Starting phenix.real_space_refine on Sun Mar 17 13:53:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xde_33145/03_2024/7xde_33145_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xde_33145/03_2024/7xde_33145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xde_33145/03_2024/7xde_33145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xde_33145/03_2024/7xde_33145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xde_33145/03_2024/7xde_33145_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xde_33145/03_2024/7xde_33145_updated.pdb" } resolution = 2.72 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= 0.009 sd= 0.228 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 92 5.16 5 C 11420 2.51 5 N 3048 2.21 5 O 3328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 80": "OE1" <-> "OE2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ASP 504": "OD1" <-> "OD2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A ASP 563": "OD1" <-> "OD2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B ASP 488": "OD1" <-> "OD2" Residue "B GLU 493": "OE1" <-> "OE2" Residue "B ASP 504": "OD1" <-> "OD2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B GLU 545": "OE1" <-> "OE2" Residue "B ASP 563": "OD1" <-> "OD2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 139": "OD1" <-> "OD2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "C ARG 405": "NH1" <-> "NH2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C GLU 432": "OE1" <-> "OE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C ARG 484": "NH1" <-> "NH2" Residue "C ASP 488": "OD1" <-> "OD2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C ASP 504": "OD1" <-> "OD2" Residue "C GLU 505": "OE1" <-> "OE2" Residue "C GLU 506": "OE1" <-> "OE2" Residue "C GLU 545": "OE1" <-> "OE2" Residue "C ASP 563": "OD1" <-> "OD2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D GLU 314": "OE1" <-> "OE2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D ARG 405": "NH1" <-> "NH2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D GLU 438": "OE1" <-> "OE2" Residue "D ARG 484": "NH1" <-> "NH2" Residue "D ASP 488": "OD1" <-> "OD2" Residue "D GLU 493": "OE1" <-> "OE2" Residue "D ASP 504": "OD1" <-> "OD2" Residue "D GLU 505": "OE1" <-> "OE2" Residue "D GLU 506": "OE1" <-> "OE2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "D ASP 563": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17896 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4430 Classifications: {'peptide': 562} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 528} Chain: "B" Number of atoms: 4430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4430 Classifications: {'peptide': 562} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 528} Chain: "C" Number of atoms: 4430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4430 Classifications: {'peptide': 562} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 528} Chain: "D" Number of atoms: 4430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4430 Classifications: {'peptide': 562} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 528} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.81, per 1000 atoms: 0.55 Number of scatterers: 17896 At special positions: 0 Unit cell: (134.747, 134.747, 79.575, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 8 15.00 O 3328 8.00 N 3048 7.00 C 11420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 6.64 Conformation dependent library (CDL) restraints added in 3.0 seconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 8 sheets defined 46.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 61 through 74 Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 105 through 111 Proline residue: A 109 - end of helix No H-bonds generated for 'chain 'A' and resid 105 through 111' Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 173 through 190 removed outlier: 3.641A pdb=" N GLY A 178 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 4.403A pdb=" N CYS A 190 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 229 through 246 Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 281 through 297 Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.702A pdb=" N LYS A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 384 Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 489 through 501 Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 516 through 536 removed outlier: 5.441A pdb=" N GLN A 520 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER A 523 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR A 535 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 61 through 74 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 93 through 102 Processing helix chain 'B' and resid 105 through 111 Proline residue: B 109 - end of helix No H-bonds generated for 'chain 'B' and resid 105 through 111' Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'B' and resid 173 through 190 removed outlier: 3.641A pdb=" N GLY B 178 " --> pdb=" O TYR B 175 " (cutoff:3.500A) Proline residue: B 180 - end of helix removed outlier: 4.403A pdb=" N CYS B 190 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 229 through 246 Processing helix chain 'B' and resid 259 through 269 Processing helix chain 'B' and resid 281 through 297 Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.702A pdb=" N LYS B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 384 Processing helix chain 'B' and resid 401 through 410 Processing