Starting phenix.real_space_refine on Tue Aug 26 03:21:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bcm_15966/08_2025/8bcm_15966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bcm_15966/08_2025/8bcm_15966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bcm_15966/08_2025/8bcm_15966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bcm_15966/08_2025/8bcm_15966.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bcm_15966/08_2025/8bcm_15966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bcm_15966/08_2025/8bcm_15966.map" } resolution = 2.15 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= 0.003 sd= 0.169 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 184 5.16 5 C 21312 2.51 5 N 5848 2.21 5 O 6176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33520 Number of models: 1 Model: "" Number of chains: 16 Chain: "D" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 857 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "C" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3333 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain breaks: 3 Chain: "E" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 857 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "K" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 857 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 857 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "L" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 857 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "O" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 857 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "M" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 857 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "P" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 857 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "B" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3333 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain breaks: 3 Chain: "A" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3333 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain breaks: 3 Chain: "H" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3333 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain breaks: 3 Chain: "F" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3333 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain breaks: 3 Chain: "I" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3333 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain breaks: 3 Chain: "G" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3333 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain breaks: 3 Chain: "J" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3333 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain breaks: 3 Time building chain proxies: 8.59, per 1000 atoms: 0.26 Number of scatterers: 33520 At special positions: 0 Unit cell: (146.91, 146.91, 122.01, 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 184 16.00 O 6176 8.00 N 5848 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 247 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS B 247 " - pdb=" SG CYS I 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS J 247 " distance=2.04 Simple disulfide: pdb=" SG CYS H 247 " - pdb=" SG CYS F 247 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 1.9 microseconds 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7776 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 32 sheets defined 51.5% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 67 through 82 removed outlier: 4.065A pdb=" N VAL D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 25 removed outlier: 3.539A pdb=" N TYR C 25 " --> pdb=" O LYS C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 25' Processing helix chain 'C' and resid 49 through 61 Processing helix chain 'C' and resid 69 through 75 Processing helix chain 'C' and resid 77 through 81 removed outlier: 3.526A pdb=" N TYR C 80 " --> pdb=" O MET C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.598A pdb=" N PHE C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 122 Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 153 through 163 removed outlier: 4.262A pdb=" N VAL C 157 " --> pdb=" O HIS C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 196 removed outlier: 3.638A pdb=" N GLY C 196 " --> pdb=" O CYS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 Processing helix chain 'C' and resid 246 through 260 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 273 through 288 Processing helix chain 'C' and resid 297 through 303 removed outlier: 4.019A pdb=" N ILE C 301 " --> pdb=" O MET C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 322 removed outlier: 3.659A pdb=" N LEU C 314 " --> pdb=" O HIS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 351 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 383 through 385 No H-bonds generated for 'chain 'C' and resid 383 through 385' Processing helix chain 'C' and resid 386 through 395 Processing helix chain 'C' and resid 413 through 434 Processing helix chain 'C' and resid 436 through 451 removed outlier: 5.903A pdb=" N GLY C 442 " --> pdb=" O TYR C 438 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 461 Processing helix chain 'E' and resid 22 through 37 Processing helix chain 'E' and resid 67 through 82 removed outlier: 4.070A pdb=" N VAL E 71 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 67 through 82 removed outlier: 4.060A pdb=" N VAL K 71 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 36 Processing helix chain 'N' and resid 67 through 82 removed outlier: 4.069A pdb=" N VAL N 71 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 37 Processing helix chain 'L' and resid 67 through 82 removed outlier: 4.078A pdb=" N VAL L 71 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 36 Processing helix chain 'O' and resid 67 through 82 removed outlier: 4.073A pdb=" N VAL O 71 " --> pdb=" O SER O 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 36 Processing helix chain 'M' and resid 67 through 82 removed outlier: 4.065A pdb=" N VAL M 71 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 37 Processing helix chain 'P' and resid 67 through 82 removed outlier: 4.085A pdb=" N VAL P 71 " --> pdb=" O SER P 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 25 removed outlier: 3.539A pdb=" N TYR B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 21 through 25' Processing helix chain 'B' and resid 49 through 61 Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.538A pdb=" N TYR B 80 " --> pdb=" O MET B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.598A pdb=" N PHE B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) 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 153 through 163 removed outlier: 4.262A pdb=" N VAL B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 removed outlier: 3.639A pdb=" N GLY B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 233 Processing helix chain 'B' and resid 246 through 260 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: 4.023A pdb=" N ILE B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.660A 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 413 through 434 Processing helix chain 'B' and resid 436 through 451 removed outlier: 5.853A pdb=" N GLY B 442 " --> pdb=" O TYR B 438 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASP B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TRP B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'A' and resid 21 through 25 removed outlier: 3.550A pdb=" N TYR A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 21 through 25' Processing helix chain 'A' and resid 49 through 61 Processing helix chain 'A' and resid 69 through 75 Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.599A pdb=" N PHE A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) 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 153 through 163 removed outlier: 4.261A pdb=" N VAL A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 removed outlier: 3.637A pdb=" N GLY A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 246 through 260 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: 4.027A pdb=" N ILE A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.660A 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 413 through 434 Processing helix chain 'A' and resid 436 through 451 removed outlier: 5.869A pdb=" N GLY A 442 " --> pdb=" O TYR A 438 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASP A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'H' and resid 21 through 25 removed outlier: 3.557A pdb=" N TYR H 25 " --> pdb=" O LYS H 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 21 through 25' Processing helix chain 'H' and resid 49 through 61 Processing helix chain 'H' and resid 69 through 75 Processing helix chain 'H' and resid 77 through 81 Processing helix chain 'H' and resid 104 through 108 removed outlier: 3.598A pdb=" N PHE H 108 " --> pdb=" O LEU H 105 " (cutoff:3.500A) 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 153 through 163 removed outlier: 4.262A pdb=" N VAL H 157 " --> pdb=" O HIS H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 196 removed outlier: 3.637A pdb=" N GLY H 196 " --> pdb=" O CYS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 233 Processing helix chain 'H' and resid 246 through 260 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: 4.028A pdb=" N ILE H 301 " --> pdb=" O MET H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 322 removed outlier: 3.659A 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 413 through 434 Processing helix chain 'H' and resid 436 through 451 removed outlier: 5.926A pdb=" N GLY H 442 " --> pdb=" O TYR H 438 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP H 443 " --> pdb=" O ARG H 439 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TRP H 451 " --> pdb=" O GLU H 447 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 461 Processing helix chain 'F' and resid 21 through 25 removed outlier: 3.549A pdb=" N TYR F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 21 through 25' Processing helix chain 'F' and resid 49 through 61 Processing helix chain 'F' and resid 69 through 75 Processing helix chain 