Starting phenix.real_space_refine on Sat Jun 28 11:09:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bcm_15966/06_2025/8bcm_15966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bcm_15966/06_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_15966/06_2025/8bcm_15966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bcm_15966/06_2025/8bcm_15966.map" model { file = "/net/cci-nas-00/data/ceres_data/8bcm_15966/06_2025/8bcm_15966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bcm_15966/06_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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 20.79, per 1000 atoms: 0.62 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: 9.18 Conformation dependent library (CDL) restraints added in 4.6 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: 4.98 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: 14.79 Time building geometry restraints manager: 10.89 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: 1.820 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: 0.030 Extract box with map and model: 1.570 Check model and map are aligned: 0.290 Set scattering table: 0.350 Process input model: 82.380 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.250 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:14.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.810 ------------------------------------------------------------------------------- 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 : 4.184 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: 1.7067 time to fit residues: 1218.5046 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 : 3.977 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.157992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.118360 restraints weight = 30590.668| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.41 r_work: 0.3237 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 : 3.929 Fit side-chains revert: symmetry clash REVERT: C 51 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7076 (p0) REVERT: C 79 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7369 (ttt-90) REVERT: K 10 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6637 (ttm110) REVERT: K 32 TYR cc_start: 0.7863 (t80) cc_final: 0.7644 (t80) REVERT: N 10 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6696 (ttm110) REVERT: N 31 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6914 (tp30) REVERT: N 35 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: O 35 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6504 (mp0) REVERT: M 31 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7015 (tp30) REVERT: M 70 GLN cc_start: 0.7132 (mt0) cc_final: 0.6923 (mt0) REVERT: B 51 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7070 (p0) REVERT: B 79 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7359 (ttt-90) REVERT: A 51 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7076 (p0) REVERT: H 51 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7086 (p0) REVERT: F 51 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7064 (p0) REVERT: F 79 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7339 (ttt-90) REVERT: I 51 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7100 (p0) REVERT: I 79 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7359 (ttt-90) REVERT: G 51 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7093 (p0) REVERT: J 51 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7064 (p0) REVERT: J 79 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7352 (ttt-90) outliers start: 84 outliers final: 13 residues processed: 620 average time/residue: 1.8790 time to fit residues: 1353.5033 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 : 4.956 ------------------------------------------------------------------------------- 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: 10.0000 chunk 45 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 241 optimal weight: 8.9990 chunk 304 optimal weight: 0.6980 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: 0.8980 overall best weight: 2.6784 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.158935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119198 restraints weight = 30587.420| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.42 r_work: 0.3245 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34356 Z= 0.162 Angle : 0.613 8.635 46504 Z= 0.325 Chirality : 0.044 0.155 4944 Planarity : 0.005 0.051 6096 Dihedral : 5.343 32.449 4593 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.46 % Allowed : 13.32 % Favored : 84.22 % 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: 1.21 (0.13), residues: 4136 helix: 1.90 (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 G 368 HIS 0.006 0.001 HIS J 153 PHE 0.024 0.002 PHE B 345 TYR 0.010 0.002 TYR G 80 ARG 0.005 0.000 ARG G 79 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 1623) hydrogen bonds : angle 5.32999 ( 4452) SS BOND : bond 0.01155 ( 4) SS BOND : angle 0.21780 ( 8) covalent geometry : bond 0.00356 (34352) covalent geometry : angle 0.61307 (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 667 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 580 time to evaluate : 4.000 Fit side-chains revert: symmetry clash REVERT: D 10 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6538 (ttm110) REVERT: C 51 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7032 (p0) REVERT: C 52 GLU cc_start: 0.7450 (tp30) cc_final: 0.7190 (tp30) REVERT: E 10 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6512 (ttm110) REVERT: K 10 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6616 (ttm110) REVERT: K 31 GLU cc_start: 0.7221 (tp30) cc_final: 0.6956 (tp30) REVERT: N 10 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6697 (ttm110) REVERT: N 31 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6943 (tp30) REVERT: N 35 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: L 10 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6515 (ttm110) REVERT: O 10 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6510 (ttm110) REVERT: O 35 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6476 (mp0) REVERT: M 10 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6542 (ttm110) REVERT: M 31 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6921 (tp30) REVERT: M 70 GLN cc_start: 0.7202 (mt0) cc_final: 0.6997 (mt0) REVERT: P 10 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6567 (ttm110) REVERT: B 51 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7019 (p0) REVERT: B 52 GLU cc_start: 0.7454 (tp30) cc_final: 0.7199 (tp30) REVERT: A 51 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7031 (p0) REVERT: A 52 GLU cc_start: 0.7457 (tp30) cc_final: 0.7212 (tp30) REVERT: H 51 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7038 (p0) REVERT: H 52 GLU cc_start: 0.7452 (tp30) cc_final: 0.7196 (tp30) REVERT: F 51 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7031 (p0) REVERT: F 52 GLU cc_start: 0.7444 (tp30) cc_final: 0.7197 (tp30) REVERT: I 51 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7042 (p0) REVERT: I 52 GLU cc_start: 0.7441 (tp30) cc_final: 0.7187 (tp30) REVERT: G 51 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7038 (p0) REVERT: G 52 GLU cc_start: 0.7454 (tp30) cc_final: 0.7249 (tp30) REVERT: J 51 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7039 (p0) REVERT: J 52 GLU cc_start: 0.7449 (tp30) cc_final: 0.7195 (tp30) outliers start: 87 outliers final: 20 residues processed: 617 average time/residue: 2.0329 time to fit residues: 1457.2852 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 : 5.140 ------------------------------------------------------------------------------- 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: 6.9990 chunk 58 optimal weight: 0.9980 chunk 259 optimal weight: 7.9990 chunk 386 optimal weight: 3.9990 chunk 313 optimal weight: 4.9990 chunk 63 optimal weight: 0.0570 chunk 158 optimal weight: 10.0000 chunk 208 optimal weight: 7.9990 chunk 415 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 overall best weight: 3.4104 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.157998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.118234 restraints weight = 30574.291| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.41 r_work: 0.3231 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 34356 Z= 0.186 Angle : 0.637 9.416 46504 Z= 0.338 Chirality : 0.045 0.181 4944 Planarity : 0.005 0.052 6096 Dihedral : 5.387 31.765 4592 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.83 % Allowed : 12.36 % Favored : 84.81 % 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: 1.12 (0.13), residues: 4136 helix: 1.81 (0.12), residues: 1744 sheet: -0.11 (0.16), residues: 816 loop : 0.12 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 368 HIS 0.006 0.001 HIS G 153 PHE 0.025 0.003 PHE H 345 TYR 0.010 0.002 TYR E 17 ARG 0.004 0.000 ARG G 79 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 1623) hydrogen bonds : angle 5.30751 ( 4452) SS BOND : bond 0.01273 ( 4) SS BOND : angle 0.26042 ( 8) covalent geometry : bond 0.00415 (34352) covalent geometry : angle 0.63704 (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 674 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 574 time to evaluate : 3.977 Fit side-chains REVERT: D 10 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6623 (ttm110) REVERT: C 51 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7056 (p0) REVERT: E 10 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6608 (ttm110) REVERT: E 31 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6959 (tp30) REVERT: E 107 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7264 (mpt-90) REVERT: K 10 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6681 (ttm110) REVERT: K 32 TYR cc_start: 0.7871 (t80) cc_final: 0.7652 (t80) REVERT: N 10 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6717 (ttm110) REVERT: N 31 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6866 (tp30) REVERT: L 10 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6632 (ttm110) REVERT: O 10 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6605 (ttm110) REVERT: O 31 GLU cc_start: 0.7286 (tp30) cc_final: 0.6734 (tp30) REVERT: O 35 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6352 (mp0) REVERT: M 10 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6639 (ttm110) REVERT: M 31 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6943 (tp30) REVERT: P 10 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6629 (ttm110) REVERT: B 51 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7068 (p0) REVERT: B 435 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.6696 (mtm-85) REVERT: A 51 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7076 (p0) REVERT: H 51 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7063 (p0) REVERT: F 51 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7074 (p0) REVERT: I 51 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7061 (p0) REVERT: G 51 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7069 (p0) REVERT: G 52 GLU cc_start: 0.7451 (tp30) cc_final: 0.7250 (tp30) REVERT: J 51 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7075 (p0) outliers start: 100 outliers final: 40 residues processed: 630 average time/residue: 1.7522 time to fit residues: 1283.6385 Evaluate side-chains 615 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 558 time to evaluate : 4.142 ------------------------------------------------------------------------------- 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 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 N residue 43 GLU Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain O residue 10 ARG Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain 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 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: 5.9990 chunk 96 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 312 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 chunk 241 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 373 optimal weight: 3.9990 chunk 217 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 375 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.156243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116639 restraints weight = 30498.153| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.39 r_work: 0.3232 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 34356 Z= 0.229 Angle : 0.680 10.448 46504 Z= 0.361 Chirality : 0.048 0.217 4944 Planarity : 0.005 0.051 6096 Dihedral : 5.529 32.636 4592 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.14 % Allowed : 11.85 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 0.94 (0.13), residues: 4136 helix: 1.63 (0.12), residues: 1744 sheet: -0.22 (0.16), residues: 824 loop : 0.10 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 368 HIS 0.006 0.001 HIS A 153 PHE 0.027 0.003 PHE F 345 TYR 0.010 0.002 TYR F 103 ARG 0.003 0.001 ARG A 435 Details of bonding type rmsd hydrogen bonds : bond 0.05032 ( 1623) hydrogen bonds : angle 5.39142 ( 4452) SS BOND : bond 0.01441 ( 4) SS BOND : angle 0.31087 ( 8) covalent geometry : bond 0.00516 (34352) covalent geometry : angle 0.68037 (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 684 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 573 time to evaluate : 4.109 Fit side-chains revert: symmetry clash REVERT: D 10 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6679 (ttm110) REVERT: C 51 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7089 (p0) REVERT: E 10 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6676 (ttm110) REVERT: E 31 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6950 (tp30) REVERT: K 10 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6692 (ttm110) REVERT: K 32 TYR cc_start: 0.7864 (t80) cc_final: 0.7628 (t80) REVERT: N 10 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6682 (ttm110) REVERT: N 31 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6924 (tp30) REVERT: L 10 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6685 (ttm110) REVERT: L 107 ARG cc_start: 0.7696 (mtm-85) cc_final: 0.7201 (mpt-90) REVERT: O 10 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6675 (ttm110) REVERT: O 35 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6402 (mp0) REVERT: M 10 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6700 (ttm110) REVERT: M 31 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6920 (tp30) REVERT: P 10 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6673 (ttm110) REVERT: B 51 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7097 (p0) REVERT: A 51 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7102 (p0) REVERT: A 77 MET cc_start: 0.6745 (mpp) cc_final: 0.5893 (mmm) REVERT: H 51 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7082 (p0) REVERT: H 77 MET cc_start: 0.6692 (mpp) cc_final: 0.6175 (mmm) REVERT: F 51 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7098 (p0) REVERT: I 51 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7088 (p0) REVERT: G 51 