helix chain 'B' and resid 423 through 425 No H-bonds generated for 'chain 'B' and resid 423 through 425' Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 489 through 501 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 516 through 536 removed outlier: 5.441A pdb=" N GLN B 520 " --> pdb=" O ALA B 517 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER B 523 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR B 535 " --> pdb=" O GLU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 554 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 61 through 74 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 105 through 111 Proline residue: C 109 - end of helix No H-bonds generated for 'chain 'C' and resid 105 through 111' Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 137 through 139 No H-bonds generated for 'chain 'C' and resid 137 through 139' Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 173 through 190 removed outlier: 3.642A pdb=" N GLY C 178 " --> pdb=" O TYR C 175 " (cutoff:3.500A) Proline residue: C 180 - end of helix removed outlier: 4.403A pdb=" N CYS C 190 " --> pdb=" O TYR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 229 through 246 Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 281 through 297 Processing helix chain 'C' and resid 314 through 330 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.702A pdb=" N LYS C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 384 Processing helix chain 'C' and resid 401 through 410 Processing helix chain 'C' and resid 423 through 425 No H-bonds generated for 'chain 'C' and resid 423 through 425' Processing helix chain 'C' and resid 430 through 436 Processing helix chain 'C' and resid 467 through 469 No H-bonds generated for 'chain 'C' and resid 467 through 469' Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 489 through 501 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 516 through 536 removed outlier: 5.440A pdb=" N GLN C 520 " --> pdb=" O ALA C 517 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER C 523 " --> pdb=" O GLN C 520 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR C 535 " --> pdb=" O GLU C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 554 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 61 through 74 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 93 through 102 Processing helix chain 'D' and resid 105 through 111 Proline residue: D 109 - end of helix No H-bonds generated for 'chain 'D' and resid 105 through 111' Processing helix chain 'D' and resid 115 through 123 Processing helix chain 'D' and resid 137 through 139 No H-bonds generated for 'chain 'D' and resid 137 through 139' Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 173 through 190 removed outlier: 3.641A pdb=" N GLY D 178 " --> pdb=" O TYR D 175 " (cutoff:3.500A) Proline residue: D 180 - end of helix removed outlier: 4.403A pdb=" N CYS D 190 " --> pdb=" O TYR D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 210 through 214 Processing helix chain 'D' and resid 229 through 246 Processing helix chain 'D' and resid 259 through 269 Processing helix chain 'D' and resid 281 through 297 Processing helix chain 'D' and resid 314 through 330 Processing helix chain 'D' and resid 334 through 340 removed outlier: 3.702A pdb=" N LYS D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 384 Processing helix chain 'D' and resid 401 through 410 Processing helix chain 'D' and resid 423 through 425 No H-bonds generated for 'chain 'D' and resid 423 through 425' Processing helix chain 'D' and resid 430 through 436 Processing helix chain 'D' and resid 467 through 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 489 through 501 Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 516 through 536 removed outlier: 5.440A pdb=" N GLN D 520 " --> pdb=" O ALA D 517 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER D 523 " --> pdb=" O GLN D 520 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR D 535 " --> pdb=" O GLU D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 554 Processing sheet with id= A, first strand: chain 'A' and resid 133 through 136 removed outlier: 6.843A pdb=" N ALA A 157 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL A 201 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL A 159 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE A 203 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR A 161 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A 251 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL A 160 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN A 253 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.256A pdb=" N ILE A 307 " --> pdb=" O TRP A 342 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE A 344 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE A 309 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR A 388 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU A 310 " --> pdb=" O THR A 388 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 390 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL A 415 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLY A 391 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE A 417 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU A 442 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA A 418 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA A 444 " --> pdb=" O ALA A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 