'F' and resid 77 through 81 removed outlier: 3.516A pdb=" N TYR F 80 " --> pdb=" O MET F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.599A pdb=" N PHE F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) 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 153 through 163 removed outlier: 4.262A pdb=" N VAL F 157 " --> pdb=" O HIS F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 196 removed outlier: 3.638A pdb=" N GLY F 196 " --> pdb=" O CYS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 Processing helix chain 'F' and resid 246 through 260 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: 4.026A pdb=" N ILE F 301 " --> pdb=" O MET F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 322 removed outlier: 3.659A 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 413 through 434 Processing helix chain 'F' and resid 436 through 451 removed outlier: 5.869A pdb=" N GLY F 442 " --> pdb=" O TYR F 438 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP F 443 " --> pdb=" O ARG F 439 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 461 Processing helix chain 'I' and resid 21 through 25 removed outlier: 3.546A pdb=" N TYR I 25 " --> pdb=" O LYS I 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 21 through 25' Processing helix chain 'I' and resid 49 through 61 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'I' and resid 77 through 81 removed outlier: 3.502A pdb=" N TYR I 80 " --> pdb=" O MET I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 108 removed outlier: 3.599A pdb=" N PHE I 108 " --> pdb=" O LEU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 122 Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 141 through 146 Processing helix chain 'I' and resid 153 through 163 removed outlier: 4.262A pdb=" N VAL I 157 " --> pdb=" O HIS I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 196 removed outlier: 3.639A pdb=" N GLY I 196 " --> pdb=" O CYS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 233 Processing helix chain 'I' and resid 246 through 260 Processing helix chain 'I' and resid 269 through 273 Processing helix chain 'I' and resid 273 through 288 Processing helix chain 'I' and resid 297 through 303 removed outlier: 4.021A pdb=" N ILE I 301 " --> pdb=" O MET I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 322 removed outlier: 3.659A pdb=" N LEU I 314 " --> pdb=" O HIS I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 351 Processing helix chain 'I' and resid 357 through 361 Processing helix chain 'I' and resid 383 through 385 No H-bonds generated for 'chain 'I' and resid 383 through 385' Processing helix chain 'I' and resid 386 through 395 Processing helix chain 'I' and resid 413 through 434 Processing helix chain 'I' and resid 436 through 451 removed outlier: 5.912A pdb=" N GLY I 442 " --> pdb=" O TYR I 438 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP I 443 " --> pdb=" O ARG I 439 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TRP I 451 " --> pdb=" O GLU I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 452 through 461 Processing helix chain 'G' and resid 21 through 25 removed outlier: 3.551A pdb=" N TYR G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 21 through 25' Processing helix chain 'G' and resid 49 through 61 Processing helix chain 'G' and resid 69 through 75 Processing helix chain 'G' and resid 77 through 81 Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.597A pdb=" N PHE G 108 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 122 Processing helix chain 'G' and resid 123 through 127 Processing helix chain 'G' and resid 141 through 146 Processing helix chain 'G' and resid 153 through 163 removed outlier: 4.262A pdb=" N VAL G 157 " --> pdb=" O HIS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 196 removed outlier: 3.638A pdb=" N GLY G 196 " --> pdb=" O CYS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 233 Processing helix chain 'G' and resid 246 through 260 Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'G' and resid 273 through 288 Processing helix chain 'G' and resid 297 through 303 removed outlier: 4.026A pdb=" N ILE G 301 " --> pdb=" O MET G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.658A pdb=" N LEU G 314 " --> pdb=" O HIS G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 351 Processing helix chain 'G' and resid 357 through 361 Processing helix chain 'G' and resid 383 through 385 No H-bonds generated for 'chain 'G' and resid 383 through 385' Processing helix chain 'G' and resid 386 through 395 Processing helix chain 'G' and resid 413 through 434 Processing helix chain 'G' and resid 436 through 451 removed outlier: 5.878A pdb=" N GLY G 442 " --> pdb=" O TYR G 438 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASP G 443 " --> pdb=" O ARG G 439 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP G 451 " --> pdb=" O GLU G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 461 Processing helix chain 'J' and resid 21 through 25 removed outlier: 3.552A pdb=" N TYR J 25 " --> pdb=" O LYS J 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 21 through 25' Processing helix chain 'J' and resid 49 through 61 Processing helix chain 'J' and resid 69 through 75 Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.503A pdb=" N TYR J 80 " --> pdb=" O MET J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 108 removed outlier: 3.599A pdb=" N PHE J 108 " --> pdb=" O LEU J 105 " (cutoff:3.500A) 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 153 through 163 removed outlier: 4.262A pdb=" N VAL J 157 " --> pdb=" O HIS J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 196 removed outlier: 3.638A pdb=" N GLY J 196 " --> pdb=" O CYS J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 233 Processing helix chain 'J' and resid 246 through 260 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: 4.021A pdb=" N ILE J 301 " --> pdb=" O MET J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 322 removed outlier: 3.659A 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 413 through 434 Processing helix chain 'J' and resid 436 through 451 removed outlier: 5.894A pdb=" N GLY J 442 " --> pdb=" O TYR J 438 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASP J 443 " --> pdb=" O ARG J 439 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TRP J 451 " --> pdb=" O GLU J 447 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 461 Processing sheet with id=AA1, first strand: chain 'D' and resid 56 through 57 removed outlier: 6.209A pdb=" N ILE D 87 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP D 93 " --> pdb=" O GLN D 99 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLN D 99 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 89 removed outlier: 5.443A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU C 37 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 169 through 173 removed outlier: 6.492A pdb=" N LEU C 170 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LYS C 201 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS C 172 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR C 200 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASN C 241 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N HIS C 238 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N MET C 266 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU C 240 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP C 268 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE C 265 " --> pdb=" O HIS C 292 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N HIS C 294 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N HIS C 267 " --> pdb=" O HIS C 294 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU C 291 " --> pdb=" O HIS C 325 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N HIS C 327 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE C 293 " --> pdb=" O HIS C 327 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN C 401 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA C 378 " --> pdb=" O GLN C 401 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET C 169 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE C 402 " --> pdb=" O MET C 169 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY C 171 " --> pdb=" O PHE C 402 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 57 removed outlier: 6.206A pdb=" N ILE E 87 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP E 93 " --> pdb=" O GLN E 99 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN E 99 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 56 through 57 removed outlier: 6.204A pdb=" N ILE K 87 " --> pdb=" O VAL K 105 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP K 93 " --> pdb=" O GLN K 99 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLN K 99 " --> pdb=" O ASP K 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 56 through 57 removed outlier: 6.211A pdb=" N ILE N 87 " --> pdb=" O VAL N 105 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP N 93 " --> pdb=" O GLN N 99 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN N 99 " --> pdb=" O ASP N 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 56 through 57 removed outlier: 6.205A pdb=" N ILE L 87 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP L 93 " --> pdb=" O GLN L 99 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN L 99 " --> pdb=" O ASP L 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 56 through 57 removed outlier: 6.209A pdb=" N ILE O 87 " --> pdb=" O VAL O 105 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP O 93 " --> pdb=" O GLN O 99 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLN O 99 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 56 through 57 removed outlier: 6.210A pdb=" N ILE M 87 " --> pdb=" O VAL M 105 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP M 93 " --> pdb=" O GLN M 99 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLN M 99 " --> pdb=" O ASP M 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 56 through 57 removed outlier: 6.215A pdb=" N ILE P 87 " --> pdb=" O VAL P 105 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP P 93 " --> pdb=" O GLN P 99 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLN P 99 " --> pdb=" O ASP P 