Starting phenix.real_space_refine on Fri Mar 22 13:14:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcm_15966/03_2024/8bcm_15966.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcm_15966/03_2024/8bcm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcm_15966/03_2024/8bcm_15966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcm_15966/03_2024/8bcm_15966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcm_15966/03_2024/8bcm_15966.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcm_15966/03_2024/8bcm_15966.pdb" } 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 Residue "D PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "E PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 74": "OE1" <-> "OE2" Residue "N PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N GLU 35": "OE1" <-> "OE2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 43": "OE1" <-> "OE2" Residue "L GLU 74": "OE1" <-> "OE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 74": "OE1" <-> "OE2" Residue "O TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 31": "OE1" <-> "OE2" Residue "M GLU 35": "OE1" <-> "OE2" Residue "M GLU 43": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 74": "OE1" <-> "OE2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 74": "OE1" <-> "OE2" Residue "P TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H ASP 78": "OD1" <-> "OD2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "I ASP 51": "OD1" <-> "OD2" Residue "I GLU 52": "OE1" <-> "OE2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "I ASP 78": "OD1" <-> "OD2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "G ASP 51": "OD1" <-> "OD2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "J GLU 52": "OE1" <-> "OE2" Residue "J GLU 60": "OE1" <-> "OE2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J GLU 392": "OE1" <-> "OE2" Residue "J GLU 440": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 16.79, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 14.32 Conformation dependent library (CDL) restraints added in 6.5 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: 4.22 Creating SS restraints... Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 67 through 82 removed outlier: 4.065A pdb=" N VAL D 71 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 25 removed outlier: 3.539A pdb=" N TYR C 25 " --> pdb=" O LYS C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 25' Processing helix chain 'C' and resid 49 through 61 Processing helix chain 'C' and resid 69 through 75 Processing helix chain 'C' and resid 77 through 81 removed outlier: 3.526A pdb=" N TYR C 80 " --> pdb=" O MET C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.598A pdb=" N PHE C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 122 Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 153 through 163 removed outlier: 4.262A pdb=" N VAL C 157 " --> pdb=" O HIS C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 196 removed outlier: 3.638A pdb=" N GLY C 196 " --> pdb=" O CYS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 Processing helix chain 'C' and resid 246 through 260 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 273 through 288 Processing helix chain 'C' and resid 297 through 303 removed outlier: 4.019A pdb=" N ILE C 301 " --> pdb=" O MET C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 322 removed outlier: 3.659A pdb=" N LEU C 314 " --> pdb=" O HIS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 351 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 383 through 385 No H-bonds generated for 'chain 'C' and resid 383 through 385' Processing helix chain 'C' and resid 386 through 395 Processing helix chain 'C' and resid 413 through 434 Processing helix chain 'C' and resid 436 through 451 removed outlier: 5.903A pdb=" N GLY C 442 " --> pdb=" O TYR C 438 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ASP C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 461 Processing helix chain 'E' and resid 22 through 37 Processing helix chain 'E' and resid 67 through 82 removed outlier: 4.070A pdb=" N VAL E 71 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 67 through 82 removed outlier: 4.060A pdb=" N VAL K 71 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 36 Processing helix chain 'N' and resid 67 through 82 removed outlier: 4.069A pdb=" N VAL N 71 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 37 Processing helix chain 'L' and resid 67 through 82 removed outlier: 4.078A pdb=" N VAL L 71 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 36 Processing helix chain 'O' and resid 67 through 82 removed outlier: 4.073A pdb=" N VAL O 71 " --> pdb=" O SER O 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 36 Processing helix chain 'M' and resid 67 through 82 removed outlier: 4.065A pdb=" N VAL M 71 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 37 Processing helix chain 'P' and resid 67 through 82 removed outlier: 4.085A pdb=" N VAL P 71 " --> pdb=" O SER P 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 25 removed outlier: 3.539A pdb=" N TYR B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 21 through 25' Processing helix chain 'B' and resid 49 through 61 Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.538A pdb=" N TYR B 80 " --> pdb=" O MET B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.598A pdb=" N PHE B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 122 Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 153 through 163 removed outlier: 4.262A pdb=" N VAL B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 removed outlier: 3.639A pdb=" N GLY B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 233 Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 297 through 303 removed outlier: 4.023A pdb=" N ILE B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.660A pdb=" N LEU B 314 " --> pdb=" O HIS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 351 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 413 through 434 Processing helix chain 'B' and resid 436 through 451 removed outlier: 5.853A pdb=" N GLY B 442 " --> pdb=" O TYR B 438 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASP B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TRP B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'A' and resid 21 through 25 removed outlier: 3.550A pdb=" N TYR A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 21 through 25' Processing helix chain 'A' and resid 49 through 61 Processing helix chain 'A' and resid 69 through 75 Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.599A pdb=" N PHE A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 153 through 163 removed outlier: 4.261A pdb=" N VAL A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 removed outlier: 3.637A pdb=" N GLY A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 297 through 303 removed outlier: 4.027A pdb=" N ILE A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.660A pdb=" N LEU A 314 " --> pdb=" O HIS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 413 through 434 Processing helix chain 'A' and resid 436 through 451 removed outlier: 5.869A pdb=" N GLY A 442 " --> pdb=" O TYR A 438 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASP A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'H' and resid 21 through 25 removed outlier: 3.557A pdb=" N TYR H 25 " --> pdb=" O LYS H 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 21 through 25' Processing helix chain 'H' and resid 49 through 61 Processing helix chain 'H' and resid 69 through 75 Processing helix chain 'H' and resid 77 through 81 Processing helix chain 'H' and resid 104 through 108 removed outlier: 3.598A pdb=" N PHE H 108 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 122 Processing helix chain 'H' and resid 123 through 127 Processing helix chain 'H' and resid 141 through 146 Processing helix chain 'H' and resid 153 through 163 removed outlier: 4.262A pdb=" N VAL H 157 " --> pdb=" O HIS H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 196 removed outlier: 3.637A pdb=" N GLY H 196 " --> pdb=" O CYS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 233 Processing helix chain 'H' and resid 246 through 260 Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'H' and resid 273 through 288 Processing helix chain 'H' and resid 297 through 303 removed outlier: 4.028A pdb=" N ILE H 301 " --> pdb=" O MET H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 322 removed outlier: 3.659A pdb=" N LEU H 314 " --> pdb=" O HIS H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 351 Processing helix chain 'H' and resid 357 through 361 Processing helix chain 'H' and resid 383 through 385 No H-bonds generated for 'chain 'H' and resid 383 through 385' Processing helix chain 'H' and resid 386 through 395 Processing helix chain 'H' and resid 413 through 434 Processing helix chain 'H' and resid 436 through 451 removed outlier: 5.926A pdb=" N GLY H 442 " --> pdb=" O TYR H 438 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP H 443 " --> pdb=" O ARG H 439 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TRP H 451 " --> pdb=" O