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7077 (p0) REVERT: G 77 MET cc_start: 0.6723 (mpp) cc_final: 0.6197 (mmm) REVERT: J 51 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7101 (p0) outliers start: 111 outliers final: 39 residues processed: 639 average time/residue: 1.7682 time to fit residues: 1314.9609 Evaluate side-chains 632 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 577 time to evaluate : 4.228 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 192 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 276 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 323 optimal weight: 8.9990 chunk 287 optimal weight: 4.9990 chunk 308 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 E 70 GLN B 156 GLN B 304 GLN A 156 GLN A 304 GLN H 156 GLN H 304 GLN F 156 GLN F 304 GLN I 156 GLN I 304 GLN G 156 GLN G 304 GLN J 156 GLN J 304 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.157370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117595 restraints weight = 30542.946| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.41 r_work: 0.3223 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 34356 Z= 0.207 Angle : 0.662 9.945 46504 Z= 0.351 Chirality : 0.046 0.196 4944 Planarity : 0.005 0.050 6096 Dihedral : 5.504 32.664 4592 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.94 % Allowed : 11.74 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.95 (0.13), residues: 4136 helix: 1.67 (0.12), residues: 1744 sheet: -0.37 (0.16), residues: 840 loop : 0.18 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 368 HIS 0.007 0.001 HIS F 153 PHE 0.026 0.003 PHE C 345 TYR 0.011 0.002 TYR N 32 ARG 0.004 0.001 ARG J 79 Details of bonding type rmsd hydrogen bonds : bond 0.04812 ( 1623) hydrogen bonds : angle 5.32670 ( 4452) SS BOND : bond 0.01352 ( 4) SS BOND : angle 0.27896 ( 8) covalent geometry : bond 0.00464 (34352) covalent geometry : angle 0.66171 (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 668 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 564 time to evaluate : 3.831 Fit side-chains REVERT: D 10 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6621 (ttm110) REVERT: D 96 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7113 (mtpm) REVERT: C 51 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7081 (p0) REVERT: E 10 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6637 (ttm110) REVERT: E 31 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6941 (tp30) REVERT: K 10 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6623 (ttm110) REVERT: K 32 TYR cc_start: 0.7866 (t80) cc_final: 0.7643 (t80) REVERT: N 10 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.6701 (ttm110) REVERT: N 31 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6943 (tp30) REVERT: L 10 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6640 (ttm110) REVERT: L 96 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7140 (mtpm) REVERT: O 10 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6640 (ttm110) REVERT: O 35 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6366 (mp0) REVERT: M 10 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6648 (ttm110) REVERT: M 31 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6951 (tp30) REVERT: M 96 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7122 (mtpm) REVERT: P 10 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6637 (ttm110) REVERT: P 96 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7126 (mtpm) REVERT: B 51 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7087 (p0) REVERT: B 71 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8274 (p) REVERT: B 435 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.6702 (mtm-85) REVERT: A 51 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7092 (p0) REVERT: A 77 MET cc_start: 0.6641 (mpp) cc_final: 0.6097 (mmm) REVERT: H 51 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7078 (p0) REVERT: H 77 MET cc_start: 0.6648 (mpp) cc_final: 0.6101 (mmm) REVERT: F 51 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7095 (p0) REVERT: I 51 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7081 (p0) REVERT: G 51 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7084 (p0) REVERT: G 77 MET cc_start: 0.6641 (mpp) cc_final: 0.6090 (mmm) REVERT: J 51 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7096 (p0) outliers start: 104 outliers final: 37 residues processed: 617 average time/residue: 1.6822 time to fit residues: 1210.9456 Evaluate side-chains 630 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 571 time to evaluate : 4.358 ------------------------------------------------------------------------------- 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 K residue 10 ARG Chi-restraints excluded: chain N residue 10 ARG 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 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 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 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 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: 