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 83 through 89 removed outlier: 5.439A pdb=" N CYS B 84 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 102 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU B 37 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE B 138 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 39 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 169 through 173 removed outlier: 6.492A pdb=" N LEU B 170 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS B 201 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS B 172 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR B 200 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASN B 241 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N HIS B 238 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N MET B 266 " --> pdb=" O HIS B 238 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU B 240 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ASP B 268 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE B 265 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N HIS B 294 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N HIS B 267 " --> pdb=" O HIS B 294 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 291 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N HIS B 327 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE B 293 " --> pdb=" O HIS B 327 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLN B 401 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA B 378 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET B 169 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE B 402 " --> pdb=" O MET B 169 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY B 171 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AB6, first strand: chain 'A' and resid 83 through 89 removed outlier: 5.445A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A 37 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 169 through 173 removed outlier: 6.492A pdb=" N LEU A 170 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LYS A 201 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS A 172 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR A 200 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASN A 241 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N HIS A 238 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N MET A 266 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU A 240 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ASP A 268 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 265 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N HIS A 294 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N HIS A 267 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 291 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N HIS A 327 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE A 293 " --> pdb=" O HIS A 327 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA A 378 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET A 169 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE A 402 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY A 171 " --> pdb=" O PHE A 402 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AB9, first strand: chain 'H' and resid 83 through 89 removed outlier: 5.444A pdb=" N CYS H 84 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA H 102 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU H 37 " --> pdb=" O ILE H 138 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE H 138 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA H 39 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 169 through 173 removed outlier: 6.491A pdb=" N LEU H 170 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LYS H 201 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS H 172 " --> pdb=" O LYS H 201 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR H 200 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASN H 241 " --> pdb=" O THR H 200 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N HIS H 238 " --> pdb=" O ILE H 264 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N MET H 266 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU H 240 " --> pdb=" O MET H 266 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ASP H 268 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE H 265 " --> pdb=" O HIS H 292 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N HIS H 294 " --> pdb=" O ILE H 265 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N HIS H 267 " --> pdb=" O HIS H 294 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU H 291 " --> pdb=" O HIS H 325 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N HIS H 327 " --> pdb=" O LEU H 291 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE H 293 " --> pdb=" O HIS H 327 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLN H 401 " --> pdb=" O PRO H 376 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA H 378 " --> pdb=" O GLN H 401 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N MET H 169 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N PHE H 402 " --> pdb=" O MET H 169 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY H 171 " --> pdb=" O PHE H 402 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 353 through 354 Processing sheet with id=AC3, first strand: chain 'F' and resid 83 through 89 removed outlier: 5.443A pdb=" N CYS F 84 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA F 102 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU F 37 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE F 138 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA F 39 " --> pdb=" O GLU F 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 169 through 173 removed outlier: 6.492A pdb=" N LEU F 170 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS F 201 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS F 172 " --> pdb=" O LYS F 201 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR F 200 " --> pdb=" O TYR F 239 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASN F 241 " --> pdb=" O THR F 200 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N HIS F 238 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N MET F 266 " --> pdb=" O HIS F 238 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU F 240 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ASP F 268 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE F 265 " --> pdb=" O HIS F 292 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N HIS F 294 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N HIS F 267 " --> pdb=" O HIS F 294 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU F 291 " --> pdb=" O HIS F 325 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N HIS F 327 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE F 293 " --> pdb=" O HIS F 327 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLN F 401 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA F 378 " --> pdb=" O GLN F 401 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET F 169 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE F 402 " --> pdb=" O MET F 169 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY F 171 " --> pdb=" O PHE F 402 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AC6, first strand: chain 'I' and resid 83 through 89 removed outlier: 5.436A pdb=" N CYS I 84 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA I 102 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU I 37 " --> pdb=" O ILE I 138 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE I 138 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA I 39 " --> pdb=" O GLU I 136 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 169 through 173 removed outlier: 6.493A pdb=" N LEU I 170 " --> pdb=" O PHE I 199 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS I 201 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS I 172 " --> pdb=" O LYS I 201 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR I 200 " --> pdb=" O TYR I 239 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASN I 241 " --> pdb=" O THR I 200 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N HIS I 238 " --> pdb=" O ILE I 264 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N MET I 266 " --> pdb=" O HIS I 238 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU I 240 " --> pdb=" O MET I 266 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASP I 268 " --> pdb=" O LEU I 240 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE I 265 " --> pdb=" O HIS I 292 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N HIS I 294 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N HIS I 267 " --> pdb=" O HIS I 294 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU I 291 " --> pdb=" O HIS I 325 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N HIS I 327 " --> pdb=" O LEU I 291 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE I 293 " --> pdb=" O HIS I 327 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLN I 401 " --> pdb=" O PRO I 376 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA I 378 " --> pdb=" O GLN I 401 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET I 169 " --> pdb=" O LEU I 400 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE I 402 " --> pdb=" O MET I 169 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY I 171 " --> pdb=" O PHE I 402 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 353 through 354 Processing sheet with id=AC9, first strand: chain 'G' and resid 83 through 89 removed outlier: 5.444A pdb=" N CYS G 84 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA G 102 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU G 37 " --> pdb=" O ILE G 138 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE G 138 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA G 39 " --> pdb=" O GLU G 136 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 169 through 173 removed outlier: 6.492A pdb=" N LEU G 170 " --> pdb=" O PHE G 199 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LYS G 201 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS G 172 " --> pdb=" O LYS G 201 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR G 200 " --> pdb=" O TYR G 239 