Starting phenix.real_space_refine on Wed Nov 20 13:49:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5a_29737/11_2024/8g5a_29737_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5a_29737/11_2024/8g5a_29737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5a_29737/11_2024/8g5a_29737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5a_29737/11_2024/8g5a_29737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5a_29737/11_2024/8g5a_29737_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5a_29737/11_2024/8g5a_29737_neut.cif" } resolution = 3.3 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 13566 2.51 5 N 3687 2.21 5 O 4317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21666 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3880 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 473} Chain: "I" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1639 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain: "M" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1647 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: C, B, L, N, H, J Residues with excluded nonbonded symmetry interactions: 51 residue: pdb=" N THR A 24 " occ=0.63 ... (5 atoms not shown) pdb=" CG2 THR A 24 " occ=0.63 residue: pdb=" N THR A 30 " occ=0.83 ... (5 atoms not shown) pdb=" CG2 THR A 30 " occ=0.83 residue: pdb=" N ASP A 32 " occ=0.72 ... (6 atoms not shown) pdb=" OD2 ASP A 32 " occ=0.72 residue: pdb=" N VAL A 78 " occ=0.43 ... (5 atoms not shown) pdb=" CG2 VAL A 78 " occ=0.43 residue: pdb=" N ARG A 207 " occ=0.48 ... (9 atoms not shown) pdb=" NH2 ARG A 207 " occ=0.48 residue: pdb=" N SER A 227 " occ=0.54 ... (4 atoms not shown) pdb=" OG SER A 227 " occ=0.54 residue: pdb=" N SER A 228 " occ=0.54 ... (4 atoms not shown) pdb=" OG SER A 228 " occ=0.54 residue: pdb=" N TRP A 234 " occ=0.52 ... (12 atoms not shown) pdb=" CH2 TRP A 234 " occ=0.52 residue: pdb=" N MET A 260 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET A 260 " occ=0.50 residue: pdb=" N ILE A 274 " occ=0.62 ... (6 atoms not shown) pdb=" CD1 ILE A 274 " occ=0.62 residue: pdb=" N ASP A 275 " occ=0.62 ... (6 atoms not shown) pdb=" OD2 ASP A 275 " occ=0.62 residue: pdb=" N MET A 346 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET A 346 " occ=0.50 ... (remaining 39 not shown) Time building chain proxies: 13.07, per 1000 atoms: 0.60 Number of scatterers: 21666 At special positions: 0 Unit cell: (155.925, 155.925, 193.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 4317 8.00 N 3687 7.00 C 13566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 483 " " NAG A 702 " - " ASN A 22 " " NAG A 703 " - " ASN A 38 " " NAG A 704 " - " ASN A 81 " " NAG B 701 " - " ASN B 483 " " NAG B 702 " - " ASN B 22 " " NAG B 703 " - " ASN B 38 " " NAG B 704 " - " ASN B 81 " " NAG C 701 " - " ASN C 483 " " NAG C 702 " - " ASN C 22 " " NAG C 703 " - " ASN C 38 " " NAG C 704 " - " ASN C 81 " Time building additional restraints: 5.66 Conformation dependent library (CDL) restraints added in 3.2 seconds 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 63 sheets defined 19.0% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.603A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 366 through 386 Processing helix chain 'A' and resid 404 through 455 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 488 through 502 removed outlier: 4.320A pdb=" N ASP A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.603A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL B 78 " --> pdb=" O HIS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 366 through 386 Processing helix chain 'B' and resid 404 through 455 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 488 through 502 removed outlier: 4.319A pdb=" N ASP B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.604A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 366 through 386 Processing helix chain 'C' and resid 404 through 455 Processing helix chain 'C' and resid 474 through 484 Processing helix chain 'C' and resid 488 through 502 removed outlier: 4.320A pdb=" N ASP C 493 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 100 through 104 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 194 through 198 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 100 through 104 Processing helix chain 'I' and resid 163 through 165 No H-bonds generated for 'chain 'I' and resid 163 through 165' Processing helix chain 'I' and resid 194 through 198 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 100 through 104 Processing helix chain 'J' and resid 163 through 165 No H-bonds generated for 'chain 'J' and resid 163 through 165' Processing helix chain 'J' and resid 194 through 198 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.665A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.503A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.665A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 