20.0000 chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 294 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 286 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 329 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 GLN C 156 GLN C 304 GLN ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 304 GLN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 304 GLN ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 GLN H 304 GLN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN F 304 GLN ** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.156011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116251 restraints weight = 30523.320| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.40 r_work: 0.3217 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 34356 Z= 0.281 Angle : 0.734 11.195 46504 Z= 0.389 Chirality : 0.051 0.247 4944 Planarity : 0.006 0.058 6096 Dihedral : 5.711 33.917 4592 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.80 % Favored : 97.15 % Rotamer: Outliers : 2.66 % Allowed : 12.19 % Favored : 85.15 % 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: 0.76 (0.13), residues: 4136 helix: 1.38 (0.11), residues: 1744 sheet: -0.28 (0.16), residues: 808 loop : 0.11 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 451 HIS 0.007 0.001 HIS I 153 PHE 0.029 0.004 PHE H 345 TYR 0.012 0.003 TYR N 17 ARG 0.004 0.001 ARG J 139 Details of bonding type rmsd hydrogen bonds : bond 0.05406 ( 1623) hydrogen bonds : angle 5.48369 ( 4452) SS BOND : bond 0.01633 ( 4) SS BOND : angle 0.35360 ( 8) covalent geometry : bond 0.00635 (34352) covalent geometry : angle 0.73388 (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 669 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 575 time to evaluate : 4.232 Fit side-chains revert: symmetry clash REVERT: D 10 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6685 (ttm110) REVERT: D 96 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7148 (mtpm) REVERT: C 51 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7088 (p0) REVERT: C 71 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8301 (p) REVERT: E 10 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6658 (ttm110) REVERT: E 31 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6918 (tp30) REVERT: E 96 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7106 (mtpm) REVERT: K 10 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6646 (ttm110) REVERT: K 32 TYR cc_start: 0.7867 (t80) cc_final: 0.7627 (t80) REVERT: K 96 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7165 (mtpm) REVERT: N 10 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6707 (ttm110) REVERT: N 31 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6958 (tp30) REVERT: N 96 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7128 (mtpm) REVERT: L 10 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6657 (ttm110) REVERT: L 96 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7154 (mtpm) REVERT: O 10 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6681 (ttm110) REVERT: O 35 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6332 (mp0) REVERT: O 96 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7170 (mtpm) REVERT: M 10 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6648 (ttm110) REVERT: M 31 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6999 (tp30) REVERT: M 96 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7113 (mtpm) REVERT: P 10 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6637 (ttm110) REVERT: P 96 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7151 (mtpm) REVERT: B 51 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7109 (p0) REVERT: A 51 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7110 (p0) REVERT: A 77 MET cc_start: 0.6660 (mpp) cc_final: 0.6134 (mmm) REVERT: H 51 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7096 (p0) REVERT: H 77 MET cc_start: 0.6671 (mpp) cc_final: 0.6156 (mmm) REVERT: F 51 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7112 (p0) REVERT: I 51 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7108 (p0) REVERT: G 51 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7110 (p0) REVERT: G 77 MET cc_start: 0.6654 (mpp) cc_final: 0.6135 (mmm) REVERT: J 51 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7114 (p0) outliers start: 94 outliers final: 46 residues processed: 629 average time/residue: 1.6516 time to fit residues: 1218.7137 Evaluate side-chains 633 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 562 time to evaluate : 3.789 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 282 LYS 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 251 MET Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain 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 282 LYS 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 282 LYS 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 282 LYS 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 282 LYS 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: 1.9990 chunk 