Starting phenix.real_space_refine on Fri May 30 03:07:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bcm_15966/05_2025/8bcm_15966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bcm_15966/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bcm_15966/05_2025/8bcm_15966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bcm_15966/05_2025/8bcm_15966.map" model { file = "/net/cci-nas-00/data/ceres_data/8bcm_15966/05_2025/8bcm_15966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bcm_15966/05_2025/8bcm_15966.cif" } resolution = 2.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 18.86, per 1000 atoms: 0.56 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: 8.49 Conformation dependent library (CDL) restraints added in 4.3 seconds 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: 4.54 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: 12.89 Time building geometry restraints manager: 9.80 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: 0.02 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.290 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 72.290 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.190 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:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.760 ------------------------------------------------------------------------------- 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 : 8.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.002 TRP L 58 HIS 0.005 0.001 HIS H 153 PHE 0.028 0.003 PHE B 345 TYR 0.010 0.002 TYR I 239 ARG 0.007 0.001 ARG H 435 Details of bonding type rmsd hydrogen bonds : bond 0.15257 ( 1623) hydrogen bonds : angle 7.02289 ( 4452) SS BOND : bond 0.01324 ( 4) SS BOND : angle 0.24995 ( 8) covalent geometry : bond 0.00492 (34352) covalent geometry : angle 0.66768 (46496) *********************** 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 : 3.594 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: 1.6547 time to fit residues: 1182.6070 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 : 3.625 ------------------------------------------------------------------------------- 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 351 optimal weight: 0.9990 chunk 315 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 107 optimal weight: 0.1980 chunk 212 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 326 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 377 optimal weight: 20.0000 overall best weight: 3.4388 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.157583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118230 restraints weight = 30611.604| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.40 r_work: 0.3229 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 34356 Z= 0.193 Angle : 0.653 9.332 46504 Z= 0.348 Chirality : 0.045 0.176 4944 Planarity : 0.005 0.049 6096 Dihedral : 5.858 40.393 4624 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.38 % Allowed : 13.55 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.13), residues: 4136 helix: 1.74 (0.12), residues: 1744 sheet: -0.18 (0.16), residues: 824 loop : 0.21 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 368 HIS 0.007 0.001 HIS B 153 PHE 0.026 0.003 PHE C 345 TYR 0.010 0.002 TYR I 103 ARG 0.003 0.001 ARG B 159 Details of bonding type rmsd hydrogen bonds : bond 0.04927 ( 1623) hydrogen bonds : angle 5.56746 ( 4452) SS BOND : bond 0.01314 ( 4) SS BOND : angle 0.22535 ( 8) covalent geometry : bond 0.00426 (34352) covalent geometry : angle 0.65339 (46496) *********************** 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 676 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 592 time to evaluate : 3.499 Fit side-chains revert: symmetry clash REVERT: C 51 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7070 (p0) REVERT: C 79 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7363 (ttt-90) REVERT: K 10 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.6635 (ttm110) REVERT: K 32 TYR cc_start: 0.7863 (t80) cc_final: 0.7645 (t80) REVERT: N 10 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6696 (ttm110) REVERT: N 31 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6908 (tp30) REVERT: N 35 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: O 35 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6503 (mp0) REVERT: M 31 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7010 (tp30) REVERT: M 70 GLN cc_start: 0.7135 (mt0) cc_final: 0.6926 (mt0) REVERT: B 51 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7067 (p0) REVERT: B 79 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7354 (ttt-90) REVERT: A 51 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7073 (p0) REVERT: H 51 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7084 (p0) REVERT: F 51 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7060 (p0) REVERT: F 79 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7333 (ttt-90) REVERT: I 51 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7092 (p0) REVERT: I 79 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7356 (ttt-90) REVERT: G 51 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7086 (p0) REVERT: J 51 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7061 (p0) REVERT: J 79 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7349 (ttt-90) outliers start: 84 outliers final: 13 residues processed: 620 average time/residue: 1.7184 time to fit residues: 1238.4324 Evaluate side-chains 623 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 594 time to evaluate : 4.040 ------------------------------------------------------------------------------- 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 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 35 GLU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 341 SER 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 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 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 79 ARG Chi-restraints excluded: chain J residue 81 LYS 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 411 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 241 optimal weight: 8.9990 chunk 304 optimal weight: 0.7980 chunk 266 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 390 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 402 optimal weight: 4.9990 chunk 93 optimal weight: 0.