GLU H 447 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 461 Processing helix chain 'F' and resid 21 through 25 removed outlier: 3.549A pdb=" N TYR F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 21 through 25' Processing helix chain 'F' and resid 49 through 61 Processing helix chain 'F' and resid 69 through 75 Processing helix chain 'F' and resid 77 through 81 removed outlier: 3.516A pdb=" N TYR F 80 " --> pdb=" O MET F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.599A pdb=" N PHE F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 122 Processing helix chain 'F' and resid 123 through 127 Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 153 through 163 removed outlier: 4.262A pdb=" N VAL F 157 " --> pdb=" O HIS F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 196 removed outlier: 3.638A pdb=" N GLY F 196 " --> pdb=" O CYS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 Processing helix chain 'F' and resid 246 through 260 Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 297 through 303 removed outlier: 4.026A pdb=" N ILE F 301 " --> pdb=" O MET F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 322 removed outlier: 3.659A pdb=" N LEU F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 351 Processing helix chain 'F' and resid 357 through 361 Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 386 through 395 Processing helix chain 'F' and resid 413 through 434 Processing helix chain 'F' and resid 436 through 451 removed outlier: 5.869A pdb=" N GLY F 442 " --> pdb=" O TYR F 438 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASP F 443 " --> pdb=" O ARG F 439 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 461 Processing helix chain 'I' and resid 21 through 25 removed outlier: 3.546A pdb=" N TYR I 25 " --> pdb=" O LYS I 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 21 through 25' Processing helix chain 'I' and resid 49 through 61 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'I' and resid 77 through 81 removed outlier: 3.502A pdb=" N TYR I 80 " --> pdb=" O MET I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 108 removed outlier: 3.599A pdb=" N PHE I 108 " --> pdb=" O LEU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 122 Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 141 through 146 Processing helix chain 'I' and resid 153 through 163 removed outlier: 4.262A pdb=" N VAL I 157 " --> pdb=" O HIS I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 196 removed outlier: 3.639A pdb=" N GLY I 196 " --> pdb=" O CYS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 233 Processing helix chain 'I' and resid 246 through 260 Processing helix chain 'I' and resid 269 through 273 Processing helix chain 'I' and resid 273 through 288 Processing helix chain 'I' and resid 297 through 303 removed outlier: 4.021A pdb=" N ILE I 301 " --> pdb=" O MET I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 322 removed outlier: 3.659A pdb=" N LEU I 314 " --> pdb=" O HIS I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 351 Processing helix chain 'I' and resid 357 through 361 Processing helix chain 'I' and resid 383 through 385 No H-bonds generated for 'chain 'I' and resid 383 through 385' Processing helix chain 'I' and resid 386 through 395 Processing helix chain 'I' and resid 413 through 434 Processing helix chain 'I' and resid 436 through 451 removed outlier: 5.912A pdb=" N GLY I 442 " --> pdb=" O TYR I 438 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP I 443 " --> pdb=" O ARG I 439 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TRP I 451 " --> pdb=" O GLU I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 452 through 461 Processing helix chain 'G' and resid 21 through 25 removed outlier: 3.551A pdb=" N TYR G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 21 through 25' Processing helix chain 'G' and resid 49 through 61 Processing helix chain 'G' and resid 69 through 75 Processing helix chain 'G' and resid 77 through 81 Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.597A pdb=" N PHE G 108 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 122 Processing helix chain 'G' and resid 123 through 127 Processing helix chain 'G' and resid 141 through 146 Processing helix chain 'G' and resid 153 through 163 removed outlier: 4.262A pdb=" N VAL G 157 " --> pdb=" O HIS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 196 removed outlier: 3.638A pdb=" N GLY G 196 " --> pdb=" O CYS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 233 Processing helix chain 'G' and resid 246 through 260 Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'G' and resid 273 through 288 Processing helix chain 'G' and resid 297 through 303 removed outlier: 4.026A pdb=" N ILE G 301 " --> pdb=" O MET G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.658A pdb=" N LEU G 314 " --> pdb=" O HIS G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 351 Processing helix chain 'G' and resid 357 through 361 Processing helix chain 'G' and resid 383 through 385 No H-bonds generated for 'chain 'G' and resid 383 through 385' Processing helix chain 'G' and resid 386 through 395 Processing helix chain 'G' and resid 413 through 434 Processing helix chain 'G' and resid 436 through 451 removed outlier: 5.878A pdb=" N GLY G 442 " --> pdb=" O TYR G 438 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASP G 443 " --> pdb=" O ARG G 439 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP G 451 " --> pdb=" O GLU G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 461 Processing helix chain 'J' and resid 21 through 25 removed outlier: 3.552A pdb=" N TYR J 25 " --> pdb=" O LYS J 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 21 through 25' Processing helix chain 'J' and resid 49 through 61 Processing helix chain 'J' and resid 69 through 75 Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.503A pdb=" N TYR J 80 " --> pdb=" O MET J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 108 removed outlier: 3.599A pdb=" N PHE J 108 " --> pdb=" O LEU J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 122 Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 141 through 146 Processing helix chain 'J' and resid 153 through 163 removed outlier: 4.262A pdb=" N VAL J 157 " --> pdb=" O HIS J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 196 removed outlier: 3.638A pdb=" N GLY J 196 " --> pdb=" O CYS J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 233 Processing helix chain 'J' and resid 246 through 260 Processing helix chain 'J' and resid 269 through 273 Processing helix chain 'J' and resid 273 through 288 Processing helix chain 'J' and resid 297 through 303 removed outlier: 4.021A pdb=" N ILE J 301 " --> pdb=" O MET J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 322 removed outlier: 3.659A pdb=" N LEU J 314 " --> pdb=" O HIS J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 351 Processing helix chain 'J' and resid 357 through 361 Processing helix chain 'J' and resid 383 through 385 No H-bonds generated for 'chain 'J' and resid 383 through 385' Processing helix chain 'J' and resid 386 through 395 Processing helix chain 'J' and resid 413 through 434 Processing helix chain 'J' and resid 436 through 451 removed outlier: 5.894A pdb=" N GLY J 442 " --> pdb=" O TYR J 438 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASP J 443 " --> pdb=" O ARG J 439 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TRP J 451 " --> pdb=" O GLU J 447 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 461 Processing sheet with id=AA1, first strand: chain 'D' and resid 56 through 57 removed outlier: 6.209A pdb=" N ILE D 87 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP D 93 " --> pdb=" O GLN D 99 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLN D 99 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 89 removed outlier: 5.443A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU C 37 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 169 through 173 removed outlier: 6.492A pdb=" N LEU C 170 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LYS C 201 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS C 172 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR C 200 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASN C 241 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N HIS C 238 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N MET C 266 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU C 240 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ASP C 268 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE C 265 " --> pdb=" O HIS C 292 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N HIS C 294 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N HIS C 267 " --> pdb=" O HIS C 294 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU C 291 " --> pdb=" O HIS C 325 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N HIS C 327 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE C 293 " --> pdb=" O HIS C 327 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN C 401 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA C 378 " --> pdb=" O GLN C 401 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET C 169 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE C 402 " --> pdb=" O MET C 169 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY C 171 " --> pdb=" O PHE C 402 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AA5, first strand: chain 'E' and resid 56 through 57 removed outlier: 6.206A pdb=" N ILE E 87 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP E 93 " --> pdb=" O GLN E 99 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN E 99 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 56 through 57 removed outlier: 6.204A pdb=" N ILE K 87 " --> pdb=" O VAL K 105 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP K 93 " --> pdb=" O GLN K 99 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLN K 99 " --> pdb=" O ASP K 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 56 through 57 removed outlier: 6.211A pdb=" N ILE N 87 " --> pdb=" O VAL N 105 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP N 93 " --> pdb=" O GLN N 99 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLN N 99 " --> pdb=" O ASP N 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 56 through 57 removed outlier: 6.205A pdb=" N ILE L 87 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP L 93 " --> pdb=" O GLN L 99 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN L 99 " --> pdb=" O ASP L 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 56 through 57 removed outlier: 6.209A pdb=" N ILE O 87 " --> pdb=" O VAL O 105 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP O 93 " --> pdb=" O GLN O 99 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLN O 99 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 56 through 57 removed outlier: 6.210A pdb=" N ILE M 87 " --> pdb=" O VAL M 105 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP M 93 " --> pdb=" O GLN M 99 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLN M 99 " --> pdb=" O ASP M 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 56 through 57 removed outlier: 6.215A pdb=" N ILE P 87 " --> pdb=" O VAL P 105 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP P 93 " --> pdb=" O GLN P 99 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLN P 99 " --> pdb=" O ASP P 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 83 through 89 removed outlier: 5.439A pdb=" N CYS B 84 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 102 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU B 37 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE B 138 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 39 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 169 through 173 removed outlier: 6.492A pdb=" N LEU B 170 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS B 201 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS B 172 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N THR B 200 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASN B 241 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N HIS B 238 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N MET B 266 " --> pdb=" O HIS B 238 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU B 240 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ASP B 268 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE B 265 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N HIS B 294 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N HIS B 267 " --> pdb=" O HIS B 294 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 291 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N HIS B 327 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE B 293 " --> pdb=" O HIS B 327 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLN B 401 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA B 378 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET B 169 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE B 402 " --> pdb=" O MET B 169 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY B 171 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AB6, first strand: chain 'A' and resid 83 through 89 removed outlier: 5.445A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A 37 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 169 through 173 removed outlier: 6.492A pdb=" N LEU A 170 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LYS A 201 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS A 172 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR A 200 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASN A 241 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N HIS A 238 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N MET A 266 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU A 240 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ASP A 268 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 265 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N HIS A 294 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N HIS A 267 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 291 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N HIS A 327 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE A 293 " --> pdb=" O HIS A 327 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA A 378 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET A 169 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE A 402 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY A 171 " --> pdb=" O PHE A 402 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AB9, first strand: chain 'H' and resid 83 through 89 removed outlier: 5.444A pdb=" N CYS H 84 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA H 102 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU H 37 " --> pdb=" O ILE H 138 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE H 138 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA H 39 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 169 through 173 removed outlier: 6.491A pdb=" N LEU H 170 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LYS H 201 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS H 172 " --> pdb=" O LYS H 201 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR H 200 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASN H 241 " --> pdb=" O THR H 200 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N HIS H 238 " --> pdb=" O ILE H 264 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N MET H 266 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU H 240 " --> pdb=" O MET H 266 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ASP H 268 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE H 265 " --> pdb=" O HIS H 292 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N HIS H 294 " --> pdb=" O ILE H 265 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N HIS H 267 " --> pdb=" O HIS H 294 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU H 291 " --> pdb=" O HIS H 325 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N HIS H 327 " --> pdb=" O LEU H 291 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE H 293 " --> pdb=" O HIS H 327 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLN H 401 " --> pdb=" O PRO H 376 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA H 378 " --> pdb=" O GLN H 401 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N MET H 169 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N PHE H 402 " --> pdb=" O MET H 169 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY H 171 " --> pdb=" O PHE H 402 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 353 through 354 Processing sheet with id=AC3, first strand: chain 'F' and resid 83 through 89 removed outlier: 5.443A pdb=" N CYS F 84 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA F 102 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU F 37 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE F 138 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA F 39 " --> pdb=" O GLU F 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 169 through 173 removed outlier: 6.492A pdb=" N LEU F 170 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS F 201 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS F 172 " --> pdb=" O LYS F 201 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR F 200 " --> pdb=" O TYR F 239 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASN F 241 " --> pdb=" O THR F 200 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N HIS F 238 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N MET F 266 " --> pdb=" O HIS F 238 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU F 240 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ASP F 268 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE F 265 " --> pdb=" O HIS F 292 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N HIS F 294 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N HIS F 267 " --> pdb=" O HIS F 294 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU F 291 " --> pdb=" O HIS F 325 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N HIS F 327 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE F 293 " --> pdb=" O