392 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6555 (tm-30) REVERT: K 92 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7639 (ttmt) REVERT: K 123 PHE cc_start: 0.7593 (t80) cc_final: 0.7380 (t80) REVERT: L 392 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6568 (tm-30) REVERT: M 123 PHE cc_start: 0.7603 (t80) cc_final: 0.7388 (t80) REVERT: N 392 GLU cc_start: 0.6811 (tm-30) cc_final: 0.6566 (tm-30) REVERT: O 123 PHE cc_start: 0.7571 (t80) cc_final: 0.7358 (t80) outliers start: 22 outliers final: 10 residues processed: 520 average time/residue: 0.7785 time to fit residues: 485.8965 Evaluate side-chains 510 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 498 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 445 ILE Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 172 CYS Chi-restraints excluded: chain J residue 445 ILE Chi-restraints excluded: chain K residue 92 LYS Chi-restraints excluded: chain L residue 172 CYS Chi-restraints excluded: chain N residue 172 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 401 optimal weight: 6.9990 chunk 246 optimal weight: 30.0000 chunk 130 optimal weight: 10.0000 chunk 412 optimal weight: 9.9990 chunk 210 optimal weight: 9.9990 chunk 327 optimal weight: 10.0000 chunk 394 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 358 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 328 optimal weight: 1.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN S 36 ASN B 304 GLN C 36 ASN D 304 GLN E 36 ASN F 304 GLN H 304 GLN I 96 ASN A J 304 GLN K 96 ASN A L 304 GLN M 36 ASN N 304 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.223797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.193549 restraints weight = 117991.957| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.68 r_work: 0.3754 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work: 0.3621 rms_B_bonded: 4.03 restraints_weight: 0.1250 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (14 function evaluations) r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 35404 Z= 0.348 Angle : 0.910 11.528 48120 Z= 0.484 Chirality : 0.053 0.209 5128 Planarity : 0.008 0.064 6240 Dihedral : 5.541 24.187 4816 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.88 % Allowed : 10.93 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.12), residues: 4320 helix: 1.13 (0.11), residues: 1744 sheet: -0.85 (0.17), residues: 688 loop : -0.17 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 167 TYR 0.034 0.005 TYR I 61 PHE 0.033 0.004 PHE D 311 TRP 0.011 0.003 TRP N 214 HIS 0.021 0.003 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.35 (35400) covalent geometry : angle 0.90877 / 0.48 (48112) SS BOND : bond 0.01113 / 0.56 ( 4) SS BOND : angle 4.10285 / 2.58 ( 8) hydrogen bonds : bond 0.05891 / 3.82 ( 1632) hydrogen bonds : angle 6.78589 / 4.83 ( 4464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 462 time to evaluate : 1.303 Fit side-chains REVERT: A 117 PHE cc_start: 0.8001 (m-80) cc_final: 0.7798 (m-80) REVERT: S 123 PHE cc_start: 0.7698 (t80) cc_final: 0.7412 (t80) REVERT: C 123 PHE cc_start: 0.7619 (t80) cc_final: 0.7408 (t80) REVERT: E 123 PHE cc_start: 0.7640 (t80) cc_final: 0.7395 (t80) REVERT: G 123 PHE cc_start: 0.7669 (t80) cc_final: 0.7377 (t80) REVERT: I 92 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7667 (ttmt) REVERT: J 117 PHE cc_start: 0.8002 (m-80) cc_final: 0.7780 (m-80) REVERT: K 92 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7644 (ttmt) REVERT: K 123 PHE cc_start: 0.7646 (t80) cc_final: 0.7361 (t80) REVERT: M 123 PHE cc_start: 0.7610 (t80) cc_final: 0.7298 (t80) REVERT: O 123 PHE cc_start: 0.7609 (t80) cc_final: 0.7291 (t80) outliers start: 32 outliers final: 11 residues processed: 478 average time/residue: 0.7236 time to fit residues: 413.1358 Evaluate side-chains 472 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 459 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 305 LYS Chi-restraints excluded: chain I residue 92 LYS Chi-restraints excluded: chain J residue 172 CYS Chi-restraints excluded: chain