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.158473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119042 restraints weight = 30719.121| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.40 r_work: 0.3249 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.0887 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= 0.156 Angle : 0.607 8.470 46504 Z= 0.322 Chirality : 0.044 0.151 4944 Planarity : 0.005 0.052 6096 Dihedral : 5.325 31.670 4593 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.55 % Allowed : 13.32 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.13), residues: 4136 helix: 1.92 (0.12), residues: 1744 sheet: -0.05 (0.16), residues: 816 loop : 0.16 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 58 HIS 0.006 0.001 HIS H 153 PHE 0.023 0.002 PHE C 345 TYR 0.010 0.002 TYR C 80 ARG 0.004 0.000 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 1623) hydrogen bonds : angle 5.31959 ( 4452) SS BOND : bond 0.01135 ( 4) SS BOND : angle 0.20796 ( 8) covalent geometry : bond 0.00343 (34352) covalent geometry : angle 0.60754 (46496) *********************** 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 670 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 580 time to evaluate : 3.744 Fit side-chains revert: symmetry clash REVERT: D 10 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6517 (ttm110) REVERT: C 51 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7028 (p0) REVERT: C 52 GLU cc_start: 0.7449 (tp30) cc_final: 0.7190 (tp30) REVERT: E 10 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6505 (ttm110) REVERT: K 10 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.6631 (ttm110) REVERT: K 31 GLU cc_start: 0.7188 (tp30) cc_final: 0.6918 (tp30) REVERT: N 10 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6700 (ttm110) REVERT: N 31 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6940 (tp30) REVERT: N 35 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: L 10 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6510 (ttm110) REVERT: O 10 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6503 (ttm110) REVERT: O 35 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6470 (mp0) REVERT: M 10 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6555 (ttm110) REVERT: M 31 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6912 (tp30) REVERT: M 70 GLN cc_start: 0.7189 (mt0) cc_final: 0.6983 (mt0) REVERT: P 10 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6536 (ttm110) REVERT: B 51 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7031 (p0) REVERT: B 52 GLU cc_start: 0.7456 (tp30) cc_final: 0.7203 (tp30) REVERT: A 51 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7021 (p0) REVERT: A 52 GLU cc_start: 0.7457 (tp30) cc_final: 0.7248 (tp30) REVERT: H 51 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7035 (p0) REVERT: H 52 GLU cc_start: 0.7453 (tp30) cc_final: 0.7198 (tp30) REVERT: F 51 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7027 (p0) REVERT: F 52 GLU cc_start: 0.7446 (tp30) cc_final: 0.7199 (tp30) REVERT: I 51 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7035 (p0) REVERT: I 52 GLU cc_start: 0.7444 (tp30) cc_final: 0.7190 (tp30) REVERT: G 51 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7031 (p0) REVERT: G 52 GLU cc_start: 0.7460 (tp30) cc_final: 0.7258 (tp30) REVERT: J 51 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7034 (p0) REVERT: J 52 GLU cc_start: 0.7455 (tp30) cc_final: 0.7201 (tp30) outliers start: 90 outliers final: 20 residues processed: 620 average time/residue: 1.7281 time to fit residues: 1247.1314 Evaluate side-chains 587 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 550 time to evaluate : 3.505 ------------------------------------------------------------------------------- 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 123 ASN Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 43 GLU 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 N residue 43 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 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 A residue 341 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain J residue 341 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 40 optimal weight: 20.0000 chunk 392 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 chunk 386 optimal weight: 4.9990 chunk 313 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 158 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 415 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.157062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117288 restraints weight = 30492.165| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.40 r_work: 0.3233 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 34356 Z= 0.226 Angle : 0.675 10.381 46504 Z= 0.358 Chirality : 0.047 0.215 4944 Planarity : 0.005 0.050 6096 Dihedral : 5.506 32.517 4592 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.77 % Allowed : 12.39 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.13), residues: 4136 helix: 1.65 (0.12), residues: 1744 sheet: -0.29 (0.16), residues: 840 loop : 0.15 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 368 HIS 0.006 0.001 HIS A 153 PHE 0.027 0.003 PHE B 345 TYR 0.010 0.002 TYR E 17 ARG 0.004 0.001 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.05031 ( 1623) hydrogen bonds : angle 5.41376 ( 4452) SS BOND : bond 0.01432 ( 4) SS BOND : angle 0.30999 ( 8) covalent geometry : bond 0.00509 (34352) covalent geometry : angle 0.67529 (46496) *********************** 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 680 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 582 time to evaluate : 3.802 Fit side-chains REVERT: D 10 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6660 (ttm110) REVERT: C 51 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7096 (p0) REVERT: E 10 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6659 (ttm110) REVERT: E 31 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6930 (tp30) REVERT: K 10 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6700 (ttm110) REVERT: K 31 GLU cc_start: 0.7153 (tp30) cc_final: 0.6877 (tp30) REVERT: K 32 TYR cc_start: 0.7880 (t80) cc_final: 0.7641 (t80) REVERT: K 35 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6724 (mp0) REVERT: N 10 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.6687 (ttm110) REVERT: N 31 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6909 (tp30) REVERT: L 10 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6656 (ttm110) REVERT: O 10 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6644 (ttm110) REVERT: O 35 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6355 (mp0) REVERT: M 10 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6652 (ttm110) REVERT: M 31 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6932 (tp30) REVERT: M 70 GLN cc_start: 0.7134 (mt0) cc_final: 0.6931 (mt0) REVERT: P 10 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6654 (ttm110) REVERT: B 51 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7078 (p0) REVERT: B 435 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.6728 (mtm-85) REVERT: A 51 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7078 (p0) REVERT: H 51 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7058 (p0) REVERT: F 51 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7086 (p0) REVERT: I 51 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7084 (p0) REVERT: G 51 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7076 (p0) REVERT: J 51 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7083 (p0) outliers start: 98 outliers final: 38 residues processed: 636 average time/residue: 1.6625 time to fit residues: 1233.6163 Evaluate side-chains 620 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 564 time to evaluate : 3.568 ------------------------------------------------------------------------------- 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 81 LYS Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain K residue 10 ARG Chi-restraints excluded: chain K residue 35 GLU 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 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 81 LYS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 341 SER 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 H residue 341 SER 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 81 LYS Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 341 SER 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 I residue 341 SER 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 G residue 341 SER 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 Chi-restraints excluded: chain J residue 341 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 138 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 312 optimal weight: 3.9990 chunk 267 optimal weight: 0.9990 chunk 241 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 chunk 373 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 375 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.116983 restraints weight = 30478.871| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.40 r_work: 0.3213 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 34356 Z= 0.236 Angle : 0.688 10.542 46504 Z= 0.365 Chirality : 0.048 0.220 4944 Planarity : 0.005 0.049 6096 Dihedral : 5.581 33.314 4592 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.31 % Allowed : 11.45 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.13), residues: 4136 helix: 1.57 (0.12), residues: 1744 sheet: -0.23 (0.16), residues: 808 loop : 0.10 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 368 HIS 0.007 0.001 HIS H 153 PHE 0.028 0.003 PHE H 345 TYR 0.010 0.002 TYR B 103 ARG 0.006 0.001 ARG J 79 Details of bonding type rmsd hydrogen bonds : bond 0.05074 ( 1623) hydrogen bonds : angle 5.41722 ( 4452) SS BOND : bond 0.01483 ( 4) SS BOND : angle 0.27463 ( 8) covalent geometry : bond 0.00531 (34352) covalent geometry : angle 0.68824 (46496) *********************** 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 697 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 580 time to evaluate : 3.972 Fit side-chains revert: symmetry clash REVERT: D 10 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.6722 (ttm110) REVERT: C 51 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7118 (p0) REVERT: E 10 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6685 (ttm110) REVERT: E 31 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6955 (tp30) REVERT: K 10 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6681 (ttm110) REVERT: K 32 TYR cc_start: 0.7878 (t80) cc_final: 0.7661 (t80) REVERT: N 10 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6718 (ttm110) REVERT: N 31 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6932 (tp30) REVERT: L 10 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6694 (ttm110) REVERT: O 10 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6724 (ttm110) REVERT: O 35 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6342 (mp0) REVERT: M 10 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6701 (ttm110) REVERT: M 31 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6937 (tp30) REVERT: M 70 GLN cc_start: 0.7117 (mt0) cc_final: 0.6915 (mt0) REVERT: P 10 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6687 (ttm110) REVERT: B 51 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7114 (p0) REVERT: A 51 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7115 (p0) REVERT: A 77 MET cc_start: 0.6751 (mpp) cc_final: 0.6222 (mmm) REVERT: H 51 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7105 (p0) REVERT: H 77 MET cc_start: 0.6726 (mpp) cc_final: 0.6205 (mmm) REVERT: F 51 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7120 (p0) REVERT: I 51 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7108 (p0) REVERT: G 51 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7105 (p0) REVERT: G 77 MET cc_start: 0.6722 (mpp) cc_final: 0.6196 (mmm) REVERT: J 51 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7120 (p0) outliers start: 117 outliers final: 40 residues processed: 650 average time/residue: 1.6604 time to fit residues: 1259.9252 Evaluate side-chains 642 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 586 time to evaluate : 3.569 ------------------------------------------------------------------------------- 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 81 LYS Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 341 SER 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 81 LYS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 341 SER 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 H residue 341 SER 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 81 LYS Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 341 SER 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 I residue 341 SER 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 G residue 341 SER 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 Chi-restraints excluded: chain J residue 341 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 240 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 276 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 323 optimal weight: 10.0000 chunk 287 optimal weight: 5.9990 chunk 308 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** B 156 GLN B 304 GLN 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 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 = 0.3833 r_free = 0.3833 target = 0.156499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116788 restraints weight = 30546.597| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.40 r_work: 0.3211 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 34356 Z= 0.244 Angle : 0.702 10.708 46504 Z= 0.372 Chirality : 0.049 0.225 4944 Planarity : 0.006 0.050 6096 Dihedral : 5.641 34.061 4592 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.83 % Allowed : 11.93 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.13), residues: 4136 helix: 1.50 (0.11), residues: 1744 sheet: -0.26 (0.16), residues: 808 loop : 0.10 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 368 HIS 0.007 0.001 HIS H 153 PHE 0.029 0.003 PHE G 345 TYR 0.011 0.002 TYR M 32 ARG 0.005 0.001 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.05137 ( 1623) hydrogen bonds : angle 5.42249 ( 4452) SS BOND : bond 0.01494 ( 4) SS BOND : angle 0.28834 ( 8) covalent geometry : bond 0.00550 (34352) covalent geometry : angle 0.70193 (46496) *********************** 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 677 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 577 time to evaluate : 3.828 Fit side-chains REVERT: D 10 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6702 (ttm110) REVERT: D 96 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7153 (mtpm) REVERT: C 51 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7086 (p0) REVERT: E 10 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6661 (ttm110) REVERT: E 31 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6927 (tp30) REVERT: E 96 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7133 (mtpm) REVERT: K 10 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6663 (ttm110) REVERT: K 32 TYR cc_start: 0.7866 (t80) cc_final: 0.7666 (t80) REVERT: K 96 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7175 (mtpm) REVERT: N 10 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6701 (ttm110) REVERT: N 31 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6947 (tp30) REVERT: N 96 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7153 (mtpm) REVERT: L 10 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6651 (ttm110) REVERT: L 96 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7176 (mtpm) REVERT: O 10 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6726 (ttm110) REVERT: O 35 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6386 (mp0) REVERT: O 96 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7160 (mtpm) REVERT: M 10 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6675 (ttm110) REVERT: M 31 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6933 (tp30) REVERT: M 70 GLN cc_start: 0.7150 (mt0) cc_final: 0.6945 (mt0) REVERT: M 96 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7151 (mtpm) REVERT: P 10 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6659 (ttm110) REVERT: P 96 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7147 (mtpm) REVERT: B 51 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7089 (p0) REVERT: B 435 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.6771 (mtm-85) REVERT: A 51 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7119 (p0) REVERT: A 77 MET cc_start: 0.6647 (mpp) cc_final: 0.6118 (mmm) REVERT: H 51 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7065 (p0) REVERT: H 77 MET cc_start: 0.6649 (mpp) cc_final: 0.6121 (mmm) REVERT: F 51 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7126 (p0) REVERT: I 51 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7084 (p0) REVERT: G 51 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7078 (p0) REVERT: G 77 MET cc_start: 0.6637 (mpp) cc_final: 0.6104 (mmm) REVERT: J 51 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7129 (p0) outliers start: 100 outliers final: 39 residues processed: 630 average time/residue: 1.6715 time to fit residues: 1229.7717 Evaluate side-chains 640 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 576 time to evaluate : 4.