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASN G 241 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N HIS G 238 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N MET G 266 " --> pdb=" O HIS G 238 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU G 240 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASP G 268 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE G 265 " --> pdb=" O HIS G 292 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N HIS G 294 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N HIS G 267 " --> pdb=" O HIS G 294 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU G 291 " --> pdb=" O HIS G 325 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N HIS G 327 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE G 293 " --> pdb=" O HIS G 327 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLN G 401 " --> pdb=" O PRO G 376 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA G 378 " --> pdb=" O GLN G 401 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET G 169 " --> pdb=" O LEU G 400 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE G 402 " --> pdb=" O MET G 169 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY G 171 " --> pdb=" O PHE G 402 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 353 through 354 Processing sheet with id=AD3, first strand: chain 'J' and resid 83 through 89 removed outlier: 5.435A pdb=" N CYS J 84 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA J 102 " --> pdb=" O CYS J 84 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU J 37 " --> pdb=" O ILE J 138 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE J 138 " --> pdb=" O LEU J 37 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA J 39 " --> pdb=" O GLU J 136 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 169 through 173 removed outlier: 6.492A pdb=" N LEU J 170 " --> pdb=" O PHE J 199 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS J 201 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS J 172 " --> pdb=" O LYS J 201 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR J 200 " --> pdb=" O TYR J 239 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASN J 241 " --> pdb=" O THR J 200 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N HIS J 238 " --> pdb=" O ILE J 264 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N MET J 266 " --> pdb=" O HIS J 238 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU J 240 " --> pdb=" O MET J 266 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASP J 268 " --> pdb=" O LEU J 240 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE J 265 " --> pdb=" O HIS J 292 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N HIS J 294 " --> pdb=" O ILE J 265 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N HIS J 267 " --> pdb=" O HIS J 294 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU J 291 " --> pdb=" O HIS J 325 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N HIS J 327 " --> pdb=" O LEU J 291 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE J 293 " --> pdb=" O HIS J 327 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLN J 401 " --> pdb=" O PRO J 376 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA J 378 " --> pdb=" O GLN J 401 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET J 169 " --> pdb=" O LEU J 400 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE J 402 " --> pdb=" O MET J 169 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY J 171 " --> pdb=" O PHE J 402 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 353 through 354 1623 hydrogen bonds defined for protein. 4452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.82 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11115 1.34 - 1.46: 6454 1.46 - 1.58: 16503 1.58 - 1.70: 0 1.70 - 1.81: 280 Bond restraints: 34352 Sorted by residual: bond pdb=" CG1 ILE B 101 " pdb=" CD1 ILE B 101 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.79e+00 bond pdb=" CG1 ILE J 101 " pdb=" CD1 ILE J 101 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.79e+00 bond pdb=" CG1 ILE C 101 " pdb=" CD1 ILE C 101 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.79e+00 bond pdb=" CG1 ILE A 101 " pdb=" CD1 ILE A 101 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.77e+00 bond pdb=" CG1 ILE F 101 " pdb=" CD1 ILE F 101 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.77e+00 ... (remaining 34347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 45599 2.00 - 3.99: 757 3.99 - 5.99: 116 5.99 - 7.98: 8 7.98 - 9.98: 16 Bond angle restraints: 46496 Sorted by residual: angle pdb=" N GLU K 13 " pdb=" CA GLU K 13 " pdb=" C GLU K 13 " ideal model delta sigma weight residual 111.07 114.66 -3.59 1.07e+00 8.73e-01 1.13e+01 angle pdb=" N GLU M 13 " pdb=" CA GLU M 13 " pdb=" C GLU M 13 " ideal model delta sigma weight residual 111.07 114.66 -3.59 1.07e+00 8.73e-01 1.12e+01 angle pdb=" N GLU N 13 " pdb=" CA GLU N 13 " pdb=" C GLU N 13 " ideal model delta sigma weight residual 111.07 114.63 -3.56 1.07e+00 8.73e-01 1.11e+01 angle pdb=" N GLU P 13 " pdb=" CA GLU P 13 " pdb=" C GLU P 13 " ideal model delta sigma weight residual 111.07 114.61 -3.54 1.07e+00 8.73e-01 1.10e+01 angle pdb=" N GLU L 13 " pdb=" CA GLU L 13 " pdb=" C GLU L 13 " ideal model delta sigma weight residual 111.07 114.57 -3.50 1.07e+00 8.73e-01 1.07e+01 ... (remaining 46491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17889 17.95 - 35.90: 1783 35.90 - 53.86: 514 53.86 - 71.81: 98 71.81 - 89.76: 80 Dihedral angle restraints: 20364 sinusoidal: 8268 harmonic: 12096 Sorted by residual: dihedral pdb=" CB CYS H 247 " pdb=" SG CYS H 247 " pdb=" SG CYS F 247 " pdb=" CB CYS F 247 " ideal model delta sinusoidal sigma weight residual -86.00 -155.06 69.06 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CB CYS C 247 " pdb=" SG CYS C 247 " pdb=" SG CYS G 247 " pdb=" CB CYS G 247 " ideal model delta sinusoidal sigma weight residual -86.00 -154.97 68.97 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " pdb=" SG CYS J 247 " pdb=" CB CYS J 247 " ideal model delta sinusoidal sigma weight residual -86.00 -154.96 68.96 1 1.00e+01 1.00e-02 6.15e+01 ... (remaining 20361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3128 0.039 - 0.078: 1352 0.078 - 0.117: 394 0.117 - 0.156: 54 0.156 - 0.194: 16 Chirality restraints: 4944 Sorted by residual: chirality pdb=" CG LEU I 318 " pdb=" CB LEU I 318 " pdb=" CD1 LEU I 318 " pdb=" CD2 LEU I 318 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CG LEU A 318 " pdb=" CB LEU A 318 " pdb=" CD1 LEU A 318 " pdb=" CD2 LEU A 318 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" CG LEU J 318 " pdb=" CB LEU J 318 " pdb=" CD1 LEU J 318 " pdb=" CD2 LEU J 318 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 4941 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 60 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO D 61 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 61 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 61 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU N 60 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.76e+00 pdb=" N PRO N 61 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO N 61 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 61 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU O 60 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO O 61 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO O 61 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO O 61 " 0.038 5.00e-02 4.00e+02 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 408 2.64 - 3.20: 29858 3.20 - 3.77: 58092 3.77 - 4.33: 82489 4.33 - 4.90: 130495 Nonbonded interactions: 301342 Sorted by model distance: nonbonded pdb=" O PHE N 12 " pdb=" OG SER N 16 " model vdw 2.070 3.040 nonbonded pdb=" O PHE P 12 " pdb=" OG SER P 16 " model vdw 2.072 3.040 nonbonded pdb=" O PHE K 12 " pdb=" OG SER K 16 " model vdw 2.074 3.040 nonbonded pdb=" O PHE E 12 " pdb=" OG SER E 16 " model vdw 2.076 3.040 nonbonded pdb=" O PHE D 12 " pdb=" OG SER D 16 " model vdw 2.076 3.040 ... (remaining 301337 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 35.050 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 34356 Z= 0.218 Angle : 0.668 9.978 46504 Z= 0.354 Chirality : 0.046 0.194 4944 Planarity : 0.005 0.071 6096 Dihedral : 16.841 89.762 12576 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.78 % Favored : 97.03 % Rotamer: Outliers : 0.85 % Allowed : 14.99 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.12), residues: 4136 helix: 1.58 (0.12), residues: 1720 sheet: 0.05 (0.17), residues: 736 loop : -0.06 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 435 TYR 0.010 0.002 TYR I 239 PHE 0.028 0.003 PHE B 345 TRP 0.020 0.002 TRP L 58 HIS 0.005 0.001 HIS H 153 Details of bonding type rmsd covalent geometry : bond 0.00492 (34352) covalent geometry : angle 0.66768 (46496) SS BOND : bond 0.01324 ( 4) SS BOND : angle 0.24995 ( 8) hydrogen bonds : bond 0.15257 ( 1623) hydrogen bonds : angle 7.02289 ( 4452) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 587 time to evaluate : 1.533 Fit side-chains REVERT: C 79 ARG cc_start: 0.7702 (ttt-90) cc_final: 0.7267 (ttt-90) REVERT: K 32 TYR cc_start: 0.8025 (t80) cc_final: 0.7808 (t80) REVERT: K 107 ARG cc_start: 0.7746 (mtm-85) cc_final: 0.7310 (mpt-90) REVERT: N 107 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7290 (mpt-90) REVERT: O 35 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6535 (mp0) REVERT: M 70 GLN cc_start: 0.7136 (mt0) cc_final: 0.6936 (mt0) REVERT: P 32 TYR cc_start: 0.8033 (t80) cc_final: 0.7826 (t80) REVERT: B 79 ARG cc_start: 0.7709 (ttt-90) cc_final: 0.7277 (ttt-90) REVERT: A 79 ARG cc_start: 0.7693 (ttt-90) cc_final: 0.7254 (ttt-90) REVERT: H 79 ARG cc_start: 0.7699 (ttt-90) cc_final: 0.7265 (ttt-90) REVERT: F 79 ARG cc_start: 0.7692 (ttt-90) cc_final: 0.7254 (ttt-90) REVERT: I 79 ARG cc_start: 0.7700 (ttt-90) cc_final: 0.7263 (ttt-90) REVERT: G 79 ARG cc_start: 0.7700 (ttt-90) cc_final: 0.7265 (ttt-90) REVERT: J 79 ARG cc_start: 0.7697 (ttt-90) cc_final: 0.7261 (ttt-90) outliers start: 30 outliers final: 24 residues processed: 612 average time/residue: 0.8830 time to fit residues: 627.9824 Evaluate side-chains 601 