133 through 136 removed outlier: 6.842A pdb=" N ALA B 157 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL B 201 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 159 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE B 203 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR B 161 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU B 251 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL B 160 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN B 253 " --> pdb=" O VAL B 160 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.255A pdb=" N ILE B 307 " --> pdb=" O TRP B 342 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE B 344 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE B 309 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR B 388 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU B 310 " --> pdb=" O THR B 388 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 390 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 415 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLY B 391 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE B 417 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU B 442 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA B 418 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA B 444 " --> pdb=" O ALA B 418 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 133 through 136 removed outlier: 6.843A pdb=" N ALA C 157 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL C 201 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL C 159 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE C 203 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR C 161 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU C 251 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL C 160 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN C 253 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 341 through 344 removed outlier: 6.256A pdb=" N ILE C 307 " --> pdb=" O TRP C 342 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N PHE C 344 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE C 309 " --> pdb=" O PHE C 344 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR C 388 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU C 310 " --> pdb=" O THR C 388 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 390 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL C 415 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLY C 391 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE C 417 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU C 442 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA C 418 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA C 444 " --> pdb=" O ALA C 418 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 133 through 136 removed outlier: 6.843A pdb=" N ALA D 157 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL D 201 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL D 159 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE D 203 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR D 161 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU D 251 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL D 160 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN D 253 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 341 through 344 removed outlier: 6.256A pdb=" N ILE D 307 " --> pdb=" O TRP D 342 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE D 344 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE D 309 " --> pdb=" O PHE D 344 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR D 388 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU D 310 " --> pdb=" O THR D 388 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE D 390 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL D 415 " --> pdb=" O ILE D 389 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLY D 391 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE D 417 " --> pdb=" O GLY D 391 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU D 442 " --> pdb=" O ILE D 416 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA D 418 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA D 444 " --> pdb=" O ALA D 418 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 596 hydrogen bonds defined for protein. 1440 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: 4.65 Time building geometry restraints manager: 7.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2972 1.31 - 1.43: 4680 1.43 - 1.56: 10460 1.56 - 1.68: 40 1.68 - 1.80: 148 Bond restraints: 18300 Sorted by residual: bond pdb=" C2D NAD C 601 " pdb=" C3D NAD C 601 " ideal model delta sigma weight residual 1.531 1.243 0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.243 0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C2D NAD D 601 " pdb=" C3D NAD D 601 " ideal model delta sigma weight residual 1.531 1.244 0.287 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C2D NAD B 601 " pdb=" C3D NAD B 601 " ideal model delta sigma weight residual 1.531 1.244 0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C1B NAD D 601 " pdb=" C2B NAD D 601 " ideal model delta sigma weight residual 1.534 1.279 0.255 2.00e-02 2.50e+03 1.62e+02 ... (remaining 18295 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.26: 452 105.26 - 112.45: 9227 112.45 - 119.63: 6131 119.63 - 126.81: 8779 126.81 - 133.99: 231 Bond angle restraints: 24820 Sorted by residual: angle