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 96 LYS 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 81 LYS Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain K residue 10 ARG Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 96 LYS Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 96 LYS Chi-restraints excluded: chain O residue 10 ARG Chi-restraints excluded: chain O residue 96 LYS Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 96 LYS Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain P residue 96 LYS 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 81 LYS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 341 SER 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 H residue 341 SER 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 81 LYS Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 341 SER 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 I residue 341 SER 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 G residue 341 SER 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 Chi-restraints excluded: chain J residue 341 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 92 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 329 optimal weight: 0.8980 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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** N 29 GLN L 70 GLN O 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.157472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117964 restraints weight = 30658.484| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.41 r_work: 0.3229 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 : 0.004 0.030 34356 Z= 0.184 Angle : 0.645 9.365 46504 Z= 0.342 Chirality : 0.045 0.177 4944 Planarity : 0.005 0.053 6096 Dihedral : 5.499 33.519 4592 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.43 % Allowed : 12.61 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.13), residues: 4136 helix: 1.70 (0.12), residues: 1744 sheet: -0.38 (0.16), residues: 840 loop : 0.20 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 58 HIS 0.007 0.001 HIS I 153 PHE 0.027 0.003 PHE G 345 TYR 0.011 0.002 TYR H 80 ARG 0.003 0.000 ARG B 79 Details of bonding type rmsd hydrogen bonds : bond 0.04607 ( 1623) hydrogen bonds : angle 5.27339 ( 4452) SS BOND : bond 0.01240 ( 4) SS BOND : angle 0.25397 ( 8) covalent geometry : bond 0.00411 (34352) covalent geometry : angle 0.64549 (46496) *********************** 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 651 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 565 time to evaluate : 3.653 Fit side-chains REVERT: D 10 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6684 (ttm110) REVERT: D 96 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7126 (mtpm) REVERT: C 51 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7082 (p0) REVERT: E 10 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6610 (ttm110) REVERT: E 31 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6928 (tp30) REVERT: E 96 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7132 (mtpm) REVERT: K 10 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6655 (ttm110) REVERT: K 32 TYR cc_start: 0.7864 (t80) cc_final: 0.7629 (t80) REVERT: K 96 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7143 (mtpm) REVERT: N 10 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6682 (ttm110) REVERT: N 31 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6947 (tp30) REVERT: N 96 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7117 (mtpm) REVERT: L 10 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6604 (ttm110) REVERT: L 96 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7143 (mtpm) REVERT: O 10 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6644 (ttm110) REVERT: O 35 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6355 (mp0) REVERT: O 96 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7117 (mtpm) REVERT: M 10 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6633 (ttm110) REVERT: M 31 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6938 (tp30) REVERT: M 96 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7116 (mtpm) REVERT: P 10 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6625 (ttm110) REVERT: P 96 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7118 (mtpm) REVERT: B 51 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7087 (p0) REVERT: B 435 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.6710 (mtm-85) REVERT: A 51 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7076 (p0) REVERT: A 77 MET cc_start: 0.6625 (mpp) cc_final: 0.6094 (mmm) REVERT: H 51 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7065 (p0) REVERT: H 77 MET cc_start: 0.6639 (mpp) cc_final: 0.6113 (mmm) REVERT: F 51 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7081 (p0) REVERT: I 51 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7086 (p0) REVERT: G 51 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7086 (p0) REVERT: G 77 MET cc_start: 0.6631 (mpp) cc_final: 0.6101 (mmm) REVERT: J 51 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7078 (p0) outliers start: 86 outliers final: 28 residues processed: 610 average time/residue: 1.6935 time to fit residues: 1203.9780 Evaluate side-chains 612 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 559 time to evaluate : 3.