J residue 305 LYS Chi-restraints excluded: chain J residue 445 ILE Chi-restraints excluded: chain K residue 92 LYS Chi-restraints excluded: chain L residue 172 CYS Chi-restraints excluded: chain N residue 172 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 337 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 290 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 304 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 318 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 166 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.2567 > 50:) chunk 246 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 ASN B 304 GLN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN D 304 GLN ** D 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN F 304 GLN H 304 GLN J 304 GLN L 304 GLN ** L 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 ASN N 304 GLN ** N 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.226380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.196796 restraints weight = 119994.369| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.72 r_work: 0.3814 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 35404 Z= 0.193 Angle : 0.723 11.861 48120 Z= 0.379 Chirality : 0.047 0.175 5128 Planarity : 0.005 0.042 6240 Dihedral : 5.285 23.312 4816 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.41 % Allowed : 11.23 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.12), residues: 4320 helix: 1.39 (0.12), residues: 1768 sheet: -0.86 (0.17), residues: 640 loop : -0.06 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 41 TYR 0.019 0.003 TYR M 61 PHE 0.019 0.003 PHE F 345 TRP 0.006 0.002 TRP E 4 HIS 0.014 0.002 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (35400) covalent geometry : angle 0.72218 / 0.38 (48112) SS BOND : bond 0.00923 / 0.46 ( 4) SS BOND : angle 2.97567 / 1.87 ( 8) hydrogen bonds : bond 0.04626 / 2.99 ( 1632) hydrogen bonds : angle 6.36294 / 4.52 ( 4464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 472 time to evaluate : 1.029 Fit side-chains REVERT: A 392 GLU cc_start: 0.6687 (tm-30) cc_final: 0.6411 (tm-30) REVERT: B 392 GLU cc_start: 0.6666 (tm-30) cc_final: 0.6400 (tm-30) REVERT: D 392 GLU cc_start: 0.6592 (tm-30) cc_final: 0.6313 (tm-30) REVERT: H 392 GLU cc_start: 0.6650 (tm-30) cc_final: 0.6397 (tm-30) REVERT: J 392 GLU cc_start: 0.6655 (tm-30) cc_final: 0.6388 (tm-30) REVERT: K 92 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7564 (ttmt) REVERT: M 123 PHE cc_start: 0.7571 (t80) cc_final: 0.7343 (t80) REVERT: O 123 PHE cc_start: 0.7570 (t80) cc_final: 0.7348 (t80) outliers start: 15 outliers final: 11 residues processed: 480 average time/residue: 0.7344 time to fit residues: 418.3116 Evaluate side-chains 473 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 461 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 445 ILE Chi-restraints excluded: chain J residue 172 CYS Chi-restraints excluded: chain J residue 445 ILE Chi-restraints excluded: chain K residue 92 LYS Chi-restraints excluded: chain L residue 172 CYS Chi-restraints excluded: chain N residue 172 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 299 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 137 optimal weight: 0.0770 chunk 239 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 397 optimal weight: 0.3980 chunk 373 optimal weight: 0.9980 chunk 151 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 ASN B 304 GLN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN D 304 GLN ** D 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN F 304 GLN H 304 GLN J 304 GLN L 304 GLN ** L 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 ASN N 304 GLN ** N 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.229261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.199782 restraints weight = 123616.311| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.86 r_work: 0.3846 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 92 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.3718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35404 