pdb=" O1A NAD B 601 " pdb=" PA NAD B 601 " pdb=" O2A NAD B 601 " ideal model delta sigma weight residual 122.64 108.96 13.68 3.00e+00 1.11e-01 2.08e+01 angle pdb=" O1A NAD D 601 " pdb=" PA NAD D 601 " pdb=" O2A NAD D 601 " ideal model delta sigma weight residual 122.64 108.98 13.66 3.00e+00 1.11e-01 2.07e+01 angle pdb=" O1A NAD C 601 " pdb=" PA NAD C 601 " pdb=" O2A NAD C 601 " ideal model delta sigma weight residual 122.64 109.00 13.64 3.00e+00 1.11e-01 2.07e+01 angle pdb=" O1A NAD A 601 " pdb=" PA NAD A 601 " pdb=" O2A NAD A 601 " ideal model delta sigma weight residual 122.64 109.03 13.61 3.00e+00 1.11e-01 2.06e+01 angle pdb=" N ARG C 197 " pdb=" CA ARG C 197 " pdb=" C ARG C 197 " ideal model delta sigma weight residual 113.15 117.96 -4.81 1.19e+00 7.06e-01 1.63e+01 ... (remaining 24815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 10066 17.01 - 34.01: 932 34.01 - 51.02: 190 51.02 - 68.03: 20 68.03 - 85.03: 20 Dihedral angle restraints: 11228 sinusoidal: 4712 harmonic: 6516 Sorted by residual: dihedral pdb=" CG ARG A 70 " pdb=" CD ARG A 70 " pdb=" NE ARG A 70 " pdb=" CZ ARG A 70 " ideal model delta sinusoidal sigma weight residual 90.00 4.97 85.03 2 1.50e+01 4.44e-03 2.12e+01 dihedral pdb=" CG ARG D 70 " pdb=" CD ARG D 70 " pdb=" NE ARG D 70 " pdb=" CZ ARG D 70 " ideal model delta sinusoidal sigma weight residual 90.00 4.97 85.03 2 1.50e+01 4.44e-03 2.12e+01 dihedral pdb=" CG ARG B 70 " pdb=" CD ARG B 70 " pdb=" NE ARG B 70 " pdb=" CZ ARG B 70 " ideal model delta sinusoidal sigma weight residual 90.00 5.00 85.00 2 1.50e+01 4.44e-03 2.12e+01 ... (remaining 11225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2368 0.070 - 0.141: 338 0.141 - 0.211: 38 0.211 - 0.281: 4 0.281 - 0.351: 4 Chirality restraints: 2752 Sorted by residual: chirality pdb=" C3D NAD D 601 " pdb=" C2D NAD D 601 " pdb=" C4D NAD D 601 " pdb=" O3D NAD D 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C3D NAD A 601 " pdb=" C2D NAD A 601 " pdb=" C4D NAD A 601 " pdb=" O3D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C3D NAD C 601 " pdb=" C2D NAD C 601 " pdb=" C4D NAD C 601 " pdb=" O3D NAD C 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 2749 not shown) Planarity restraints: 3196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 460 " -0.012 2.00e-02 2.50e+03 1.74e-02 5.30e+00 pdb=" CG PHE D 460 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE D 460 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE D 460 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 460 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE D 460 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 460 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 460 " -0.012 2.00e-02 2.50e+03 1.73e-02 5.25e+00 pdb=" CG PHE B 460 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 460 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE B 460 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 460 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 460 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 460 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 460 " 0.011 2.00e-02 2.50e+03 1.72e-02 5.15e+00 pdb=" CG PHE A 460 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 460 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 460 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 460 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 460 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 460 " -0.001 2.00e-02 2.50e+03 ... (remaining 3193 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 264 2.67 - 3.23: 17195 3.23 - 3.78: 28715 3.78 - 4.34: 41512 4.34 - 4.90: 67338 Nonbonded interactions: 155024 Sorted by model distance: nonbonded pdb=" OD1 ASP D 236 " pdb=" OH TYR D 269 " model vdw 2.110 2.440 nonbonded pdb=" OD1 ASP A 236 " pdb=" OH TYR A 269 " model vdw 2.110 2.440 nonbonded pdb=" OD1 ASP C 236 " pdb=" OH TYR C 269 " model vdw 2.111 2.440 nonbonded pdb=" OD1 ASP B 236 " pdb=" OH TYR B 269 " model vdw 2.111 2.440 nonbonded pdb=" OD1 ASP B 139 " pdb=" OH TYR C 570 " model vdw 2.153 2.440 ... (remaining 155019 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 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.580 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 47.040 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.011 0.288 18300 Z= 0.783 Angle : 0.824 13.680 24820 Z= 0.404 Chirality : 0.053 0.351 2752 Planarity : 0.004 0.032 3196 Dihedral : 13.604 85.035 7052 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.63 % Allowed : 0.00 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.38 (0.18), residues: 2240 helix: 0.18 (0.16), residues: 1032 sheet: 0.70 (0.35), residues: 208 loop : 0.46 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 572 HIS 0.005 0.002 HIS B 125 PHE 0.036 0.003 PHE D 460 TYR 0.033 0.002 TYR D 231 ARG 0.018 0.001 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 252 time to evaluate : 1.905 Fit side-chains REVERT: A 239 MET cc_start: 0.8637 (mmm) cc_final: 0.8350 (mmm) REVERT: A 384 LEU cc_start: 0.8122 (mt) cc_final: 0.7897 (mt) REVERT: B 239 MET cc_start: 0.8629 (mmm) cc_final: 0.8344 (mmm) REVERT: B 384 LEU cc_start: 0.8155 (mt) cc_final: 0.7925 (mt) REVERT: B 551 LYS cc_start: 0.8564 (ttpp) cc_final: 0.8362 (ttpp) REVERT: C 239 MET cc_start: 0.8636 (mmm) cc_final: 0.8341 (mmm) REVERT: C 384 LEU cc_start: 0.8123 (mt) cc_final: 0.7896 (mt) REVERT: C 551 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8365 (ttpp) REVERT: D 239 MET cc_start: 0.8630 (mmm) cc_final: 0.8340 (mmm) REVERT: D 384 LEU cc_start: 0.8118 (mt) cc_final: 0.7901 (mt) REVERT: D 551 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8367 (ttpp) outliers start: 12 outliers final: 0 residues processed: 252 average time/residue: 1.3945 time to fit residues: 389.8075 Evaluate side-chains 182 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 67 optimal weight: 0.0770 chunk 106 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 203 optimal weight: 20.0000 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN B 382 ASN C 382 ASN D 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18300 Z= 0.169 Angle : 0.497 5.581 24820 Z= 0.249 Chirality : 0.042 0.169 2752 Planarity : 0.004 0.027 3196 Dihedral : 7.443 83.290 2684 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.47 % Allowed : 9.43 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.71 (0.18), residues: 2240 helix: 0.47 (0.17), residues: 1036 sheet: 0.67 (0.37), residues: 208 loop : 0.67 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 558 HIS 0.003 0.000 HIS A 125 PHE 0.018 0.002 PHE B 471 TYR 0.011 0.001 TYR D 222 ARG 0.003 0.000 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 207 time to evaluate : 2.045 Fit side-chains REVERT: A 70 ARG cc_start: 0.7597 (ptm-80) cc_final: 0.7393 (ppt170) REVERT: A 209 ASN cc_start: 0.8081 (t0) cc_final: 0.7855 (t0) REVERT: A 239 MET cc_start: 0.8469 (mmm) cc_final: 0.8263 (mmm) REVERT: A 384 LEU cc_start: 0.8166 (mt) cc_final: 0.7930 (mt) REVERT: B 70 ARG cc_start: 0.7604 (ptm-80) cc_final: 0.7397 (ppt170) REVERT: B 209 ASN cc_start: 0.8077 (t0) cc_final: 0.7854 (t0) REVERT: B 239 MET cc_start: 0.8468 (mmm) cc_final: 0.8261 (mmm) REVERT: B 384 LEU cc_start: 0.8153 (mt) cc_final: 0.7933 (mt) REVERT: C 70 ARG cc_start: 0.7599 (ptm-80) cc_final: 0.7397 (ppt170) REVERT: C 209 ASN cc_start: 0.8082 (t0) cc_final: 0.7855 (t0) REVERT: C 239 MET cc_start: 0.8489 (mmm) cc_final: 0.8275 (mmm) REVERT: C 384 LEU cc_start: 0.8165 (mt) cc_final: 0.7934 (mt) REVERT: D 70 ARG cc_start: 0.7600 (ptm-80) cc_final: 0.7398 (ppt170) REVERT: D 209 ASN cc_start: 0.8079 (t0) cc_final: 0.7854 (t0) REVERT: D 239 MET cc_start: 0.8475 (mmm) cc_final: 0.8265 (mmm) REVERT: D 384 LEU cc_start: 0.8162 (mt) cc_final: 0.7927 (mt) outliers start: 28 outliers final: 16 residues processed: 219 average time/residue: 1.3100 time to fit residues: 320.6558 Evaluate side-chains 207 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 203 optimal weight: 0.0470 chunk 220 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 202 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 chunk 163 optimal weight: 0.0870 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18300 Z= 0.126 Angle : 0.449 5.691 24820 Z= 0.226 Chirality : 0.040 0.157 2752 Planarity : 0.004 0.027 3196 Dihedral : 7.063 75.600 2684 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.52 % Allowed : 10.06 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.96 (0.18), residues: 2240 helix: 0.77 (0.17), residues: 1036 sheet: 0.42 (0.34), residues: 232 loop : 0.79 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 558 HIS 0.001 0.000 HIS B 125 PHE 0.015 0.001 PHE D 471 TYR 0.008 0.001 TYR A 347 ARG 0.004 0.000 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 223 time to evaluate : 2.001 Fit side-chains REVERT: A 384 LEU cc_start: 0.8152 (mt) cc_final: 0.7909 (mt) REVERT: B 219 MET cc_start: 0.8360 (mtt) cc_final: 0.8017 (mtt) REVERT: B 384 LEU cc_start: 0.8117 (mt) cc_final: 0.7902 (mt) REVERT: C 219 MET cc_start: 0.8396 (mtt) cc_final: 0.8034 (mtt) REVERT: C 384 LEU cc_start: 0.8154 (mt) cc_final: 0.7914 (mt) REVERT: D 384 LEU cc_start: 0.8148 (mt) cc_final: 0.7905 (mt) outliers start: 29 outliers final: 19 residues processed: 229 average time/residue: 1.3828 time to fit residues: 353.3980 Evaluate side-chains 229 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 210 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 193 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 18300 Z= 0.412 Angle : 0.584 5.697 24820 Z= 0.294 Chirality : 0.048 0.250 2752 Planarity : 0.005 0.035 3196 Dihedral : 7.433 79.864 2684 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.73 % Allowed : 11.74 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.79 (0.18), residues: 2240 helix: 0.56 (0.17), residues: 1040 sheet: 0.50 (0.36), residues: 208 loop : 0.72 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 558 HIS 0.006 0.001 HIS A 125 PHE 0.030 0.002 PHE A 471 TYR 0.015 0.002 TYR D 97 ARG 0.005 0.001 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 206 time to evaluate : 2.188 Fit side-chains REVERT: A 70 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7457 (ppt170) REVERT: A 91 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7222 (ptp-170) REVERT: A 209 ASN cc_start: 0.8072 (t0) cc_final: 0.7821 (t0) REVERT: A 219 MET cc_start: 0.8328 (mtt) cc_final: 0.7985 (mtt) REVERT: A 239 MET cc_start: 0.8750 (mmm) cc_final: 0.8544 (mmm) REVERT: A 325 MET cc_start: 0.8163 (mtp) cc_final: 0.7880 (mtm) REVERT: A 384 LEU cc_start: 0.8119 (mt) cc_final: 0.7878 (mt) REVERT: B 70 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7454 (ppt170) REVERT: B 219 MET cc_start: 0.8402 (mtt) cc_final: 0.8096 (mtt) REVERT: B 239 MET cc_start: 0.8741 (mmm) cc_final: 0.8537 (mmm) REVERT: B 325 MET cc_start: 0.8160 (mtp) cc_final: 0.7878 (mtm) REVERT: B 384 LEU cc_start: 0.8121 (mt) cc_final: 0.7874 (mt) REVERT: C 70 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7457 (ppt170) REVERT: C 91 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7226 (ptp-170) REVERT: C 219 MET cc_start: 0.8364 (mtt) cc_final: 0.8020 (mtt) REVERT: C 239 MET cc_start: 0.8743 (mmm) cc_final: 0.8541 (mmm) REVERT: C 325 MET cc_start: 0.8162 (mtp) cc_final: 0.7882 (mtm) REVERT: C 384 LEU cc_start: 0.8122 (mt) cc_final: 0.7884 (mt) REVERT: D 70 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7456 (ppt170) REVERT: D 91 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7226 (ptp-170) REVERT: D 209 ASN cc_start: 0.8067 (t0) cc_final: 0.7819 (t0) REVERT: D 239 MET cc_start: 0.8743 (mmm) cc_final: 0.8542 (mmm) REVERT: D 325 MET cc_start: 0.8152 (mtp) cc_final: 0.7872 (mtm) REVERT: D 384 LEU cc_start: 0.8116 (mt) cc_final: 0.7876 (mt) outliers start: 52 outliers final: 26 residues processed: 222 average time/residue: 1.2754 time to fit residues: 318.2615 Evaluate side-chains 230 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 197 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 184 optimal weight: 0.4980 chunk 149 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 chunk 194 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN B 382 ASN C 382 ASN D 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18300 Z= 0.205 Angle : 0.483 5.618 24820 Z= 0.245 Chirality : 0.042 0.173 2752 Planarity : 0.004 0.030 3196 Dihedral : 7.107 80.263 2684 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.56 % Allowed : 11.43 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.86 (0.18), residues: 2240 helix: 0.67 (0.17), residues: 1040 sheet: 0.42 (0.37), residues: 208 loop : 0.74 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 558 HIS 0.003 0.000 HIS B 125 PHE 0.019 0.002 PHE D 471 TYR 0.010 0.001 TYR B 97 ARG 0.005 0.000 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 196 time to evaluate : 2.130 Fit side-chains REVERT: A 70 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7405 (ppt170) REVERT: A 219 MET cc_start: 0.8322 (mtt) cc_final: 0.7987 (mtt) REVERT: A 239 MET cc_start: 0.8654 (mmm) cc_final: 0.8430 (mmm) REVERT: A 325 MET cc_start: 0.8119 (mtp) cc_final: 0.7820 (mtm) REVERT: A 384 LEU cc_start: 0.8108 (mt) cc_final: 0.7855 (mt) REVERT: B 70 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7405 (ppt170) REVERT: B 219 MET cc_start: 0.8409 (mtt) cc_final: 0.8058 (mtt) REVERT: B 239 MET cc_start: 0.8644 (mmm) cc_final: 0.8423 (mmm) REVERT: B 325 MET cc_start: 0.8114 (mtp) cc_final: 0.7815 (mtm) REVERT: B 384 LEU cc_start: 0.8152 (mt) cc_final: 0.7894 (mt) REVERT: C 70 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7405 (ppt170) REVERT: C 219 MET cc_start: 0.8399 (mtt) cc_final: 0.8024 (mtt) REVERT: C 239 MET cc_start: 0.8660 (mmm) cc_final: 0.8429 (mmm) REVERT: C 325 MET cc_start: 0.8121 (mtp) cc_final: 0.7823 (mtm) REVERT: C 384 LEU cc_start: 0.8109 (mt) cc_final: 0.7861 (mt) REVERT: D 70 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7408 (ppt170) REVERT: D 239 MET cc_start: 0.8645 (mmm) cc_final: 0.8423 (mmm) REVERT: D 325 MET cc_start: 0.8110 (mtp) cc_final: 0.7812 (mtm) REVERT: D 384 LEU cc_start: 0.8106 (mt) cc_final: 0.7857 (mt) outliers start: 68 outliers final: 39 residues processed: 241 average time/residue: 1.2925 time to fit residues: 349.1370 Evaluate side-chains 240 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 197 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 91 ARG Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 91 ARG Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN B 382 ASN C 382 ASN D 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18300 Z= 0.265 Angle : 0.510 5.654 24820 Z= 0.257 Chirality : 0.044 0.181 2752 Planarity : 0.004 0.031 3196 Dihedral : 6.989 82.251 2684 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.30 % Allowed : 11.58 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.80 (0.18), residues: 2240 helix: 0.61 (0.17), residues: 1044 sheet: 0.43 (0.37), residues: 208 loop : 0.71 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 558 HIS 0.003 0.001 HIS A 125 PHE 0.023 0.002 PHE B 471 TYR 0.012 0.001 TYR A 97 ARG 0.005 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 191 time to evaluate : 1.688 Fit side-chains REVERT: A 70 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7430 (ppt170) REVERT: A 219 MET cc_start: 0.8326 (mtt) cc_final: 0.7963 (mtt) REVERT: A 239 MET cc_start: 0.8677 (mmm) cc_final: 0.8384 (mmm) REVERT: A 325 MET cc_start: 0.8188 (mtp) cc_final: 0.7878 (mtm) REVERT: A 384 LEU cc_start: 0.8105 (mt) cc_final: 0.7865 (mt) REVERT: B 70 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7427 (ppt170) REVERT: B 219 MET cc_start: 0.8429 (mtt) cc_final: 0.8067 (mtt) REVERT: B 239 MET cc_start: 0.8669 (mmm) cc_final: 0.8379 (mmm) REVERT: B 325 MET cc_start: 0.8185 (mtp) cc_final: 0.7875 (mtm) REVERT: B 384 LEU cc_start: 0.8117 (mt) cc_final: 0.7870 (mt) REVERT: C 70 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7430 (ppt170) REVERT: C 219 MET cc_start: 0.8362 (mtt) cc_final: 0.8006 (mtt) REVERT: C 239 MET cc_start: 0.8671 (mmm) cc_final: 0.8380 (mmm) REVERT: C 325 MET cc_start: 0.8190 (mtp) cc_final: 0.7881 (mtm) REVERT: C 384 LEU cc_start: 0.8108 (mt) cc_final: 0.7889 (mt) REVERT: D 70 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7432 (ppt170) REVERT: D 239 MET cc_start: 0.8670 (mmm) cc_final: 0.8378 (mmm) REVERT: D 