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 96 LYS Chi-restraints excluded: chain K residue 10 ARG Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 96 LYS Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 96 LYS Chi-restraints excluded: chain O residue 10 ARG Chi-restraints excluded: chain O residue 96 LYS Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 96 LYS Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 51 ASP 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 A residue 341 SER 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 H residue 341 SER 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 F residue 341 SER 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 I residue 341 SER 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 G residue 341 SER Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain J residue 341 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 332 optimal weight: 0.0670 chunk 46 optimal weight: 7.9990 chunk 303 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 328 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 308 optimal weight: 0.1980 chunk 404 optimal weight: 20.0000 chunk 377 optimal weight: 5.9990 chunk 410 optimal weight: 8.9990 overall best weight: 2.4322 ------------------------------------------------------------------------------- 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** L 70 GLN O 70 GLN P 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.159104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119422 restraints weight = 30561.774| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.41 r_work: 0.3247 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1102 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= 0.152 Angle : 0.607 9.196 46504 Z= 0.322 Chirality : 0.044 0.150 4944 Planarity : 0.005 0.057 6096 Dihedral : 5.350 31.978 4592 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.09 % Allowed : 12.78 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.13), residues: 4136 helix: 1.89 (0.12), residues: 1744 sheet: -0.19 (0.17), residues: 736 loop : 0.10 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 58 HIS 0.007 0.001 HIS J 153 PHE 0.023 0.002 PHE G 345 TYR 0.010 0.002 TYR N 32 ARG 0.003 0.000 ARG M 10 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 1623) hydrogen bonds : angle 5.13017 ( 4452) SS BOND : bond 0.01098 ( 4) SS BOND : angle 0.25214 ( 8) covalent geometry : bond 0.00336 (34352) covalent geometry : angle 0.60684 (46496) *********************** 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 657 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 583 time to evaluate : 3.503 Fit side-chains REVERT: D 10 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6601 (ttm110) REVERT: C 51 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7051 (p0) REVERT: C 71 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8241 (p) REVERT: E 10 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6633 (ttm110) REVERT: E 31 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6931 (tp30) REVERT: K 10 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6639 (ttm110) REVERT: K 32 TYR cc_start: 0.7894 (t80) cc_final: 0.7667 (t80) REVERT: N 10 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6638 (ttm110) REVERT: N 31 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6925 (tp30) REVERT: L 10 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6616 (ttm110) REVERT: O 10 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6632 (ttm110) REVERT: O 35 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6353 (mp0) REVERT: M 10 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6600 (ttm110) REVERT: M 31 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6980 (tp30) REVERT: P 10 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6621 (ttm110) REVERT: B 51 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7053 (p0) REVERT: B 71 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8234 (p) REVERT: B 435 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.6747 (mtm-85) REVERT: A 51 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7047 (p0) REVERT: A 71 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8245 (p) REVERT: A 77 MET cc_start: 0.6588 (mpp) cc_final: 0.6041 (mmm) REVERT: H 51 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7024 (p0) REVERT: H 77 MET cc_start: 0.6619 (mpp) cc_final: 0.6077 (mmm) REVERT: F 51 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7066 (p0) REVERT: F 71 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8233 (p) REVERT: I 51 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7056 (p0) REVERT: I 71 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8242 (p) REVERT: G 51 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7046 (p0) REVERT: G 77 MET cc_start: 0.6621 (mpp) cc_final: 0.5749 (mmm) REVERT: J 51 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7055 (p0) REVERT: J 71 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8234 (p) outliers start: 74 outliers final: 24 residues processed: 618 average time/residue: 1.6546 time to fit residues: 1197.2537 Evaluate side-chains 617 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 569 time to evaluate : 3.680 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 341 SER 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 M residue 31 GLU Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain P residue 43 GLU 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 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 71 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 341 SER 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 F residue 251 MET Chi-restraints excluded: chain F residue 341 SER 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 I residue 341 SER 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 G residue 341 SER 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 251 MET Chi-restraints excluded: chain J residue 341 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 11 optimal weight: 7.9990 chunk 369 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 301 optimal weight: 6.9990 chunk 287 