126 Processing helix chain 'M' and resid 183 through 189 removed outlier: 3.503A pdb=" N LYS M 188 " --> pdb=" O ALA M 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.665A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 126 Processing helix chain 'N' and resid 183 through 189 removed outlier: 3.503A pdb=" N LYS N 188 " --> pdb=" O ALA N 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.610A pdb=" N CYS A 277 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.965A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.757A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 removed outlier: 4.934A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AB3, first strand: chain 'B' and resid 360 through 365 Processing sheet with id=AB4, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.610A pdb=" N CYS B 277 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 58 through 61 Processing sheet with id=AB9, first strand: chain 'B' and resid 100 through 101 removed outlier: 4.965A pdb=" N ILE B 179 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 101 removed outlier: 7.757A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 169 removed outlier: 4.934A pdb=" N ARG B 201 " --> pdb=" O ASN B 248 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 281 through 282 Processing sheet with id=AC5, first strand: chain 'C' and resid 360 through 365 Processing sheet with id=AC6, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AC7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.611A pdb=" N CYS C 277 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AD2, first strand: chain 'C' and resid 100 through 101 removed outlier: 4.965A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.756A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AD5, first strand: chain 'C' and resid 164 through 169 removed outlier: 4.935A pdb=" N ARG C 201 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AD7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.510A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.510A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 127 through 131 removed outlier: 5.305A pdb=" N ALA H 144 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL H 191 " --> pdb=" O ALA H 144 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLY H 146 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL H 189 " --> pdb=" O GLY H 146 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER H 186 " --> pdb=" O PRO H 174 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL H 188 " --> pdb=" O THR H 172 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR H 172 " --> pdb=" O VAL H 188 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 158 through 161 removed outlier: 4.076A pdb=" N TYR H 201 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.509A pdb=" N GLU I 10 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE I 34 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.509A pdb=" N GLU I 10 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR I 109 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 127 through 131 removed outlier: 5.305A pdb=" N ALA I 144 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL I 191 " --> pdb=" O ALA I 144 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLY I 146 " --> pdb=" O VAL I 189 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL I 189 " --> pdb=" O GLY I 146 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU I 148 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER I 187 " --> pdb=" O LEU I 148 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS I 150 " --> pdb=" O LEU I 185 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU I 185 " --> pdb=" O LYS I 150 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N SER I 186 " --> pdb=" O PRO I 174 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL I 188 " --> pdb=" O THR I 172 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR I 172 " --> pdb=" O VAL I 188 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 158 through 161 removed outlier: 4.075A pdb=" N TYR I 201 " --> pdb=" O VAL I 218 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.509A pdb=" N GLU J 10 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE J 34 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.509A pdb=" N GLU J 10 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR J 109 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 127 through 131 removed outlier: 5.305A pdb=" N ALA J 144 " --> pdb=" O VAL J 191 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL J 191 " --> pdb=" O ALA J 144 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLY J 146 " --> pdb=" O VAL J 189 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL J 189 