325 MET cc_start: 0.8177 (mtp) cc_final: 0.7869 (mtm) REVERT: D 384 LEU cc_start: 0.8158 (mt) cc_final: 0.7919 (mt) outliers start: 63 outliers final: 40 residues processed: 224 average time/residue: 1.2667 time to fit residues: 320.0619 Evaluate side-chains 227 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 183 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 122 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN B 382 ASN C 382 ASN D 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18300 Z= 0.169 Angle : 0.460 5.654 24820 Z= 0.232 Chirality : 0.041 0.163 2752 Planarity : 0.004 0.029 3196 Dihedral : 6.740 84.405 2684 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.78 % Allowed : 12.42 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.91 (0.18), residues: 2240 helix: 0.75 (0.17), residues: 1040 sheet: 0.24 (0.35), residues: 232 loop : 0.79 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 558 HIS 0.002 0.000 HIS C 125 PHE 0.016 0.001 PHE C 471 TYR 0.008 0.001 TYR B 347 ARG 0.005 0.000 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 204 time to evaluate : 1.978 Fit side-chains REVERT: A 70 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7387 (ppt170) REVERT: A 219 MET cc_start: 0.8319 (mtt) cc_final: 0.7956 (mtt) REVERT: A 239 MET cc_start: 0.8603 (mmm) cc_final: 0.8355 (mmm) REVERT: A 325 MET cc_start: 0.8158 (mtp) cc_final: 0.7840 (mtm) REVERT: A 384 LEU cc_start: 0.8189 (mt) cc_final: 0.7964 (mt) REVERT: B 70 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7376 (ppt170) REVERT: B 219 MET cc_start: 0.8414 (mtt) cc_final: 0.8034 (mtt) REVERT: B 239 MET cc_start: 0.8596 (mmm) cc_final: 0.8352 (mmm) REVERT: B 325 MET cc_start: 0.8155 (mtp) cc_final: 0.7838 (mtm) REVERT: B 384 LEU cc_start: 0.8107 (mt) cc_final: 0.7867 (mt) REVERT: C 70 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7388 (ppt170) REVERT: C 219 MET cc_start: 0.8375 (mtt) cc_final: 0.8006 (mtt) REVERT: C 239 MET cc_start: 0.8596 (mmm) cc_final: 0.8352 (mmm) REVERT: C 325 MET cc_start: 0.8162 (mtp) cc_final: 0.7839 (mtm) REVERT: C 384 LEU cc_start: 0.8102 (mt) cc_final: 0.7880 (mt) REVERT: D 70 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7387 (ppt170) REVERT: D 239 MET cc_start: 0.8594 (mmm) cc_final: 0.8351 (mmm) REVERT: D 325 MET cc_start: 0.8149 (mtp) cc_final: 0.7832 (mtm) REVERT: D 384 LEU cc_start: 0.8184 (mt) cc_final: 0.7961 (mt) outliers start: 53 outliers final: 37 residues processed: 229 average time/residue: 1.2103 time to fit residues: 312.5074 Evaluate side-chains 236 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 65 optimal weight: 0.0570 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 537 ASN B 382 ASN B 537 ASN C 382 ASN C 537 ASN D 382 ASN D 537 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18300 Z= 0.145 Angle : 0.449 5.638 24820 Z= 0.225 Chirality : 0.041 0.160 2752 Planarity : 0.004 0.029 3196 Dihedral : 6.560 89.355 2684 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.25 % Allowed : 13.10 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.98 (0.18), residues: 2240 helix: 0.83 (0.17), residues: 1040 sheet: 0.25 (0.35), residues: 232 loop : 0.80 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 342 HIS 0.001 0.000 HIS A 125 PHE 0.016 0.001 PHE A 471 TYR 0.008 0.001 TYR A 469 ARG 0.006 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 212 time to evaluate : 2.338 Fit side-chains REVERT: A 219 MET cc_start: 0.8313 (mtt) cc_final: 0.7939 (mtt) REVERT: A 239 MET cc_start: 0.8510 (mmm) cc_final: 0.8244 (mmm) REVERT: A 325 MET cc_start: 0.8082 (mtp) cc_final: 0.7768 (mtm) REVERT: A 384 LEU cc_start: 0.8096 (mt) cc_final: 0.7863 (mt) REVERT: B 219 MET cc_start: 0.8357 (mtt) cc_final: 0.7979 (mtt) REVERT: B 239 MET cc_start: 0.8505 (mmm) cc_final: 0.8238 (mmm) REVERT: B 325 MET cc_start: 0.8082 (mtp) cc_final: 0.7767 (mtm) REVERT: B 384 LEU cc_start: 0.8102 (mt) cc_final: 0.7853 (mt) REVERT: C 219 MET cc_start: 0.8337 (mtt) cc_final: 0.7975 (mtt) REVERT: C 239 MET cc_start: 0.8505 (mmm) cc_final: 0.8242 (mmm) REVERT: C 325 MET cc_start: 0.8086 (mtp) cc_final: 0.7772 (mtm) REVERT: C 384 LEU cc_start: 0.8098 (mt) cc_final: 0.7867 (mt) REVERT: D 239 MET cc_start: 0.8502 (mmm) cc_final: 0.8235 (mmm) REVERT: D 325 MET cc_start: 0.8075 (mtp) cc_final: 0.7758 (mtm) REVERT: D 384 LEU cc_start: 0.8102 (mt) cc_final: 0.7851 (mt) outliers start: 43 outliers final: 42 residues processed: 235 average time/residue: 1.0945 time to fit residues: 293.2880 Evaluate side-chains 236 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.3980 chunk 206 optimal weight: 0.5980 chunk 188 optimal weight: 8.9990 chunk 201 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 537 ASN B 382 ASN B 537 ASN C 382 ASN C 537 ASN D 382 ASN D 537 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18300 Z= 0.180 Angle : 0.463 5.629 24820 Z= 0.232 Chirality : 0.042 0.170 2752 Planarity : 0.004 0.029 3196 Dihedral : 6.465 87.475 2684 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.73 % Allowed : 13.47 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.99 (0.18), residues: 2240 helix: 0.84 (0.17), residues: 1040 sheet: 0.23 (0.35), residues: 232 loop : 0.80 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 558 HIS 0.002 0.000 HIS B 125 PHE 0.019 0.001 PHE D 471 TYR 0.008 0.001 TYR C 347 ARG 0.005 0.000 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 199 time to evaluate : 1.698 Fit side-chains REVERT: A 70 