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 386 optimal weight: 3.9990 chunk 344 optimal weight: 2.9990 chunk 267 optimal weight: 0.6980 chunk 261 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 O 70 GLN P 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.161890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122381 restraints weight = 30933.613| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.42 r_work: 0.3287 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34356 Z= 0.117 Angle : 0.556 9.482 46504 Z= 0.295 Chirality : 0.042 0.132 4944 Planarity : 0.005 0.062 6096 Dihedral : 5.101 27.806 4592 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.58 % Allowed : 13.49 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.13), residues: 4136 helix: 2.16 (0.12), residues: 1752 sheet: -0.38 (0.17), residues: 792 loop : 0.33 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 58 HIS 0.004 0.001 HIS J 153 PHE 0.019 0.002 PHE J 345 TYR 0.009 0.001 TYR A 80 ARG 0.004 0.000 ARG E 10 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 1623) hydrogen bonds : angle 4.91507 ( 4452) SS BOND : bond 0.00918 ( 4) SS BOND : angle 0.13483 ( 8) covalent geometry : bond 0.00252 (34352) covalent geometry : angle 0.55561 (46496) *********************** 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: 56 poor density : 579 time to evaluate : 3.824 Fit side-chains REVERT: D 10 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6609 (ttm110) REVERT: D 107 ARG cc_start: 0.7636 (mtt90) cc_final: 0.7271 (mtt-85) REVERT: C 51 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6964 (p0) REVERT: C 71 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8169 (p) REVERT: E 10 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6638 (ttm110) REVERT: E 31 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6936 (tp30) REVERT: E 35 GLU cc_start: 0.7007 (mp0) cc_final: 0.6738 (mp0) REVERT: K 10 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6725 (ttm110) REVERT: N 10 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6636 (ttm110) REVERT: N 31 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6885 (tp30) REVERT: N 35 GLU cc_start: 0.6969 (mp0) cc_final: 0.6625 (mp0) REVERT: N 45 ASN cc_start: 0.8125 (t0) cc_final: 0.7636 (t0) REVERT: N 96 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6909 (mtpm) REVERT: N 107 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7460 (mtt180) REVERT: L 10 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6641 (ttm110) REVERT: L 96 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6900 (mtpm) REVERT: L 107 ARG cc_start: 0.7555 (mtt90) cc_final: 0.7271 (mtt-85) REVERT: O 10 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6637 (ttm110) REVERT: O 31 GLU cc_start: 0.7261 (tp30) cc_final: 0.6686 (tp30) REVERT: O 35 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6346 (mp0) REVERT: M 10 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.6636 (ttm110) REVERT: M 31 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6912 (tp30) REVERT: M 35 GLU cc_start: 0.6983 (mp0) cc_final: 0.6631 (mp0) REVERT: P 10 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6629 (ttm110) REVERT: P 96 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6921 (mtpm) REVERT: B 51 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.6961 (p0) REVERT: B 71 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8160 (p) REVERT: B 435 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.6712 (mtm-85) REVERT: A 51 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.6973 (p0) REVERT: A 71 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8194 (p) REVERT: A 77 MET cc_start: 0.6480 (mpp) cc_final: 0.5649 (mmm) REVERT: H 51 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6948 (p0) REVERT: H 71 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8198 (p) REVERT: H 77 MET cc_start: 0.6500 (mpp) cc_final: 0.5671 (mmm) REVERT: F 51 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6955 (p0) REVERT: F 71 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8165 (p) REVERT: I 51 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.6978 (p0) REVERT: I 71 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8184 (p) REVERT: G 51 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6961 (p0) REVERT: G 71 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8207 (p) REVERT: G 77 MET cc_start: 0.6503 (mpp) cc_final: 0.5646 (mmm) REVERT: J 51 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6969 (p0) REVERT: J 71 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8156 (p) outliers start: 56 outliers final: 16 residues processed: 602 average time/residue: 1.6709 time to fit residues: 1172.8340 Evaluate side-chains 600 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 553 time to evaluate : 3.543 ------------------------------------------------------------------------------- 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 251 MET Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain E residue 31 GLU 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 N residue 96 LYS Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 96 LYS 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 P residue 43 GLU Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 71 THR 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 71 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 341 SER 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 I residue 341 SER Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain J residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 149 optimal weight: 8.9990 chunk 20 optimal weight: 0.1980 chunk 150 optimal weight: 10.0000 chunk 392 optimal weight: 0.4980 chunk 364 optimal weight: 10.0000 chunk 321 optimal weight: 9.9990 chunk 382 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 325 