HIS F 327 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLN F 401 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA F 378 " --> pdb=" O GLN F 401 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET F 169 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE F 402 " --> pdb=" O MET F 169 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY F 171 " --> pdb=" O PHE F 402 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AC6, first strand: chain 'I' and resid 83 through 89 removed outlier: 5.436A pdb=" N CYS I 84 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA I 102 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU I 37 " --> pdb=" O ILE I 138 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE I 138 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA I 39 " --> pdb=" O GLU I 136 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 169 through 173 removed outlier: 6.493A pdb=" N LEU I 170 " --> pdb=" O PHE I 199 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS I 201 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS I 172 " --> pdb=" O LYS I 201 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR I 200 " --> pdb=" O TYR I 239 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASN I 241 " --> pdb=" O THR I 200 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N HIS I 238 " --> pdb=" O ILE I 264 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N MET I 266 " --> pdb=" O HIS I 238 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU I 240 " --> pdb=" O MET I 266 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ASP I 268 " --> pdb=" O LEU I 240 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE I 265 " --> pdb=" O HIS I 292 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N HIS I 294 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N HIS I 267 " --> pdb=" O HIS I 294 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU I 291 " --> pdb=" O HIS I 325 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N HIS I 327 " --> pdb=" O LEU I 291 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE I 293 " --> pdb=" O HIS I 327 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLN I 401 " --> pdb=" O PRO I 376 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA I 378 " --> pdb=" O GLN I 401 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET I 169 " --> pdb=" O LEU I 400 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE I 402 " --> pdb=" O MET I 169 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY I 171 " --> pdb=" O PHE I 402 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 353 through 354 Processing sheet with id=AC9, first strand: chain 'G' and resid 83 through 89 removed outlier: 5.444A pdb=" N CYS G 84 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA G 102 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU G 37 " --> pdb=" O ILE G 138 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE G 138 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA G 39 " --> pdb=" O GLU G 136 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 169 through 173 removed outlier: 6.492A pdb=" N LEU G 170 " --> pdb=" O PHE G 199 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LYS G 201 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS G 172 " --> pdb=" O LYS G 201 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR G 200 " --> pdb=" O TYR G 239 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASN G 241 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N HIS G 238 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N MET G 266 " --> pdb=" O HIS G 238 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU G 240 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASP G 268 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE G 265 " --> pdb=" O HIS G 292 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N HIS G 294 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N HIS G 267 " --> pdb=" O HIS G 294 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU G 291 " --> pdb=" O HIS G 325 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N HIS G 327 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE G 293 " --> pdb=" O HIS G 327 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLN G 401 " --> pdb=" O PRO G 376 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA G 378 " --> pdb=" O GLN G 401 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET G 169 " --> pdb=" O LEU G 400 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE G 402 " --> pdb=" O MET G 169 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY G 171 " --> pdb=" O PHE G 402 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 353 through 354 Processing sheet with id=AD3, first strand: chain 'J' and resid 83 through 89 removed outlier: 5.435A pdb=" N CYS J 84 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA J 102 " --> pdb=" O CYS J 84 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU J 37 " --> pdb=" O ILE J 138 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE J 138 " --> pdb=" O LEU J 37 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA J 39 " --> pdb=" O GLU J 136 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 169 through 173 removed outlier: 6.492A pdb=" N LEU J 170 " --> pdb=" O PHE J 199 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LYS J 201 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS J 172 " --> pdb=" O LYS J 201 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N THR J 200 " --> pdb=" O TYR J 239 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASN J 241 " --> pdb=" O THR J 200 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N HIS J 238 " --> pdb=" O ILE J 264 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N MET J 266 " --> pdb=" O HIS J 238 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU J 240 " --> pdb=" O MET J 266 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASP J 268 " --> pdb=" O LEU J 240 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE J 265 " --> pdb=" O HIS J 292 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N HIS J 294 " --> pdb=" O ILE J 265 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N HIS J 267 " --> pdb=" O HIS J 294 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU J 291 " --> pdb=" O HIS J 325 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N HIS J 327 " --> pdb=" O LEU J 291 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE J 293 " --> pdb=" O HIS J 327 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLN J 401 " --> pdb=" O PRO J 376 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA J 378 " --> pdb=" O GLN J 401 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET J 169 " --> pdb=" O LEU J 400 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE J 402 " --> pdb=" O MET J 169 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY J 171 " --> pdb=" O PHE J 402 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 353 through 354 1623 hydrogen bonds defined for protein. 4452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.99 Time building geometry restraints manager: 15.36 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: 99.40 - 106.33: 1035 106.33 - 113.26: 18045 113.26 - 120.19: 12611 120.19 - 127.11: 14321 127.11 - 134.04: 484 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 2.440 nonbonded pdb=" O PHE P 12 " pdb=" OG SER P 16 " model vdw 2.072 2.440 nonbonded pdb=" O PHE K 12 " pdb=" OG SER K 16 " model vdw 2.074 2.440 nonbonded pdb=" O PHE E 12 " pdb=" OG SER E 16 " model vdw 2.076 2.440 nonbonded pdb=" O PHE D 12 " pdb=" OG SER D 16 " model vdw 2.076 2.440 ... (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 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 7.630 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 88.160 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.230 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.260 ------------------------------------------------------------------------------- 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 34352 Z= 0.319 Angle : 0.668 9.978 46496 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 *********************** 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 fitting. rotamer outliers: 30 poor density : 587 time to evaluate : 3.851 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: 1.6539 time to fit residues: 1180.9571 Evaluate side-chains 601 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 577 time to evaluate : 4.148 ------------------------------------------------------------------------------- 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: 1.9990 chunk 174 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 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: 2.