Z= 0.146 Angle : 0.659 12.520 48120 Z= 0.344 Chirality : 0.044 0.171 5128 Planarity : 0.005 0.040 6240 Dihedral : 5.023 22.274 4816 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.36 % Allowed : 11.42 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.12), residues: 4320 helix: 1.69 (0.12), residues: 1768 sheet: -1.05 (0.17), residues: 584 loop : 0.04 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 41 TYR 0.014 0.002 TYR I 61 PHE 0.020 0.002 PHE B 345 TRP 0.010 0.001 TRP E 4 HIS 0.012 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (35400) covalent geometry : angle 0.65854 / 0.34 (48112) SS BOND : bond 0.00923 / 0.46 ( 4) SS BOND : angle 2.75977 / 1.73 ( 8) hydrogen bonds : bond 0.04018 / 2.60 ( 1632) hydrogen bonds : angle 6.05439 / 4.30 ( 4464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 499 time to evaluate : 1.105 Fit side-chains REVERT: A 392 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6478 (tm-30) REVERT: B 356 LYS cc_start: 0.6372 (ttmm) cc_final: 0.6141 (ttmt) REVERT: B 392 GLU cc_start: 0.6730 (tm-30) cc_final: 0.6476 (tm-30) REVERT: C 18 LEU cc_start: 0.7486 (mt) cc_final: 0.7149 (mp) REVERT: D 392 GLU cc_start: 0.6595 (tm-30) cc_final: 0.6320 (tm-30) REVERT: F 392 GLU cc_start: 0.6731 (tm-30) cc_final: 0.6458 (tm-30) REVERT: H 392 GLU cc_start: 0.6701 (tm-30) cc_final: 0.6461 (tm-30) REVERT: J 392 GLU cc_start: 0.6705 (tm-30) cc_final: 0.6447 (tm-30) REVERT: L 392 GLU cc_start: 0.6580 (tm-30) cc_final: 0.6315 (tm-30) REVERT: M 123 PHE cc_start: 0.7580 (t80) cc_final: 0.7373 (t80) REVERT: N 392 GLU cc_start: 0.6730 (tm-30) cc_final: 0.6449 (tm-30) REVERT: O 123 PHE cc_start: 0.7568 (t80) cc_final: 0.7356 (t80) outliers start: 13 outliers final: 10 residues processed: 507 average time/residue: 0.7040 time to fit residues: 424.5114 Evaluate side-chains 496 residues out of total 3440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 486 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 445 ILE Chi-restraints excluded: chain J residue 172 CYS Chi-restraints excluded: chain J residue 445 ILE Chi-restraints excluded: chain L residue 172 CYS Chi-restraints excluded: chain N residue 172 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 266 optimal weight: 6.9990 chunk 241 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 293 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 ASN B 304 GLN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN D 304 GLN ** D 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN F 304 GLN H 304 GLN J 304 GLN L 304 GLN ** L 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 ASN N 304 GLN ** N 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.226567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.196692 restraints weight = 120770.089| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.76 r_work: 0.3814 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work: 0.3687 rms_B_bonded: 3.68 restraints_weight: 0.1250 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 92 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 92 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 35404 Z= 0.203 Angle : 0.735 11.369 48120 Z= 0.387 Chirality : 0.047 0.179 5128 Planarity : 0.006 0.040 6240 Dihedral : 5.197 23.691 4816 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.50 % Allowed : 11.26 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.12), residues: 4320 helix: 1.51 (0.12), residues: 1768 sheet: -0.87 (0.17), residues: 640 loop : 0.06 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 41 TYR 0.021 0.003 TYR O 61 PHE 0.023 0.003 PHE F 311 TRP 0.006 0.002 TRP J 451 HIS 0.014 0.002 HIS D 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (35400) covalent geometry : angle 0.73431 / 0.39 (48112) SS BOND : bond 0.00899 / 0.45 ( 4) SS BOND : angle 2.94070 / 1.85 ( 8) hydrogen bonds : bond 0.04624 / 3.00 ( 1632) hydrogen bonds : angle 6.27312 / 4.46 ( 4464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19915.71 seconds wall clock time: 338 minutes 56.60 seconds (20336.60 seconds total)