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.158646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118920 restraints weight = 30586.056| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.41 r_work: 0.3240 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: 0.8721 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34356 Z= 0.184 Angle : 0.635 9.426 46504 Z= 0.336 Chirality : 0.045 0.173 4944 Planarity : 0.005 0.062 6096 Dihedral : 5.297 28.397 4592 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.47 % Allowed : 14.08 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.13), residues: 4136 helix: 1.91 (0.12), residues: 1744 sheet: -0.35 (0.17), residues: 784 loop : 0.18 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 58 HIS 0.007 0.001 HIS A 153 PHE 0.027 0.003 PHE H 345 TYR 0.013 0.002 TYR G 80 ARG 0.003 0.000 ARG H 131 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 1623) hydrogen bonds : angle 5.15125 ( 4452) SS BOND : bond 0.01247 ( 4) SS BOND : angle 0.23975 ( 8) covalent geometry : bond 0.00412 (34352) covalent geometry : angle 0.63465 (46496) ********************** 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 618 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 566 time to evaluate : 3.907 Fit side-chains REVERT: D 10 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6574 (ttm110) REVERT: D 107 ARG cc_start: 0.7653 (mtt90) cc_final: 0.7295 (mtt-85) REVERT: C 51 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.6976 (p0) REVERT: C 71 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8251 (p) REVERT: E 10 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6588 (ttm110) REVERT: E 31 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6980 (tp30) REVERT: K 10 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6635 (ttm110) REVERT: N 10 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6659 (ttm110) REVERT: N 31 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6887 (tp30) REVERT: L 10 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.6598 (ttm110) REVERT: O 10 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6590 (ttm110) REVERT: O 31 GLU cc_start: 0.7267 (tp30) cc_final: 0.6755 (tp30) REVERT: O 35 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6335 (mp0) REVERT: O 96 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6640 (mptp) REVERT: M 10 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6597 (ttm110) REVERT: M 31 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6922 (tp30) REVERT: M 96 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7186 (mtpt) REVERT: P 10 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6595 (ttm110) REVERT: B 51 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.6997 (p0) REVERT: B 71 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8199 (p) REVERT: B 435 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.6793 (mtm-85) REVERT: A 51 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7000 (p0) REVERT: A 77 MET cc_start: 0.6492 (mpp) cc_final: 0.6009 (mmm) REVERT: H 51 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.6983 (p0) REVERT: H 71 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8239 (p) REVERT: H 77 MET cc_start: 0.6514 (mpp) cc_final: 0.6033 (mmm) REVERT: F 51 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.6993 (p0) REVERT: I 51 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.6977 (p0) REVERT: G 51 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7020 (p0) REVERT: G 71 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8232 (p) REVERT: G 77 MET cc_start: 0.6507 (mpp) cc_final: 0.6024 (mmm) REVERT: J 51 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.6995 (p0) REVERT: J 71 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8218 (p) outliers start: 52 outliers final: 17 residues processed: 590 average time/residue: 1.6745 time to fit residues: 1149.4008 Evaluate side-chains 607 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 565 time to evaluate : 3.956 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 341 SER 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 O residue 96 LYS Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 31 GLU Chi-restraints excluded: chain M residue 96 LYS Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain P residue 43 GLU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 71 THR 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 A residue 341 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 341 SER Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 341 SER Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain J residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 135 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 381 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.157389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.117566 restraints weight = 30556.994| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.41 r_work: 0.3219 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 34356 Z= 0.229 Angle : 0.683 10.340 46504 Z= 0.363 Chirality : 0.048 0.208 4944 Planarity : 0.006 0.055 6096 Dihedral : 5.503 30.072 4592 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.47 % Allowed : 14.23 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.13), residues: 4136 helix: 1.64 (0.12), residues: 1744 sheet: -0.47 (0.16), residues: 792 loop : 0.13 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP O 58 HIS 0.006 0.001 HIS H 153 PHE 0.030 0.003 PHE C 345 TYR 0.014 0.002 TYR G 80 ARG 0.003 0.001 ARG J 435 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 1623) hydrogen bonds : angle 5.30854 ( 4452) SS BOND : bond 0.01408 ( 4) SS BOND : angle 0.31869 ( 8) covalent geometry : bond 0.00514 (34352) covalent geometry : angle 0.68305 (46496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33552.14 seconds wall clock time: 575 minutes 2.53 seconds (34502.53 seconds total)