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 34352 Z= 0.200 Angle : 0.583 8.228 46496 Z= 0.310 Chirality : 0.043 0.149 4944 Planarity : 0.005 0.051 6096 Dihedral : 5.622 34.701 4624 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.44 % Favored : 97.36 % Rotamer: Outliers : 2.18 % Allowed : 14.14 % Favored : 83.68 % 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: 1.28 (0.13), residues: 4136 helix: 1.92 (0.12), residues: 1744 sheet: 0.08 (0.17), residues: 720 loop : 0.16 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 58 HIS 0.005 0.001 HIS A 153 PHE 0.024 0.002 PHE H 345 TYR 0.010 0.002 TYR I 239 ARG 0.004 0.000 ARG K 10 *********************** 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 659 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 582 time to evaluate : 4.081 Fit side-chains revert: symmetry clash REVERT: C 51 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6803 (p0) REVERT: C 52 GLU cc_start: 0.6951 (tp30) cc_final: 0.6692 (tp30) REVERT: C 252 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8383 (mtpp) REVERT: E 31 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6772 (tp30) REVERT: N 31 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6729 (tp30) REVERT: O 35 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6500 (mp0) REVERT: M 31 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6729 (tp30) REVERT: P 32 TYR cc_start: 0.8039 (t80) cc_final: 0.7833 (t80) REVERT: B 51 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6808 (p0) REVERT: B 52 GLU cc_start: 0.6956 (tp30) cc_final: 0.6705 (tp30) REVERT: B 252 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8408 (mtpp) REVERT: A 51 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6797 (p0) REVERT: A 52 GLU cc_start: 0.6962 (tp30) cc_final: 0.6703 (tp30) REVERT: A 252 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8385 (mtpp) REVERT: H 51 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6794 (p0) REVERT: H 52 GLU cc_start: 0.6960 (tp30) cc_final: 0.6698 (tp30) REVERT: H 252 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8380 (mtpp) REVERT: F 51 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6797 (p0) REVERT: F 52 GLU cc_start: 0.6958 (tp30) cc_final: 0.6707 (tp30) REVERT: F 79 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7180 (ttt-90) REVERT: F 252 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8385 (mtpp) REVERT: I 51 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6805 (p0) REVERT: I 52 GLU cc_start: 0.6949 (tp30) cc_final: 0.6690 (tp30) REVERT: I 252 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8382 (mtpp) REVERT: G 51 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6799 (p0) REVERT: G 52 GLU cc_start: 0.6923 (tp30) cc_final: 0.6715 (tp30) REVERT: G 252 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8389 (mtpp) REVERT: J 51 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6800 (p0) REVERT: J 52 GLU cc_start: 0.6953 (tp30) cc_final: 0.6690 (tp30) REVERT: J 252 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8374 (mtpp) outliers start: 77 outliers final: 9 residues processed: 605 average time/residue: 1.7788 time to fit residues: 1245.9412 Evaluate side-chains 602 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 576 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 LYS 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 252 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 252 LYS 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 F residue 252 LYS Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain J residue 252 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 209 optimal weight: 20.0000 chunk 117 optimal weight: 8.9990 chunk 314 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 378 optimal weight: 20.0000 chunk 408 optimal weight: 4.9990 chunk 337 optimal weight: 3.9990 chunk 375 optimal weight: 0.2980 chunk 129 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 overall best weight: 4.8588 ------------------------------------------------------------------------------- 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 304 GLN J 156 GLN J 304 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 34352 Z= 0.342 Angle : 0.668 10.689 46496 Z= 0.354 Chirality : 0.048 0.227 4944 Planarity : 0.005 0.047 6096 Dihedral : 5.498 30.674 4592 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.54 % Favored : 97.27 % Rotamer: Outliers : 2.57 % Allowed : 12.67 % Favored : 84.76 % 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: 0.94 (0.12), residues: 4136 helix: 1.58 (0.12), residues: 1744 sheet: -0.24 (0.16), residues: 824 loop : 0.18 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 368 HIS 0.006 0.001 HIS G 153 PHE 0.028 0.003 PHE J 345 TYR 0.011 0.002 TYR G 80 ARG 0.006 0.001 ARG A 79 *********************** 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 656 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 565 time to evaluate : 4.608 Fit side-chains revert: symmetry clash REVERT: C 51 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6816 (p0) REVERT: C 252 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8436 (mtpp) REVERT: E 107 ARG cc_start: 0.7750 (mtm-85) cc_final: 0.7472 (mpt-90) REVERT: K 10 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6787 (ttm110) REVERT: N 10 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6808 (ttm110) REVERT: N 31 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6750 (tp30) REVERT: L 107 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7455 (mpt-90) REVERT: O 35 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6403 (mp0) REVERT: M 31 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6770 (tp30) REVERT: P 32 TYR cc_start: 0.8015 (t80) cc_final: 0.7789 (t80) REVERT: B 51 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6824 (p0) REVERT: B 252 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8441 (mtpp) REVERT: A 51 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6827 (p0) REVERT: A 252 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8439 (mtpp) REVERT: H 51 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6825 (p0) REVERT: H 252 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8434 (mtpp) REVERT: F 51 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6832 (p0) REVERT: F 252 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8431 (mtpp) REVERT: I 51 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6821 (p0) REVERT: I 252 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8453 (mtpp) REVERT: G 51 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6816 (p0) REVERT: G 252 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8435 (mtpp) REVERT: J 51 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6832 (p0) REVERT: J 252 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8421 (mtpp) outliers start: 91 outliers final: 29 residues processed: 609 average time/residue: 1.6640 time to fit residues: 1180.8079 Evaluate side-chains 614 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 567 time to evaluate : 3.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 252 LYS 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 O residue 43 GLU Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain P residue 43 GLU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 435 ARG 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 252 LYS 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 252 LYS 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 252 LYS 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 252 LYS 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 252 LYS 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 252 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 373 optimal weight: 5.9990 chunk 284 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 chunk 379 optimal weight: 8.9990 chunk 402 optimal weight: 0.9990 chunk 198 optimal weight: 0.1980 chunk 359 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34352 Z= 0.219 Angle : 0.590 8.742 46496 Z= 0.312 Chirality : 0.043 0.159 4944 Planarity : 0.004 0.052 6096 Dihedral : 5.310 30.096 4592 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.13 % Favored : 97.68 % Rotamer: Outliers : 2.18 % Allowed : 13.26 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.13), residues: 4136 helix: 1.86 (0.12), residues: 1744 sheet: -0.03 (0.17), residues: 736 loop : 0.10 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 58 HIS 0.006 0.001 HIS B 153 PHE 0.025 0.002 PHE F 345 TYR 0.009 0.002 TYR I 239 ARG 0.002 0.000 ARG G 79 *********************** 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 649 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 572 time to evaluate : 4.032 Fit side-chains revert: symmetry clash REVERT: C 51 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6835 (p0) REVERT: C 252 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8421 (mtpp) REVERT: E 31 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6770 (tp30) REVERT: K 10 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6761 (ttm110) REVERT: N 10 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6737 (ttm110) REVERT: N 31 GLU cc_start: 0.6919 (tm-30) cc_final: 0.6702 (tp30) REVERT: O 35 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6370 (mp0) REVERT: M 31 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6699 (tp30) REVERT: P 32 TYR cc_start: 0.8026 (t80) cc_final: 0.7822 (t80) REVERT: B 51 