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU J 148 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER J 187 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS J 150 " --> pdb=" O LEU J 185 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU J 185 " --> pdb=" O LYS J 150 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER J 186 " --> pdb=" O PRO J 174 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL J 188 " --> pdb=" O THR J 172 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR J 172 " --> pdb=" O VAL J 188 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 158 through 161 removed outlier: 4.075A pdb=" N TYR J 201 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.176A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.988A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.539A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.690A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AG1, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.176A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.989A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 114 through 118 removed outlier: 3.539A pdb=" N VAL M 133 " --> pdb=" O PHE M 118 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER M 131 " --> pdb=" O LEU M 181 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU M 181 " --> pdb=" O SER M 131 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL M 133 " --> pdb=" O LEU M 179 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU M 179 " --> pdb=" O VAL M 133 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU M 135 " --> pdb=" O SER M 177 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER M 177 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASN M 137 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU M 175 " --> pdb=" O ASN M 137 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 153 through 155 removed outlier: 4.690A pdb=" N TRP M 148 " --> pdb=" O GLN M 155 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.175A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.989A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 114 through 118 removed outlier: 3.540A pdb=" N VAL N 133 " --> pdb=" O PHE N 118 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SER N 131 " --> pdb=" O LEU N 181 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU N 181 " --> pdb=" O SER N 131 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL N 133 " --> pdb=" O LEU N 179 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU N 179 " --> pdb=" O VAL N 133 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU N 135 " --> pdb=" O SER N 177 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER N 177 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ASN N 137 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU N 175 " --> pdb=" O ASN N 137 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 153 through 155 removed outlier: 4.690A pdb=" N TRP N 148 " --> pdb=" O GLN N 155 " (cutoff:3.500A) 948 hydrogen bonds defined for protein. 2412 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: 9.89 Time building geometry restraints manager: 6.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7071 1.34 - 1.46: 5311 1.46 - 1.58: 9629 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 22143 Sorted by residual: bond pdb=" C ARG A 456 " pdb=" O ARG A 456 " ideal model delta sigma weight residual 1.236 1.299 -0.062 1.15e-02 7.56e+03 2.95e+01 bond pdb=" C ARG C 456 " pdb=" O ARG C 456 " ideal model delta sigma weight residual 1.236 1.299 -0.062 1.15e-02 7.56e+03 2.94e+01 bond pdb=" C ARG B 456 " pdb=" O ARG B 456 " ideal model delta sigma weight residual 1.236 1.298 -0.062 1.15e-02 7.56e+03 2.93e+01 bond pdb=" C ALA C 334 " pdb=" O ALA C 334 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.21e-02 6.83e+03 2.48e+01 bond pdb=" C ALA A 334 " pdb=" O ALA A 334 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.21e-02 6.83e+03 2.48e+01 ... (remaining 22138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 29635 2.39 - 4.78: 359 4.78 - 7.17: 48 7.17 - 9.56: 6 9.56 - 11.94: 6 Bond angle restraints: 30054 Sorted by residual: angle pdb=" OG1 THR C 328 " pdb=" CB THR C 328 " pdb=" CG2 THR C 328 " ideal model delta sigma weight residual 109.30 120.82 -11.52 2.00e+00 2.50e-01 3.32e+01 angle pdb=" OG1 THR B 328 " pdb=" CB THR B 328 " pdb=" CG2 THR B 328 " ideal model delta sigma weight residual 109.30 120.81 -11.51 2.00e+00 2.50e-01 3.31e+01 angle pdb=" OG1 THR A 328 " pdb=" CB THR A 328 " pdb=" CG2 THR A 328 " ideal model delta sigma weight residual 109.30 120.79 -11.49 2.00e+00 2.50e-01 3.30e+01 angle pdb=" CA ILE C 335 " pdb=" C ILE C 335 " pdb=" O ILE C 335 " ideal model delta sigma weight residual 120.48 114.68 5.80 1.10e+00 8.26e-01 2.78e+01 angle pdb=" CA ILE B 335 " pdb=" C ILE B 