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 577 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain N residue 95 ILE Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain M residue 95 ILE Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 341 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 GLN P 70 GLN B 304 GLN A 304 GLN H 304 GLN F 304 GLN I 304 GLN G 304 GLN J 304 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119863 restraints weight = 30697.349| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.42 r_work: 0.3254 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 34356 Z= 0.147 Angle : 0.603 7.809 46504 Z= 0.322 Chirality : 0.043 0.146 4944 Planarity : 0.005 0.052 6096 Dihedral : 5.624 34.429 4624 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.35 % Allowed : 13.86 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.13), residues: 4136 helix: 1.93 (0.12), residues: 1752 sheet: -0.13 (0.16), residues: 840 loop : 0.34 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 10 TYR 0.010 0.001 TYR I 239 PHE 0.024 0.002 PHE J 345 TRP 0.010 0.001 TRP A 368 HIS 0.006 0.001 HIS H 153 Details of bonding type rmsd covalent geometry : bond 0.00315 (34352) covalent geometry : angle 0.60258 (46496) SS BOND : bond 0.01086 ( 4) SS BOND : angle 0.19179 ( 8) hydrogen bonds : bond 0.04511 ( 1623) hydrogen bonds : angle 5.46796 ( 4452) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 595 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: C 51 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7021 (p0) REVERT: C 52 GLU cc_start: 0.7408 (tp30) cc_final: 0.7142 (tp30) REVERT: C 79 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7308 (ttt-90) REVERT: E 31 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6901 (tp30) REVERT: E 35 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: K 32 TYR cc_start: 0.7841 (t80) cc_final: 0.7598 (t80) REVERT: N 31 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6910 (tp30) REVERT: O 35 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6520 (mp0) REVERT: M 31 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6899 (tp30) REVERT: M 70 GLN cc_start: 0.7206 (mt0) cc_final: 0.6991 (mt0) REVERT: P 32 TYR cc_start: 0.7883 (t80) cc_final: 0.7672 (t80) REVERT: B 51 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7024 (p0) REVERT: B 52 GLU cc_start: 0.7404 (tp30) cc_final: 0.7143 (tp30) REVERT: B 79 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7298 (ttt-90) REVERT: A 51 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7019 (p0) REVERT: A 52 GLU cc_start: 0.7444 (tp30) cc_final: 0.7188 (tp30) REVERT: H 51 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7005 (p0) REVERT: H 52 GLU cc_start: 0.7443 (tp30) cc_final: 0.7177 (tp30) REVERT: F 51 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7018 (p0) REVERT: F 52 GLU cc_start: 0.7445 (tp30) cc_final: 0.7188 (tp30) REVERT: F 79 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7291 (ttt-90) REVERT: I 51 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.7025 (p0) REVERT: I 52 GLU cc_start: 0.7399 (tp30) cc_final: 0.7134 (tp30) REVERT: I 79 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7300 (ttt-90) REVERT: G 51 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7016 (p0) REVERT: G 52 GLU cc_start: 0.7359 (tp30) cc_final: 0.7118 (tp30) REVERT: J 51 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7023 (p0) REVERT: J 52 GLU cc_start: 0.7448 (tp30) cc_final: 0.7185 (tp30) REVERT: J 79 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7291 (ttt-90) outliers start: 83 outliers final: 16 residues processed: 621 average time/residue: 0.9379 time to fit residues: 674.0078 Evaluate side-chains 616 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 586 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 123 ASN Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 79 ARG Chi-restraints excluded: chain I residue 123 ASN Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 123 ASN Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 79 ARG Chi-restraints excluded: chain J residue 123 ASN Chi-restraints excluded: chain J residue 251 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 20 optimal weight: 10.0000 chunk 206 optimal weight: 0.0030 chunk 82 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 372 optimal weight: 30.0000 chunk 256 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 275 optimal weight: 0.2980 chunk 264 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 overall best weight: 3.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 304 GLN K 29 GLN L 29 GLN P 29 GLN B 156 GLN B 304 GLN A 156 GLN A 304 GLN H 156 GLN H 304 GLN F 156 GLN F 304 GLN I 156 GLN I 304 GLN G 156 GLN G 304 GLN J 156 GLN J 304 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118809 restraints weight = 30587.570| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.42 r_work: 0.3237 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 34356 Z= 0.176 Angle : 0.625 9.020 46504 Z= 0.332 Chirality : 0.044 0.168 4944 Planarity : 0.005 0.050 6096 Dihedral : 5.302 30.389 4592 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.18 % Allowed : 13.09 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.13), residues: 4136 helix: 1.90 (0.12), residues: 1744 sheet: -0.02 (0.16), residues: 816 loop : 0.16 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 79 TYR 0.009 0.002 TYR H 80 PHE 0.025 0.002 PHE H 345 TRP 0.010 0.001 TRP F 368 HIS 0.006 0.001 HIS G 153 Details of bonding type rmsd covalent geometry : bond 0.00390 (34352) covalent geometry : angle 0.62550 (46496) SS BOND : bond 0.01201 ( 4) SS BOND : angle 0.27293 ( 8) hydrogen bonds : bond 0.04643 ( 1623) hydrogen bonds : angle 5.37377 ( 4452) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 574 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: D 10 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6501 (ttm110) REVERT: D 31 GLU cc_start: 0.7128 (tp30) cc_final: 0.6911 (tp30) REVERT: C 51 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7034 (p0) REVERT: C 52 GLU cc_start: 0.7453 (tp30) cc_final: 0.7238 (tp30) REVERT: N 10 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6758 (ttm110) REVERT: N 31 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6904 (tp30) REVERT: N 35 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: L 107 ARG cc_start: 0.7785 (mtt90) cc_final: 0.7555 (mpt-90) REVERT: O 35 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6491 (mp0) REVERT: M 10 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6487 (ttm110) REVERT: M 31 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6942 (tp30) REVERT: M 70 GLN cc_start: 0.7197 (mt0) cc_final: 0.6992 (mt0) REVERT: P 10 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6466 (ttm110) REVERT: P 32 TYR cc_start: 0.7895 (t80) cc_final: 0.7675 (t80) REVERT: B 51 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7045 (p0) REVERT: B 52 GLU cc_start: 0.7459 (tp30) cc_final: 0.7247 (tp30) REVERT: A 51 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7033 (p0) REVERT: A 52 GLU cc_start: 0.7447 (tp30) cc_final: 0.7244 (tp30) REVERT: H 51 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7036 (p0) REVERT: H 52 GLU cc_start: 0.7447 (tp30) cc_final: 0.7233 (tp30) REVERT: F 51 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7028 (p0) REVERT: F 52 GLU cc_start: 0.7444 (tp30) cc_final: 0.7237 (tp30) REVERT: I 51 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7041 (p0) REVERT: I 52 GLU cc_start: 0.7438 (tp30) cc_final: 0.7223 (tp30) REVERT: G 51 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7044 (p0) REVERT: J 51 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7036 (p0) REVERT: J 52 GLU cc_start: 0.7449 (tp30) cc_final: 0.7238 (tp30) outliers start: 77 outliers final: 15 residues processed: 605 average time/residue: 0.9482 time to fit residues: 661.6395 Evaluate side-chains 593 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 565 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 81 LYS Chi-restraints excluded: chain J residue 251 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 262 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 307 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 289 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 240 optimal weight: 4.9990 chunk 117 optimal weight: 0.1980 chunk 222 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 285 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 304 GLN B 156 GLN B 304 GLN A 156 GLN A 304 GLN H 156 GLN H 304 GLN F 156 GLN F 304 GLN I 156 GLN I 304 GLN G 156 GLN G 304 GLN J 156 GLN J 304 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119924 restraints weight = 30635.656| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.41 r_work: 0.3256 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 34356 Z= 0.145 Angle : 0.591 8.125 46504 Z= 0.313 Chirality : 0.043 0.147 4944 Planarity : 0.004 0.054 6096 Dihedral : 5.208 29.269 4592 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.01 % Allowed : 13.60 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.13), residues: 4136 helix: 1.99 (0.12), residues: 1752 sheet: -0.17 (0.17), residues: 776 loop : 0.25 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 79 TYR 0.009 0.002 TYR L 32 PHE 0.023 0.002 PHE B 345 TRP 0.009 0.001 TRP O 58 HIS 0.006 0.001 HIS C 153 Details of bonding type rmsd covalent geometry : bond 0.00318 (34352) covalent geometry : angle 0.59076 (46496) SS BOND : bond 0.01064 ( 4) SS BOND : angle 0.23810 ( 8) hydrogen bonds : bond 0.04238 ( 1623) hydrogen bonds : angle 5.18278 ( 4452) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 584 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: D 10 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6494 (ttm110) REVERT: D 31 GLU cc_start: 0.7146 (tp30) cc_final: 0.6871 (tp30) REVERT: D 35 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: C 51 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7017 (p0) REVERT: C 52 GLU cc_start: 0.7446 (tp30) cc_final: 0.7234 (tp30) REVERT: E 31 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6943 (tp30) REVERT: K 32 TYR cc_start: 0.7862 (t80) cc_final: 0.7634 (t80) REVERT: N 10 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6748 (ttm110) REVERT: N 31 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6847 (tp30) REVERT: O 35 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6446 (mp0) REVERT: M 10 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6545 (ttm110) REVERT: M 31 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6906 (tp30) REVERT: M 35 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: P 10 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6523 (ttm110) REVERT: P 31 GLU cc_start: 0.7128 (tp30) cc_final: 0.6900 (tp30) REVERT: B 51 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7027 (p0) REVERT: B 52 GLU cc_start: 0.7448 (tp30) cc_final: 0.7237 (tp30) REVERT: A 51 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7011 (p0) REVERT: A 52 GLU cc_start: 0.7467 (tp30) cc_final: 0.7263 (tp30) REVERT: H 51 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7009 (p0) REVERT: H 52 GLU cc_start: 0.7452 (tp30) cc_final: 0.7239 (tp30) REVERT: F 51 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7025 (p0) REVERT: F 52 GLU cc_start: 0.7449 (tp30) cc_final: 0.7241 (tp30) REVERT: I 51 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7021 (p0) REVERT: I 52 GLU cc_start: 0.7442 (tp30) cc_final: 0.7229 (tp30) REVERT: G 51 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7027 (p0) REVERT: J 51 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7023 (p0) REVERT: J 52 GLU cc_start: 0.7455 (tp30) cc_final: 0.7246 (tp30) outliers start: 71 outliers final: 23 residues processed: 611 average time/residue: 0.9307 time to fit residues: 656.8722 Evaluate side-chains 603 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 566 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain L residue 43 GLU Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 251 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 30.0000 chunk 177 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 249 optimal weight: 0.8980 chunk 342 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 GLN C 156 GLN C 304 GLN E 29 GLN O 29 GLN M 29 GLN B 156 GLN B 304 GLN A 156 GLN A 304 GLN H 156 GLN H 304 GLN F 156 GLN F 304 GLN I 156 GLN I 304 GLN G 156 GLN G 304 GLN J 156 GLN J 304 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.157665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117829 restraints weight = 30545.121| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.41 r_work: 0.3241 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 34356 Z= 0.205 Angle : 0.654 9.971 46504 Z= 0.347 Chirality : 0.046 0.199 4944 Planarity : 0.005 0.054 6096 Dihedral : 5.386 29.410 4592 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.63 % Allowed : 12.58 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.13), residues: 4136 helix: 1.78 (0.12), residues: 1744 sheet: -0.14 (0.16), residues: 816 loop : 0.09 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 358 TYR 0.010 0.002 TYR I 103 PHE 0.027 0.003 PHE A 345 TRP 0.010 0.001 TRP I 368 HIS 0.006 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00457 (34352) covalent geometry : angle 0.65428 (46496) SS BOND : bond 0.01308 ( 4) SS BOND : angle 0.37192 ( 8) hydrogen bonds : bond 0.04819 ( 1623) hydrogen bonds : angle 5.29852 ( 4452) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 585 time to evaluate : 1.386 Fit side-chains REVERT: D 10 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.6596 (ttm110) REVERT: D 31 GLU cc_start: 0.7133 (tp30) cc_final: 0.6893 (tp30) REVERT: C 51 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7084 (p0) REVERT: E 31 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6934 (tp30) REVERT: K 10 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6923 (ttm110) REVERT: K 32 TYR cc_start: 0.7869 (t80) cc_final: 0.7663 (t80) REVERT: N 10 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6843 (ttm110) REVERT: N 31 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6879 (tp30) REVERT: O 35 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6370 (mp0) REVERT: M 10 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6615 (ttm110) REVERT: M 31 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6908 (tp30) REVERT: P 10 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6613 (ttm110) REVERT: B 51 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7105 (p0) REVERT: B 71 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8266 (p) REVERT: B 435 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.6684 (mtm-85) REVERT: A 51 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7069 (p0) REVERT: A 77 MET cc_start: 0.6733 (mpp) cc_final: 0.5902 (mmm) REVERT: H 51 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7076 (p0) REVERT: H 77 MET cc_start: 0.6730 (mpp) cc_final: 0.6186 (mmm) REVERT: F 51 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7068 (p0) REVERT: I 51 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7071 (p0) REVERT: G 51 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7064 (p0) REVERT: G 77 MET cc_start: 0.6725 (mpp) cc_final: 0.5874 (mmm) REVERT: J 51 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7069 (p0) REVERT: J 71 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8253 (p) outliers start: 93 outliers final: 25 residues processed: 634 average time/residue: 0.8101 time to fit residues: 595.6757 Evaluate side-chains 615 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 574 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain K residue 10 ARG Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 43 GLU Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 81 LYS Chi-restraints excluded: chain J residue 251 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 95 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 220 optimal weight: 0.9980 chunk 330 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 399 optimal weight: 6.9990 chunk 314 optimal weight: 4.9990 chunk 327 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 304 GLN B 156 GLN B 304 GLN A 156 GLN A 304 GLN H 156 GLN H 304 GLN F 156 GLN F 304 GLN I 156 GLN I 304 GLN G 156 GLN G 304 GLN ** G 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN J 304 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116881 restraints weight = 30333.296| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.40 r_work: 0.3227 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 34356 Z= 0.251 Angle : 0.703 10.807 46504 Z= 0.373 Chirality : 0.049 0.230 4944 Planarity : 0.006 0.050 6096 Dihedral : 5.557 30.322 4592 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.57 % Allowed : 12.44 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.13), residues: 4136 helix: 1.53 (0.11), residues: 1744 sheet: -0.29 (0.16), residues: 808 loop : 0.10 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 358 TYR 0.011 0.002 TYR N 32 PHE 0.028 0.003 PHE B 345 TRP 0.010 0.002 TRP H 368 HIS 0.006 0.001 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00566 (34352) covalent geometry : angle 0.70349 (46496) SS BOND : bond 0.01498 ( 4) SS BOND : angle 0.35442 ( 8) hydrogen bonds : bond 0.05182 ( 1623) hydrogen bonds : angle 5.40748 ( 4452) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 582 time to evaluate : 1.065 Fit side-chains REVERT: D 10 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.6705 (ttm110) REVERT: C 51 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7097 (p0) REVERT: C 71 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8292 (p) REVERT: E 10 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6965 (ttm110) REVERT: E 31 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6885 (tp30) REVERT: K 10 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6910 (ttm110) REVERT: K 32 TYR cc_start: 0.7870 (t80) cc_final: 0.7642 (t80) REVERT: N 10 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6794 (ttm110) REVERT: N 31 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6997 (tp30) REVERT: L 10 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.6976 (ttm110) REVERT: O 10 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6929 (ttm110) REVERT: O 35 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6384 (mp0) REVERT: M 10 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6676 (ttm110) REVERT: M 31 GLU cc_start: 0.7334 (tm-30) cc_final: 0.6976 (tp30) REVERT: P 10 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6673 (ttm110) REVERT: B 51 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7107 (p0) REVERT: B 435 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.6710 (mtm-85) REVERT: A 51 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7108 (p0) REVERT: A 71 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8286 (p) REVERT: A 77 MET cc_start: 0.6751 (mpp) cc_final: 0.6203 (mmm) REVERT: H 51 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7099 (p0) REVERT: H 77 MET cc_start: 0.6726 (mpp) cc_final: 0.6190 (mmm) REVERT: F 51 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7106 (p0) REVERT: F 71 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8283 (p) REVERT: I 51 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7098 (p0) REVERT: G 51 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7094 (p0) REVERT: G 77 MET cc_start: 0.6690 (mpp) cc_final: 0.6160 (mmm) REVERT: J 51 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7107 (p0) outliers start: 91 outliers final: 32 residues processed: 621 average time/residue: 0.7512 time to fit residues: 542.3780 Evaluate side-chains 647 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 595 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain K residue 10 ARG Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain O residue 10 ARG Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 81 LYS Chi-restraints excluded: chain J residue 251 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 55 optimal weight: 7.9990 chunk 213 optimal weight: 8.9990 chunk 390 optimal weight: 3.9990 chunk 306 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 381 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 332 optimal weight: 0.9990 chunk 297 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 304 GLN ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN N 29 GLN B 156 GLN B 304 