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6820 (p0) REVERT: B 252 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8416 (mtpp) REVERT: A 51 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6829 (p0) REVERT: A 52 GLU cc_start: 0.6953 (tp30) cc_final: 0.6733 (tp30) REVERT: A 252 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8416 (mtpp) REVERT: H 51 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6820 (p0) REVERT: H 52 GLU cc_start: 0.6953 (tp30) cc_final: 0.6732 (tp30) REVERT: H 252 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8412 (mtpp) REVERT: F 51 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6832 (p0) REVERT: F 79 ARG cc_start: 0.7653 (ttt-90) cc_final: 0.7251 (ttt-90) REVERT: F 252 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8416 (mtpp) REVERT: I 51 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6811 (p0) REVERT: I 52 GLU cc_start: 0.6953 (tp30) cc_final: 0.6737 (tp30) REVERT: I 252 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8418 (mtpp) REVERT: G 51 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6812 (p0) REVERT: G 52 GLU cc_start: 0.6932 (tp30) cc_final: 0.6712 (tp30) REVERT: G 252 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8417 (mtpp) REVERT: J 51 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6836 (p0) REVERT: J 252 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8404 (mtpp) outliers start: 77 outliers final: 21 residues processed: 605 average time/residue: 1.7825 time to fit residues: 1247.5049 Evaluate side-chains 601 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 562 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain K residue 10 ARG Chi-restraints excluded: chain N 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 251 MET Chi-restraints excluded: chain B residue 252 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 251 MET Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 252 LYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 81 LYS Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain J residue 252 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 334 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 299 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 343 optimal weight: 0.6980 chunk 277 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 360 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 GLN C 156 GLN C 304 GLN E 29 GLN O 29 GLN M 29 GLN B 156 GLN B 304 GLN A 156 GLN A 304 GLN ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 GLN H 304 GLN F 156 GLN F 304 GLN ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN I 304 GLN ** I 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 304 GLN ** G 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN J 304 GLN ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 34352 Z= 0.150 Angle : 0.528 8.840 46496 Z= 0.278 Chirality : 0.041 0.135 4944 Planarity : 0.004 0.056 6096 Dihedral : 4.991 26.810 4592 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.96 % Favored : 97.85 % Rotamer: Outliers : 1.87 % Allowed : 13.52 % Favored : 84.62 % 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: 1.43 (0.13), residues: 4136 helix: 2.17 (0.12), residues: 1752 sheet: -0.30 (0.16), residues: 784 loop : 0.37 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 58 HIS 0.004 0.001 HIS A 153 PHE 0.021 0.002 PHE B 345 TYR 0.009 0.001 TYR F 239 ARG 0.002 0.000 ARG I 79 *********************** 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 638 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 572 time to evaluate : 3.833 Fit side-chains revert: symmetry clash REVERT: C 252 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8347 (mtpp) REVERT: E 31 GLU cc_start: 0.6956 (tm-30) cc_final: 0.6755 (tp30) REVERT: K 10 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6680 (ttm110) REVERT: N 31 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6712 (tp30) REVERT: O 35 GLU cc_start: 0.6769 (mt-10) cc_final: 0.6349 (mp0) REVERT: O 107 ARG cc_start: 0.7615 (mtt90) cc_final: 0.7400 (mtt-85) REVERT: B 252 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8358 (mtpp) REVERT: A 252 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8348 (mtpp) REVERT: H 252 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8339 (mtpp) REVERT: F 252 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8343 (mtpp) REVERT: I 252 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8348 (mtpp) REVERT: G 252 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8349 (mtpp) REVERT: J 252 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8335 (mtpp) outliers start: 66 outliers final: 10 residues processed: 592 average time/residue: 1.8025 time to fit residues: 1232.2990 Evaluate side-chains 581 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 561 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain K residue 10 ARG Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain P residue 43 GLU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 252 LYS Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain J residue 252 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 135 optimal weight: 7.9990 chunk 362 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 402 optimal weight: 3.9990 chunk 334 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 34352 Z= 0.301 Angle : 0.637 10.136 46496 Z= 0.335 Chirality : 0.046 0.199 4944 Planarity : 0.005 0.057 6096 Dihedral : 5.304 26.908 4592 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.47 % Favored : 97.34 % Rotamer: Outliers : 1.95 % Allowed : 13.72 % 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: 1.14 (0.13), residues: 4136 helix: 1.84 (0.12), residues: 1744 sheet: -0.12 (0.17), residues: 736 loop : 0.12 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 368 HIS 0.007 0.001 HIS B 153 PHE 0.027 0.003 PHE I 345 TYR 0.010 0.002 TYR F 103 ARG 0.006 0.001 ARG M 107 *********************** 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 633 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 564 time to evaluate : 4.297 Fit side-chains REVERT: C 252 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8427 (mtpp) REVERT: E 31 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6710 (tp30) REVERT: K 10 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6691 (ttm110) REVERT: N 10 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6818 (ttm110) REVERT: N 31 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6718 (tp30) REVERT: O 31 GLU cc_start: 0.7015 (tp30) cc_final: 0.6538 (tp30) REVERT: O 35 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6330 (mp0) REVERT: O 107 ARG cc_start: 0.7678 (mtt90) cc_final: 0.7475 (mtt-85) REVERT: B 252 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8420 (mtpp) REVERT: B 435 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.6691 (mtm-85) REVERT: A 77 MET cc_start: 0.6345 (mpp) cc_final: 0.5506 (mmm) REVERT: A 252 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8428 (mtpp) REVERT: H 77 MET cc_start: 0.6341 (mpp) cc_final: 0.5501 (mmm) REVERT: H 252 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8418 (mtpp) REVERT: F 252 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8422 (mtpp) REVERT: I 252 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8424 (mtpp) REVERT: G 77 MET cc_start: 0.6341 (mpp) cc_final: 0.5502 (mmm) REVERT: G 252 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8424 (mtpp) REVERT: J 252 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8410 (mtpp) outliers start: 69 outliers final: 25 residues processed: 604 average time/residue: 1.7438 time to fit residues: 1224.1118 Evaluate side-chains 605 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 569 time to evaluate : 3.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain K residue 10 ARG Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 23 THR 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 252 LYS Chi-restraints excluded: chain H residue 23 THR 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 252 LYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain J residue 252 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 388 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 229 optimal weight: 3.9990 chunk 293 optimal weight: 20.0000 chunk 227 optimal weight: 4.9990 chunk 338 optimal weight: 9.9990 chunk 224 optimal weight: 0.8980 chunk 400 optimal weight: 6.9990 chunk 250 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 304 GLN ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN N 29 GLN B 156 GLN B 304 GLN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 304 GLN ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 GLN H 304 GLN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN F 304 GLN I 156 GLN I 304 GLN ** I 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 304 GLN ** G 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN J 304 GLN ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34352 Z= 0.205 Angle : 0.577 9.343 46496 Z= 0.303 Chirality : 0.043 0.149 4944 Planarity : 0.004 0.057 6096 Dihedral : 5.172 26.396 4592 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.32 % Favored : 97.49 % Rotamer: Outliers : 1.87 % Allowed : 13.86 % Favored : 84.28 % 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: 1.25 (0.13), residues: 4136 helix: 1.97 (0.12), residues: 1744 sheet: -0.14 (0.17), residues: 736 loop : 0.17 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 58 HIS 0.006 0.001 HIS F 153 PHE 0.023 0.002 PHE B 345 TYR 0.010 0.002 TYR M 32 ARG 0.007 0.000 ARG M 107 *********************** 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 636 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 570 time to evaluate : 3.854 Fit side-chains revert: symmetry clash REVERT: D 10 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6815 (ttm110) REVERT: D 96 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6809 (mtpt) REVERT: C 252 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8389 (mtpp) REVERT: E 10 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6810 (ttm110) REVERT: K 10 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6685 (ttm110) REVERT: N 10 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6730 (ttm110) REVERT: N 96 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.7052 (mtpt) REVERT: L 10 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6803 (ttm110) REVERT: O 10 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6821 (ttm110) REVERT: O 35 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6331 (mp0) REVERT: O 96 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6820 (mtpt) REVERT: M 10 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6796 (ttm110) REVERT: M 96 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6794 (mtpt) REVERT: P 10 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6814 (ttm110) REVERT: P 96 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6810 (mtpt) REVERT: B 252 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8410 (mtpp) REVERT: A 77 MET cc_start: 0.6282 (mpp) cc_final: 0.5472 (mmm) REVERT: A 252 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8391 (mtpp) REVERT: H 77 MET cc_start: 0.6278 (mpp) cc_final: 0.5468 (mmm) REVERT: H 252 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8386 (mtpp) REVERT: F 79 ARG cc_start: 0.7607 (ttt-90) cc_final: 0.7198 (ttt-90) REVERT: F 252 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8399 (mtpp) REVERT: I 252 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8391 (mtpp) REVERT: G 77 MET cc_start: 0.6280 (mpp) cc_final: 0.5467 (mmm) REVERT: G 252 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8392 (mtpp) REVERT: J 252 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8388 (mtpp) outliers start: 66 outliers final: 21 residues processed: 605 average time/residue: 1.7586 time to fit residues: 1239.3743 Evaluate side-chains 594 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 552 time to evaluate : 3.933 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain E residue 10 ARG Chi-restraints excluded: chain K residue 10 ARG Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 96 LYS Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain O residue 10 ARG Chi-restraints excluded: chain O residue 96 LYS Chi-restraints excluded: chain M residue 10 ARG Chi-restraints excluded: chain M residue 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 65 THR Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 252 LYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain J residue 252 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 248 optimal weight: 0.5980 chunk 160 optimal weight: 0.8980 chunk 239 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 273 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 315 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 304 GLN ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN B 156 GLN B 304 GLN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 304 GLN ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 GLN H 304 GLN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN F 304 GLN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34352 Z= 0.192 Angle : 0.566 9.268 46496 Z= 0.297 Chirality : 0.043 0.144 4944 Planarity : 0.004 0.059 6096 Dihedral : 5.096 25.556 4592 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.42 % Favored : 97.41 % Rotamer: Outliers : 1.92 % Allowed : 14.00 % Favored : 84.08 % 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: 1.30 (0.13), residues: 4136 helix: 2.02 (0.12), residues: 1744 sheet: -0.14 (0.17), residues: 736 loop : 0.19 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 58 HIS 0.006 0.001 HIS A 153 PHE 0.022 0.002 PHE C 345 TYR 0.010 0.002 TYR N 32 ARG 0.003 0.000 ARG C 358 *********************** 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 633 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 565 time to evaluate : 4.025 Fit side-chains REVERT: D 10 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6786 (ttm110) REVERT: D 96 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6782 (mtpt) REVERT: C 252 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8389 (mtpp) REVERT: E 10 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6806 (ttm110) REVERT: E 96 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6791 (mtpt) REVERT: K 10 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6636 (ttm110) REVERT: K 96 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6810 (mtpt) REVERT: N 10 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6675 (ttm110) REVERT: N 96 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6786 (mtpt) REVERT: L 10 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6804 (ttm110) REVERT: L 96 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6796 (mtpt) REVERT: O 10 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6811 (ttm110) REVERT: O 35 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6337 (mp0) REVERT: O 96 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6786 (mtpt) REVERT: O 107 ARG cc_start: 0.7667 (mtt90) cc_final: 0.7353 (mtt-85) REVERT: M 10 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6802 (ttm110) REVERT: M 96 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6779 (mtpt) REVERT: P 10 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6808 (ttm110) REVERT: P 96 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6783 (mtpt) REVERT: B 252 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8380 (mtpp) REVERT: B 435 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.6682 (mtm-85) REVERT: A 77 MET cc_start: 0.6226 (mpp) cc_final: 0.5435 (mmm) REVERT: A 252 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8385 (mtpp) REVERT: H 77 MET cc_start: 0.6224 (mpp) cc_final: 0.5432 (mmm) REVERT: H 252 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8383 (mtpp) REVERT: F 79 ARG cc_start: 0.7685 (ttt-90) cc_final: 0.7105 (ttt-90) REVERT: F 252 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8385 (mtpp) REVERT: I 252 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8387 (mtpp) REVERT: G 77 MET cc_start: 0.6224 (mpp) cc_final: 0.5432 (mmm) REVERT: G 252 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8389 (mtpp) REVERT: J 252 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8374 (mtpp) outliers start: 68 outliers final: 21 residues processed: 608 average time/residue: 1.7598 time to fit residues: 1237.4891 Evaluate side-chains 605 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 559 time to evaluate : 4.235 ------------------------------------------------------------------------------- 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 251 MET Chi-restraints excluded: chain C residue 252 LYS 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 251 MET Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 252 LYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain J residue 252 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 364 optimal weight: 10.0000 chunk 384 optimal weight: 1.9990 chunk 350 optimal weight: 0.0670 chunk 373 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 chunk 293 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 337 optimal weight: 3.9990 chunk 353 optimal weight: 3.9990 chunk 372 optimal weight: 20.0000 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 304 GLN ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 304 GLN A 156 GLN A 304 GLN H 156 GLN H 304 GLN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN F 304 GLN I 156 GLN I 304 GLN ** I 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 304 GLN ** G 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN J 304 GLN ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 : 0.003 0.028 34352 Z= 0.227 Angle : 0.592 9.480 46496 Z= 0.311 Chirality : 0.044 0.158 4944 Planarity : 0.005 0.061 6096 Dihedral : 5.167 25.914 4592 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.39 % Favored : 97.41 % Rotamer: Outliers : 1.78 % Allowed : 14.03 % Favored : 84.19 % 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: 1.93 (0.12), residues: 1744 sheet: -0.14 (0.17), residues: 736 loop : 0.15 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 58 HIS 0.006 0.001 HIS I 