46 optimal weight: 8.9990 chunk 303 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 328 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 272 optimal weight: 7.9990 chunk 308 optimal weight: 1.9990 chunk 404 optimal weight: 9.9990 chunk 377 optimal weight: 2.9990 chunk 410 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 304 GLN ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119615 restraints weight = 30557.863| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.41 r_work: 0.3249 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1104 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= 0.148 Angle : 0.610 9.687 46504 Z= 0.323 Chirality : 0.044 0.156 4944 Planarity : 0.005 0.048 6096 Dihedral : 5.372 32.464 4592 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.92 % Allowed : 13.09 % Favored : 84.98 % 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: 1.11 (0.13), residues: 4136 helix: 1.82 (0.12), residues: 1752 sheet: -0.18 (0.17), residues: 736 loop : 0.11 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 58 HIS 0.006 0.001 HIS G 153 PHE 0.025 0.002 PHE A 345 TYR 0.010 0.002 TYR L 32 ARG 0.003 0.000 ARG F 295 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 1623) hydrogen bonds : angle 5.14925 ( 4452) SS BOND : bond 0.01102 ( 4) SS BOND : angle 0.21023 ( 8) covalent geometry : bond 0.00324 (34352) covalent geometry : angle 0.60991 (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 656 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 588 time to evaluate : 4.130 Fit side-chains REVERT: D 10 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6624 (ttm110) REVERT: C 51 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7033 (p0) REVERT: C 71 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8294 (p) REVERT: E 10 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6591 (ttm110) REVERT: E 31 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6905 (tp30) REVERT: K 10 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6614 (ttm110) REVERT: K 32 TYR cc_start: 0.7835 (t80) cc_final: 0.7632 (t80) REVERT: N 10 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.6660 (ttm110) REVERT: N 31 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6933 (tp30) REVERT: L 10 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6606 (ttm110) REVERT: O 10 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6646 (ttm110) REVERT: O 35 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6352 (mp0) REVERT: M 10 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6604 (ttm110) REVERT: M 31 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6927 (tp30) REVERT: M 35 GLU cc_start: 0.6964 (mp0) cc_final: 0.6748 (mp0) REVERT: P 10 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6612 (ttm110) REVERT: B 51 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7061 (p0) REVERT: B 71 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8291 (p) REVERT: B 435 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.6745 (mtm-85) REVERT: A 51 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7059 (p0) REVERT: A 71 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8277 (p) REVERT: A 77 MET cc_start: 0.6599 (mpp) cc_final: 0.6061 (mmm) REVERT: H 51 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7043 (p0) REVERT: H 71 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8286 (p) REVERT: H 77 MET cc_start: 0.6646 (mpp) cc_final: 0.6097 (mmm) REVERT: F 51 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7064 (p0) REVERT: F 71 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8286 (p) REVERT: I 51 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7053 (p0) REVERT: I 71 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8283 (p) REVERT: G 51 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7064 (p0) REVERT: G 71 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8267 (p) REVERT: G 77 MET cc_start: 0.6629 (mpp) cc_final: 0.6077 (mmm) REVERT: J 51 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7067 (p0) REVERT: J 71 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8259 (p) outliers start: 68 outliers final: 18 residues processed: 617 average time/residue: 1.7423 time to fit residues: 1253.4712 Evaluate side-chains 625 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 581 time to evaluate : 3.920 ------------------------------------------------------------------------------- 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 K residue 10 ARG Chi-restraints excluded: chain K residue 43 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 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 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 65 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 11 optimal weight: 6.9990 chunk 369 optimal weight: 9.9990 chunk 317 optimal weight: 9.9990 chunk 301 optimal weight: 6.9990 chunk 287 optimal weight: 0.8980 chunk 250 optimal weight: 0.7980 chunk 174 optimal weight: 0.0050 chunk 386 optimal weight: 5.9990 chunk 344 optimal weight: 2.9990 