GLN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 304 GLN ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 GLN H 304 GLN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN F 304 GLN ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN I 304 GLN ** I 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 304 GLN ** G 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN J 304 GLN ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.159019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119273 restraints weight = 30704.053| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.41 r_work: 0.3243 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 34356 Z= 0.153 Angle : 0.612 9.207 46504 Z= 0.324 Chirality : 0.044 0.151 4944 Planarity : 0.005 0.054 6096 Dihedral : 5.339 29.062 4592 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.01 % Allowed : 13.18 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.13), residues: 4136 helix: 1.84 (0.12), residues: 1744 sheet: -0.16 (0.17), residues: 736 loop : 0.09 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 358 TYR 0.009 0.002 TYR E 32 PHE 0.023 0.002 PHE J 345 TRP 0.013 0.001 TRP M 58 HIS 0.007 0.001 HIS C 153 Details of bonding type rmsd covalent geometry : bond 0.00338 (34352) covalent geometry : angle 0.61215 (46496) SS BOND : bond 0.01091 ( 4) SS BOND : angle 0.26538 ( 8) hydrogen bonds : bond 0.04318 ( 1623) hydrogen bonds : angle 5.16665 ( 4452) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 572 time to evaluate : 1.359 Fit side-chains REVERT: D 10 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6631 (ttm110) REVERT: C 51 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7060 (p0) REVERT: C 71 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8272 (p) REVERT: E 10 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6955 (ttm110) REVERT: E 31 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6915 (tp30) REVERT: K 10 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6937 (ttm110) REVERT: K 32 TYR cc_start: 0.7855 (t80) cc_final: 0.7647 (t80) REVERT: N 10 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6811 (ttm110) REVERT: N 31 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6898 (tp30) REVERT: N 35 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: L 10 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6955 (ttm110) REVERT: O 10 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6956 (ttm110) REVERT: O 35 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6339 (mp0) REVERT: M 10 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.6626 (ttm110) REVERT: M 31 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6898 (tp30) REVERT: P 10 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6614 (ttm110) REVERT: B 51 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7076 (p0) REVERT: B 71 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8271 (p) REVERT: B 435 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.6725 (mtm-85) REVERT: A 51 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7066 (p0) REVERT: A 71 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8280 (p) REVERT: A 77 MET cc_start: 0.6605 (mpp) cc_final: 0.5727 (mmm) REVERT: H 51 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7073 (p0) REVERT: H 71 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8280 (p) REVERT: H 77 MET cc_start: 0.6655 (mpp) cc_final: 0.6114 (mmm) REVERT: F 51 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7077 (p0) REVERT: F 71 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8260 (p) REVERT: I 51 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7072 (p0) REVERT: I 71 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8286 (p) REVERT: G 51 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7072 (p0) REVERT: G 71 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8279 (p) REVERT: G 77 MET cc_start: 0.6631 (mpp) cc_final: 0.6084 (mmm) REVERT: J 51 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7069 (p0) REVERT: J 71 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8247 (p) outliers start: 71 outliers final: 13 residues processed: 601 average time/residue: 0.7246 time to fit residues: 505.7704 Evaluate side-chains 602 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 562 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain K residue 10 ARG Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 35 GLU Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain O residue 10 ARG Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 282 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 18 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 304 GLN E 70 GLN B 156 GLN B 304 GLN A 156 GLN A 304 GLN H 156 GLN H 304 GLN F 156 GLN F 304 GLN I 156 GLN I 304 GLN G 156 GLN G 304 GLN J 156 GLN J 304 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.156239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116435 restraints weight = 30412.520| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.40 r_work: 0.3204 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 34356 Z= 0.280 Angle : 0.726 11.196 46504 Z= 0.386 Chirality : 0.051 0.248 4944 Planarity : 0.006 0.058 6096 Dihedral : 5.636 31.441 4592 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.95 % Allowed : 13.18 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.13), residues: 4136 helix: 1.43 (0.11), residues: 1744 sheet: -0.30 (0.16), residues: 808 loop : 0.12 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 79 TYR 0.011 0.002 TYR G 80 PHE 0.030 0.004 PHE H 345 TRP 0.011 0.002 TRP A 368 HIS 0.006 0.002 HIS G 153 Details of bonding type rmsd covalent geometry : bond 0.00634 (34352) covalent geometry : angle 0.72616 (46496) SS BOND : bond 0.01567 ( 4) SS BOND : angle 0.41844 ( 8) hydrogen bonds : bond 0.05359 ( 1623) hydrogen bonds : angle 5.44434 ( 4452) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 567 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: D 10 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6682 (ttm110) REVERT: C 51 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7099 (p0) REVERT: C 71 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8292 (p) REVERT: E 10 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6925 (ttm110) REVERT: E 31 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6902 (tp30) REVERT: K 10 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6921 (ttm110) REVERT: K 32 TYR cc_start: 0.7877 (t80) cc_final: 0.7648 (t80) REVERT: N 10 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6794 (ttm110) REVERT: N 31 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6950 (tp30) REVERT: L 10 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6916 (ttm110) REVERT: O 10 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6903 (ttm110) REVERT: O 35 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6308 (mp0) REVERT: M 10 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6628 (ttm110) REVERT: M 31 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6968 (tp30) REVERT: P 10 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6625 (ttm110) REVERT: B 51 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7093 (p0) REVERT: A 51 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7113 (p0) REVERT: A 77 MET cc_start: 0.6687 (mpp) cc_final: 0.6145 (mmm) REVERT: H 51 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7082 (p0) REVERT: H 71 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8291 (p) REVERT: H 77 MET cc_start: 0.6684 (mpp) cc_final: 0.6152 (mmm) REVERT: F 51 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7114 (p0) REVERT: F 71 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8291 (p) REVERT: I 51 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7114 (p0) REVERT: I 71 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8286 (p) REVERT: G 51 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7092 (p0) REVERT: G 77 MET cc_start: 0.6656 (mpp) cc_final: 0.6144 (mmm) REVERT: J 51 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7113 (p0) outliers start: 69 outliers final: 32 residues processed: 603 average time/residue: 0.7251 time to fit residues: 510.7412 Evaluate side-chains 620 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 568 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 282 LYS Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain K residue 10 ARG Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain O residue 10 ARG Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 282 LYS Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 282 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 81 LYS Chi-restraints excluded: chain J residue 282 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 333 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 392 optimal weight: 7.9990 chunk 93 optimal weight: 0.0570 chunk 321 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 GLN C 156 GLN C 304 GLN ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN B 156 GLN B 304 GLN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 304 GLN ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 GLN H 304 GLN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN F 304 GLN ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN I 304 GLN ** I 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 304 GLN ** G 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN J 304 GLN ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.158647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118940 restraints weight = 30523.785| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.41 r_work: 0.3239 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34356 Z= 0.168 Angle : 0.628 9.515 46504 Z= 0.333 Chirality : 0.045 0.163 4944 Planarity : 0.005 0.053 6096 Dihedral : 5.405 29.180 4592 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.67 % Allowed : 13.35 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.13), residues: 4136 helix: 1.76 (0.12), residues: 1744 sheet: -0.19 (0.17), residues: 736 loop : 0.07 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 358 TYR 0.011 0.002 TYR N 32 PHE 0.023 0.002 PHE J 345 TRP 0.014 0.002 TRP O 58 HIS 0.007 0.001 HIS H 153 Details