153 PHE 0.024 0.002 PHE H 345 TYR 0.010 0.002 TYR O 86 ARG 0.003 0.000 ARG G 358 *********************** 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 621 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 558 time to evaluate : 4.088 Fit side-chains REVERT: D 10 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6727 (ttm110) REVERT: D 96 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6783 (mtpt) REVERT: C 252 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8410 (mtpp) REVERT: E 10 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6771 (ttm110) REVERT: E 96 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6802 (mtpt) REVERT: K 10 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6614 (ttm110) REVERT: K 96 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6799 (mtpt) REVERT: N 10 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6661 (ttm110) REVERT: N 96 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6791 (mtpt) REVERT: L 10 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6758 (ttm110) REVERT: L 96 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6797 (mtpt) REVERT: O 10 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6755 (ttm110) REVERT: O 35 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6324 (mp0) REVERT: O 96 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6797 (mtpt) REVERT: M 10 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6768 (ttm110) REVERT: M 96 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6803 (mtpt) REVERT: P 10 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6752 (ttm110) REVERT: P 96 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6781 (mtpt) REVERT: B 252 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8418 (mtpp) REVERT: B 435 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.6666 (mtm-85) REVERT: A 77 MET cc_start: 0.6189 (mpp) cc_final: 0.5378 (mmm) REVERT: A 252 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8412 (mtpp) REVERT: H 77 MET cc_start: 0.6187 (mpp) cc_final: 0.5784 (mmm) REVERT: H 252 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8389 (mtpp) REVERT: F 79 ARG cc_start: 0.7648 (ttt-90) cc_final: 0.7227 (ttt-90) REVERT: F 252 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8412 (mtpp) REVERT: I 252 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8412 (mtpp) REVERT: G 77 MET cc_start: 0.6187 (mpp) cc_final: 0.5374 (mmm) REVERT: G 252 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8413 (mtpp) REVERT: J 252 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8401 (mtpp) outliers start: 63 outliers final: 28 residues processed: 597 average time/residue: 1.7726 time to fit residues: 1224.9540 Evaluate side-chains 608 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 555 time to evaluate : 3.594 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 282 LYS 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 65 THR Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 252 LYS Chi-restraints excluded: chain H residue 282 LYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 282 LYS Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain J residue 252 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 245 optimal weight: 9.9990 chunk 395 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 414 optimal weight: 20.0000 chunk 381 optimal weight: 10.0000 chunk 330 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 254 optimal weight: 8.9990 chunk 202 optimal weight: 0.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 B 156 GLN B 304 GLN A 156 GLN A 304 GLN H 156 GLN H 304 GLN 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 J 156 GLN J 304 GLN ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 34352 Z= 0.410 Angle : 0.716 11.236 46496 Z= 0.378 Chirality : 0.051 0.251 4944 Planarity : 0.006 0.053 6096 Dihedral : 5.555 28.109 4592 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.64 % Favored : 97.17 % Rotamer: Outliers : 1.64 % Allowed : 14.23 % 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: 0.81 (0.12), residues: 4136 helix: 1.45 (0.11), residues: 1744 sheet: -0.41 (0.16), residues: 824 loop : 0.20 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 58 HIS 0.006 0.002 HIS J 153 PHE 0.031 0.004 PHE B 345 TYR 0.012 0.003 TYR F 103 ARG 0.005 0.001 ARG B 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 560 time to evaluate : 3.918 Fit side-chains REVERT: D 10 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6817 (ttm110) REVERT: D 96 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6868 (mtpt) REVERT: C 252 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8451 (mtpp) REVERT: E 10 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6805 (ttm110) REVERT: E 96 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6877 (mtpt) REVERT: K 10 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6605 (ttm110) REVERT: K 96 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6862 (mtpt) REVERT: N 10 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.6701 (ttm110) REVERT: N 96 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6861 (mtpt) REVERT: L 10 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6822 (ttm110) REVERT: L 96 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6872 (mtpt) REVERT: O 10 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6810 (ttm110) REVERT: O 35 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6326 (mp0) REVERT: O 96 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6880 (mtpt) REVERT: M 10 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6825 (ttm110) REVERT: M 96 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6857 (mtpt) REVERT: P 10 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6789 (ttm110) REVERT: P 96 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6863 (mtpt) REVERT: B 252 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8442 (mtpp) REVERT: B 435 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.6624 (mtm-85) REVERT: A 77 MET cc_start: 0.6294 (mpp) cc_final: 0.5902 (mmm) REVERT: A 252 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8453 (mtpp) REVERT: H 77 MET cc_start: 0.6291 (mpp) cc_final: 0.5903 (mmm) REVERT: H 252 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8449 (mtpp) REVERT: F 252 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8452 (mtpp) REVERT: I 252 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8452 (mtpp) REVERT: G 77 MET cc_start: 0.6295 (mpp) cc_final: 0.5900 (mmm) REVERT: G 252 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8455 (mtpp) REVERT: J 252 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8442 (mtpp) outliers start: 58 outliers final: 28 residues processed: 593 average time/residue: 1.7892 time to fit residues: 1242.1404 Evaluate side-chains 608 residues out of total 3536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 555 time to evaluate : 4.013 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 282 LYS 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 65 THR Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 435 ARG Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 252 LYS Chi-restraints excluded: chain H residue 282 LYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 251 MET Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 282 LYS Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 251 MET Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 251 MET Chi-restraints excluded: chain J residue 252 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 262 optimal weight: 3.9990 chunk 351 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 304 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 330 optimal weight: 20.0000 chunk 138 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 L 70 GLN B 156 GLN B 304 GLN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 304 GLN ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 GLN H 304 GLN F 156 GLN F 304 GLN ** F 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN I 304 GLN ** I 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 304 GLN ** G 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 156 GLN J 304 GLN ** J 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.159487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119924 restraints weight = 30654.312| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.40 r_work: 0.3265 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 34352 Z= 0.202 Angle : 0.582 9.821 46496 Z= 0.307 Chirality : 0.043 0.147 4944 Planarity : 0.004 0.057 6096 Dihedral : 5.248 26.487 4592 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.39 % Allowed : 14.45 % Favored : 84.16 % 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: 1.15 (0.13), residues: 4136 helix: 1.86 (0.12), residues: 1744 sheet: -0.14 (0.17), residues: 736 loop : 0.13 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 58 HIS 0.006 0.001 HIS J 153 PHE 0.023 0.002 PHE F 345 TYR 0.010 0.002 TYR M 32 ARG 0.003 0.000 ARG I 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17013.98 seconds wall clock time: 299 minutes 18.90 seconds (17958.90 seconds total)