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7387 (ppt170) REVERT: A 219 MET cc_start: 0.8332 (mtt) cc_final: 0.7960 (mtt) REVERT: A 239 MET cc_start: 0.8545 (mmm) cc_final: 0.8280 (mmm) REVERT: A 325 MET cc_start: 0.8108 (mtp) cc_final: 0.7771 (mtm) REVERT: A 347 TYR cc_start: 0.7774 (m-10) cc_final: 0.7389 (m-80) REVERT: A 384 LEU cc_start: 0.8103 (mt) cc_final: 0.7874 (mt) REVERT: B 70 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7372 (ppt170) REVERT: B 219 MET cc_start: 0.8389 (mtt) cc_final: 0.8011 (mtt) REVERT: B 239 MET cc_start: 0.8539 (mmm) cc_final: 0.8273 (mmm) REVERT: B 325 MET cc_start: 0.8106 (mtp) cc_final: 0.7769 (mtm) REVERT: B 347 TYR cc_start: 0.7769 (m-10) cc_final: 0.7387 (m-80) REVERT: B 384 LEU cc_start: 0.8067 (mt) cc_final: 0.7851 (mt) REVERT: C 70 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7384 (ppt170) REVERT: C 219 MET cc_start: 0.8332 (mtt) cc_final: 0.7961 (mtt) REVERT: C 239 MET cc_start: 0.8538 (mmm) cc_final: 0.8272 (mmm) REVERT: C 325 MET cc_start: 0.8112 (mtp) cc_final: 0.7776 (mtm) REVERT: C 347 TYR cc_start: 0.7748 (m-10) cc_final: 0.7359 (m-80) REVERT: C 384 LEU cc_start: 0.8108 (mt) cc_final: 0.7875 (mt) REVERT: D 70 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7387 (ppt170) REVERT: D 239 MET cc_start: 0.8536 (mmm) cc_final: 0.8273 (mmm) REVERT: D 325 MET cc_start: 0.8098 (mtp) cc_final: 0.7760 (mtm) REVERT: D 347 TYR cc_start: 0.7769 (m-10) cc_final: 0.7385 (m-80) REVERT: D 384 LEU cc_start: 0.8109 (mt) cc_final: 0.7875 (mt) outliers start: 52 outliers final: 46 residues processed: 232 average time/residue: 1.0861 time to fit residues: 288.3769 Evaluate side-chains 244 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 194 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.3980 chunk 212 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 chunk 147 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 205 optimal weight: 0.0270 chunk 177 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 382 ASN B 382 ASN C 92 ASN C 382 ASN D 92 ASN D 382 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18300 Z= 0.138 Angle : 0.446 5.667 24820 Z= 0.224 Chirality : 0.040 0.158 2752 Planarity : 0.004 0.028 3196 Dihedral : 6.143 82.884 2684 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.20 % Allowed : 14.20 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.04 (0.18), residues: 2240 helix: 0.93 (0.17), residues: 1036 sheet: 0.23 (0.35), residues: 232 loop : 0.78 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 342 HIS 0.001 0.000 HIS A 125 PHE 0.015 0.001 PHE D 471 TYR 0.008 0.001 TYR B 347 ARG 0.006 0.000 ARG B 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 207 time to evaluate : 2.143 Fit side-chains REVERT: A 70 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7355 (ppt170) REVERT: A 239 MET cc_start: 0.8515 (mmm) cc_final: 0.8218 (mmm) REVERT: A 347 TYR cc_start: 0.7680 (m-10) cc_final: 0.7305 (m-80) REVERT: A 384 LEU cc_start: 0.8104 (mt) cc_final: 0.7870 (mt) REVERT: B 219 MET cc_start: 0.8277 (mtt) cc_final: 0.7924 (mtt) REVERT: B 239 MET cc_start: 0.8509 (mmm) cc_final: 0.8212 (mmm) REVERT: B 347 TYR cc_start: 0.7675 (m-10) cc_final: 0.7301 (m-80) REVERT: B 384 LEU cc_start: 0.8078 (mt) cc_final: 0.7856 (mt) REVERT: C 70 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7355 (ppt170) REVERT: C 219 MET cc_start: 0.8269 (mtt) cc_final: 0.7921 (mtt) REVERT: C 239 MET cc_start: 0.8509 (mmm) cc_final: 0.8212 (mmm) REVERT: C 347 TYR cc_start: 0.7673 (m-10) cc_final: 0.7295 (m-80) REVERT: C 384 LEU cc_start: 0.8111 (mt) cc_final: 0.7879 (mt) REVERT: D 70 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7356 (ppt170) REVERT: D 239 MET cc_start: 0.8507 (mmm) cc_final: 0.8210 (mmm) REVERT: D 347 TYR cc_start: 0.7675 (m-10) cc_final: 0.7300 (m-80) REVERT: D 384 LEU cc_start: 0.8106 (mt) cc_final: 0.7877 (mt) outliers start: 42 outliers final: 37 residues processed: 232 average time/residue: 1.0453 time to fit residues: 277.8924 Evaluate side-chains 233 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 193 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 421 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 421 ASN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 441 CYS Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 441 CYS Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 421 ASN Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 441 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 0.0470 chunk 177 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN B 382 ASN C 382 ASN D 382 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104991 restraints weight = 19191.827| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.94 r_work: 0.3044 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18300 Z= 0.165 Angle : 0.457 5.653 24820 Z= 0.228 Chirality : 0.042 0.166 2752 Planarity : 0.004 0.029 3196 Dihedral : 6.036 78.431 2684 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.25 % Allowed : 14.15 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.00 (0.18), residues: 2240 helix: 0.87 (0.17), residues: 1040 sheet: 0.20 (0.35), residues: 232 loop : 0.78 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 558 HIS 0.002 0.000 HIS D 125 PHE 0.017 0.001 PHE C 471 TYR 0.008 0.001 TYR B 347 ARG 0.005 0.000 ARG C 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5914.75 seconds wall clock time: 105 minutes 31.68 seconds (6331.68 seconds total)