of bonding type rmsd covalent geometry : bond 0.00375 (34352) covalent geometry : angle 0.62818 (46496) SS BOND : bond 0.01158 ( 4) SS BOND : angle 0.27606 ( 8) hydrogen bonds : bond 0.04451 ( 1623) hydrogen bonds : angle 5.20171 ( 4452) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 576 time to evaluate : 1.338 Fit side-chains REVERT: D 10 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6647 (ttm110) REVERT: C 51 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7077 (p0) REVERT: C 71 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8273 (p) REVERT: E 10 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.6955 (ttm110) REVERT: E 31 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6929 (tp30) REVERT: K 10 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.6941 (ttm110) REVERT: K 32 TYR cc_start: 0.7856 (t80) cc_final: 0.7646 (t80) REVERT: N 10 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6799 (ttm110) REVERT: N 31 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6901 (tp30) REVERT: N 107 ARG cc_start: 0.7755 (mtm-85) cc_final: 0.7377 (mtt180) REVERT: L 10 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6954 (ttm110) REVERT: O 10 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.6914 (ttm110) REVERT: O 35 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6329 (mp0) REVERT: M 10 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6629 (ttm110) REVERT: M 31 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6949 (tp30) REVERT: M 35 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: P 10 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6631 (ttm110) REVERT: B 51 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7082 (p0) REVERT: B 71 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8295 (p) REVERT: B 435 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.6716 (mtm-85) REVERT: A 51 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7078 (p0) REVERT: A 71 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8275 (p) REVERT: A 77 MET cc_start: 0.6614 (mpp) cc_final: 0.5718 (mmm) REVERT: H 51 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7070 (p0) REVERT: H 71 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8283 (p) REVERT: H 77 MET cc_start: 0.6657 (mpp) cc_final: 0.6103 (mmm) REVERT: F 51 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7082 (p0) REVERT: F 71 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8253 (p) REVERT: I 51 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7084 (p0) REVERT: I 71 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8289 (p) REVERT: G 51 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7042 (p0) REVERT: G 71 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8272 (p) REVERT: G 77 MET cc_start: 0.6626 (mpp) cc_final: 0.6075 (mmm) REVERT: J 51 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7075 (p0) REVERT: J 71 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8267 (p) outliers start: 59 outliers final: 20 residues processed: 608 average time/residue: 0.7032 time to fit residues: 498.8318 Evaluate side-chains 613 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 566 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain K residue 10 ARG Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain O residue 10 ARG Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 46 optimal weight: 0.2980 chunk 214 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 119 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 93 optimal weight: 0.0050 chunk 69 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 380 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 GLN C 156 GLN C 304 GLN ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN N 70 GLN L 70 GLN B 156 GLN B 304 GLN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 304 GLN ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 GLN H 304 GLN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN F 304 GLN ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN I 304 GLN ** I 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 304 GLN ** G 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN J 304 GLN ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.160743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121103 restraints weight = 30766.460| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.42 r_work: 0.3270 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34356 Z= 0.128 Angle : 0.579 9.680 46504 Z= 0.306 Chirality : 0.042 0.136 4944 Planarity : 0.005 0.060 6096 Dihedral : 5.193 27.512 4592 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.22 % Allowed : 14.31 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.13), residues: 4136 helix: 2.02 (0.12), residues: 1752 sheet: -0.40 (0.17), residues: 792 loop : 0.28 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 358 TYR 0.010 0.001 TYR G 239 PHE 0.021 0.002 PHE B 345 TRP 0.016 0.001 TRP O 58 HIS 0.005 0.001 HIS J 153 Details of bonding type rmsd covalent geometry : bond 0.00278 (34352) covalent geometry : angle 0.57877 (46496) SS BOND : bond 0.00946 ( 4) SS BOND : angle 0.25068 ( 8) hydrogen bonds : bond 0.03933 ( 1623) hydrogen bonds : angle 5.01053 ( 4452) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 574 time to evaluate : 1.378 Fit side-chains REVERT: D 10 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6599 (ttm110) REVERT: C 51 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.6991 (p0) REVERT: C 71 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8180 (p) REVERT: E 10 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6911 (ttm110) REVERT: E 31 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6841 (tp30) REVERT: K 10 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6891 (ttm110) REVERT: K 32 TYR cc_start: 0.7870 (t80) cc_final: 0.7655 (t80) REVERT: K 107 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7492 (mtt90) REVERT: N 10 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6764 (ttm110) REVERT: N 31 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6926 (tp30) REVERT: L 10 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6896 (ttm110) REVERT: O 10 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6923 (ttm110) REVERT: O 35 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6339 (mp0) REVERT: M 10 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6616 (ttm110) REVERT: M 31 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6940 (tp30) REVERT: M 35 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6725 (mp0) REVERT: M 107 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7469 (mtt90) REVERT: P 10 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6618 (ttm110) REVERT: B 51 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6981 (p0) REVERT: B 71 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8223 (p) REVERT: B 435 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.6686 (mtm-85) REVERT: A 51 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6947 (p0) REVERT: A 71 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8213 (p) REVERT: A 77 MET cc_start: 0.6545 (mpp) cc_final: 0.5722 (mmm) REVERT: H 51 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.6944 (p0) REVERT: H 71 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8213 (p) REVERT: H 77 MET cc_start: 0.6523 (mpp) cc_final: 0.6008 (mmm) REVERT: F 51 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.6996 (p0) REVERT: F 71 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8185 (p) REVERT: I 51 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7008 (p0) REVERT: I 71 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8179 (p) REVERT: G 51 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.6984 (p0) REVERT: G 71 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8216 (p) REVERT: G 77 MET cc_start: 0.6513 (mpp) cc_final: 0.5651 (mmm) REVERT: J 51 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.6964 (p0) REVERT: J 71 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8217 (p) outliers start: 43 outliers final: 9 residues processed: 592 average time/residue: 0.8015 time to fit residues: 550.4844 Evaluate side-chains 602 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 565 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain K residue 10 ARG Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain O residue 10 ARG Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 275 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 117 optimal weight: 0.0370 chunk 108 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 254 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 304 GLN ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 304 GLN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 304 GLN ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 GLN H 304 GLN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN F 304 GLN I 156 GLN I 304 GLN ** I 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 304 GLN ** G 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN J 304 GLN ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.160316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120619 restraints weight = 30679.548| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.42 r_work: 0.3261 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34356 Z= 0.139 Angle : 0.590 9.093 46504 Z= 0.312 Chirality : 0.043 0.160 4944 Planarity : 0.005 0.062 6096 Dihedral : 5.175 26.906 4592 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.33 % Allowed : 14.08 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.13), residues: 4136 helix: 2.03 (0.12), residues: 1752 sheet: -0.34 (0.17), residues: 784 loop : 0.21 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 10 TYR 0.011 0.002 TYR G 80 PHE 0.026 0.002 PHE G 345 TRP 0.014 0.001 TRP O 58 HIS 0.007 0.001 HIS G 153 Details of bonding type rmsd covalent geometry : bond 0.00304 (34352) covalent geometry : angle 0.59004 (46496) SS BOND : bond 0.01023 ( 4) SS BOND : angle 0.24594 ( 8) hydrogen bonds : bond 0.04103 ( 1623) hydrogen bonds : angle 5.02434 ( 4452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17238.07 seconds wall clock time: 293 minutes 2.46 seconds (17582.46 seconds total)