chunk 267 optimal weight: 0.5980 chunk 261 optimal weight: 0.5980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 E 70 GLN N 70 GLN L 29 GLN L 70 GLN O 29 GLN O 70 GLN P 70 GLN B 156 GLN B 304 GLN B 327 HIS A 156 GLN A 304 GLN A 327 HIS H 156 GLN H 304 GLN H 327 HIS F 156 GLN F 304 GLN F 327 HIS I 156 GLN I 304 GLN I 327 HIS G 156 GLN G 304 GLN G 327 HIS J 156 GLN J 304 GLN J 327 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.164089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.124957 restraints weight = 31090.093| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.42 r_work: 0.3314 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 34356 Z= 0.104 Angle : 0.534 9.577 46504 Z= 0.284 Chirality : 0.041 0.136 4944 Planarity : 0.005 0.060 6096 Dihedral : 5.009 27.455 4592 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.33 % Allowed : 13.72 % Favored : 84.95 % 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: 1.46 (0.13), residues: 4136 helix: 2.24 (0.12), residues: 1752 sheet: -0.33 (0.17), residues: 792 loop : 0.35 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 58 HIS 0.004 0.001 HIS M 47 PHE 0.016 0.001 PHE C 345 TYR 0.008 0.001 TYR I 239 ARG 0.004 0.000 ARG P 10 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 1623) hydrogen bonds : angle 4.80978 ( 4452) SS BOND : bond 0.00811 ( 4) SS BOND : angle 0.03813 ( 8) covalent geometry : bond 0.00221 (34352) covalent geometry : angle 0.53425 (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 637 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 590 time to evaluate : 4.085 Fit side-chains REVERT: C 51 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6973 (p0) REVERT: C 71 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8148 (p) REVERT: C 358 ARG cc_start: 0.8682 (mmm-85) cc_final: 0.8425 (mmm-85) REVERT: E 31 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6932 (tp30) REVERT: E 35 GLU cc_start: 0.7024 (mp0) cc_final: 0.6759 (mp0) REVERT: N 31 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6881 (tp30) REVERT: N 107 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7463 (mtt90) REVERT: O 35 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6336 (mp0) REVERT: M 31 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6876 (tp30) REVERT: M 107 ARG cc_start: 0.7608 (mtt90) cc_final: 0.7205 (mtt-85) REVERT: B 51 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.6950 (p0) REVERT: B 71 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8160 (p) REVERT: B 435 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.6671 (mtm-85) REVERT: A 51 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7005 (p0) REVERT: A 71 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8183 (p) REVERT: A 77 MET cc_start: 0.6477 (mpp) cc_final: 0.5629 (mmm) REVERT: H 51 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.6934 (p0) REVERT: H 71 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8137 (p) REVERT: H 77 MET cc_start: 0.6495 (mpp) cc_final: 0.5643 (mmm) REVERT: F 51 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7002 (p0) REVERT: F 71 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8149 (p) REVERT: I 51 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6969 (p0) REVERT: I 71 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8146 (p) REVERT: G 51 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.6937 (p0) REVERT: G 71 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8187 (p) REVERT: G 77 MET cc_start: 0.6498 (mpp) cc_final: 0.5647 (mmm) REVERT: J 51 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6964 (p0) REVERT: J 71 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8158 (p) outliers start: 47 outliers final: 16 residues processed: 611 average time/residue: 1.6948 time to fit residues: 1207.2140 Evaluate side-chains 607 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 573 time to evaluate : 4.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 M residue 31 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 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 65 THR 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: 9.9990 chunk 20 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 392 optimal weight: 0.0010 chunk 364 optimal weight: 9.9990 chunk 321 optimal weight: 7.9990 chunk 382 optimal weight: 0.0370 chunk 199 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 325 optimal weight: 20.0000 overall best weight: 1.9868 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.160814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121199 restraints weight = 30844.111| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.42 r_work: 0.3271 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34356 Z= 0.139 Angle : 0.583 8.932 46504 Z= 0.309 Chirality : 0.043 0.159 4944 Planarity : 0.005 0.063 6096 Dihedral : 5.090 25.977 4592 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.24 % Allowed : 14.42 % Favored : 84.33 % 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: 1.37 (0.13), residues: 4136 helix: 2.17 (0.12), residues: 1752 sheet: -0.37 (0.17), residues: 792 loop : 0.29 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 58 HIS 0.007 0.001 HIS H 153 PHE 0.024 0.002 PHE H 345 TYR 0.014 0.002 TYR B 239 ARG 0.003 0.000 ARG L 10 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 1623) hydrogen bonds : angle 4.96006 ( 4452) SS BOND : bond 0.01083 ( 4) SS BOND : angle 0.10126 ( 8) covalent geometry : bond 0.00306 (34352) covalent geometry : angle 0.58255 (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 610 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 566 time to evaluate : 3.666 Fit side-chains REVERT: C 51 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.6949 (p0) REVERT: C 71 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8153 (p) REVERT: E 31 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6818 (tp30) REVERT: E 35 GLU cc_start: 0.6956 (mp0) cc_final: 0.6715 (mp0) REVERT: N 10 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6655 (ttm110) REVERT: N 31 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6920 (tp30) REVERT: N 107 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7385 (mtt180) REVERT: O 10 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.6660 (ttm110) REVERT: O 31 GLU cc_start: 0.7252 (tp30) cc_final: 0.6668 (tp30) REVERT: O 35 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6316 (mp0) REVERT: M 31 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6934 (tp30) REVERT: M 45 ASN cc_start: 0.8201 (t0) cc_final: 0.7757 (t0) REVERT: P 45 ASN cc_start: 0.8212 (t0) cc_final: 0.7761 (t0) REVERT: B 51 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.6963 (p0) REVERT: B 71 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8154 (p) REVERT: B 435 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.6771 (mtm-85) REVERT: A 51 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6977 (p0) REVERT: A 71 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8201 (p) REVERT: A 77 MET cc_start: 0.6505 (mpp) cc_final: 0.5963 (mmm) REVERT: H 51 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6957 (p0) REVERT: H 71 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8183 (p) REVERT: H 77 MET cc_start: 0.6527 (mpp) cc_final: 0.5987 (mmm) REVERT: F 51 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6957 (p0) REVERT: F 71 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8145 (p) REVERT: I 51 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6980 (p0) REVERT: I 71 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8140 (p) REVERT: G 51 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.6945 (p0) REVERT: G 71 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8208 (p) REVERT: G 77 MET cc_start: 0.6471 (mpp) cc_final: 0.5675 (mmm) REVERT: J 51 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.6955 (p0) REVERT: J 71 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8154 (p) outliers start: 44 outliers final: 16 residues processed: 584 average time/residue: 1.7605 time to fit residues: 1192.3466 Evaluate side-chains 599 residues out of total 3536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 563 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 31 GLU Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain O residue 10 ARG 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 65 THR 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: 8.9990 chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 0.0050 chunk 8 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 293 optimal weight: 30.0000 chunk 164 optimal weight: 7.9990 chunk 219 optimal weight: 8.9990 chunk 381 optimal weight: 8.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 304 GLN B 156 GLN B 304 GLN A 156 GLN A 304 GLN H 156 GLN H 304 GLN F 156 GLN F 304 GLN I 156 GLN I 304 GLN G 156 GLN G 304 GLN J 156 GLN J 304 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119960 restraints weight = 30820.461| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.41 r_work: 0.3252 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1217 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= 0.159 Angle : 0.611 9.059 46504 Z= 0.324 Chirality : 0.044 0.153 4944 Planarity : 0.005 0.062 6096 Dihedral : 5.179 27.122 4592 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.39 % Allowed : 14.48 % Favored : 84.13 % 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: 1.21 (0.13), residues: 4136 helix: 2.04 (0.12), residues: 1752 sheet: -0.40 (0.17), residues: 784 loop : 0.17 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 58 HIS 0.007 0.001 HIS G 153 PHE 0.023 0.002 PHE F 345 TYR 0.015 0.002 TYR B 239 ARG 0.004 0.000 ARG J 131 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 1623) hydrogen bonds : angle 5.06483 ( 4452) SS BOND : bond 0.01153 ( 4) SS BOND : angle 0.19182 ( 8) covalent geometry : bond 0.00353 (34352) covalent geometry : angle 0.61118 (46496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36531.52 seconds wall clock time: 624 minutes 23.57 seconds (37463.57 seconds total)