335 " pdb=" O ILE B 335 " ideal model delta sigma weight residual 120.48 114.70 5.78 1.10e+00 8.26e-01 2.76e+01 ... (remaining 30049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 12141 16.07 - 32.14: 882 32.14 - 48.21: 230 48.21 - 64.28: 67 64.28 - 80.35: 36 Dihedral angle restraints: 13356 sinusoidal: 5361 harmonic: 7995 Sorted by residual: dihedral pdb=" CA GLU N 93 " pdb=" C GLU N 93 " pdb=" N TYR N 94 " pdb=" CA TYR N 94 " ideal model delta harmonic sigma weight residual -180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLU M 93 " pdb=" C GLU M 93 " pdb=" N TYR M 94 " pdb=" CA TYR M 94 " ideal model delta harmonic sigma weight residual -180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLU L 93 " pdb=" C GLU L 93 " pdb=" N TYR L 94 " pdb=" CA TYR L 94 " ideal model delta harmonic sigma weight residual -180.00 -159.12 -20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 13353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.304: 3339 0.304 - 0.607: 12 0.607 - 0.911: 0 0.911 - 1.214: 0 1.214 - 1.518: 6 Chirality restraints: 3357 Sorted by residual: chirality pdb=" C4 NAG B 702 " pdb=" C3 NAG B 702 " pdb=" C5 NAG B 702 " pdb=" O4 NAG B 702 " both_signs ideal model delta sigma weight residual False -2.53 -1.01 -1.52 2.00e-01 2.50e+01 5.76e+01 chirality pdb=" C4 NAG A 702 " pdb=" C3 NAG A 702 " pdb=" C5 NAG A 702 " pdb=" O4 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.53 -1.02 -1.52 2.00e-01 2.50e+01 5.74e+01 chirality pdb=" C4 NAG C 702 " pdb=" C3 NAG C 702 " pdb=" C5 NAG C 702 " pdb=" O4 NAG C 702 " both_signs ideal model delta sigma weight residual False -2.53 -1.02 -1.51 2.00e-01 2.50e+01 5.74e+01 ... (remaining 3354 not shown) Planarity restraints: 3894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 331 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LEU A 331 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU A 331 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 332 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 331 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LEU C 331 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU C 331 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE C 332 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 331 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C LEU B 331 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU B 331 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE B 332 " 0.020 2.00e-02 2.50e+03 ... (remaining 3891 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 211 2.60 - 3.18: 19097 3.18 - 3.75: 33234 3.75 - 4.33: 48456 4.33 - 4.90: 81552 Nonbonded interactions: 182550 Sorted by model distance: nonbonded pdb=" SG CYS C 64 " pdb=" SG CYS C 76 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS B 64 " pdb=" SG CYS B 76 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS B 281 " pdb=" SG CYS B 305 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS C 281 " pdb=" SG CYS C 305 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS I 22 " pdb=" SG CYS I 96 " model vdw 2.028 3.760 ... (remaining 182545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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=0.43 max=1.00 mean=0.99 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 52.310 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22143 Z= 0.331 Angle : 0.693 11.945 30054 Z= 0.402 Chirality : 0.081 1.518 3357 Planarity : 0.005 0.093 3882 Dihedral : 13.255 80.348 8226 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.88 % Allowed : 0.75 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -0.23 (0.16), residues: 2763 helix: 1.84 (0.25), residues: 429 sheet: -0.21 (0.16), residues: 1017 loop : -0.71 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 47 HIS 0.004 0.001 HIS I 207 PHE 0.015 0.001 PHE N 116 TYR 0.030 0.002 TYR N 192 ARG 0.005 0.000 ARG M 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 280 time to evaluate : 2.494 Fit side-chains revert: symmetry clash REVERT: A 338 PHE cc_start: 0.5781 (OUTLIER) cc_final: 0.4566 (m-80) REVERT: A 444 MET cc_start: 0.8771 (tpt) cc_final: 0.8529 (tpt) REVERT: A 470 TYR cc_start: 0.8260 (m-80) cc_final: 0.8036 (m-80) REVERT: B 338 PHE cc_start: 0.5729 (OUTLIER) cc_final: 0.4506 (m-80) REVERT: B 444 MET cc_start: 0.8772 (tpt) cc_final: 0.8434 (tpt) REVERT: B 470 TYR cc_start: 0.8247 (m-80) cc_final: 0.8002 (m-80) REVERT: C 338 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.4760 (m-80) REVERT: H 112 GLN cc_start: 0.7800 (pm20) cc_final: 0.7464 (pm20) REVERT: H 216 LYS cc_start: 0.5340 (mmmm) cc_final: 0.5088 (tppt) REVERT: J 35 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7835 (mt-10) REVERT: L 24 ARG cc_start: 0.6211 (ttm-80) cc_final: 0.5822 (tmm-80) REVERT: L 79 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6399 (mm-30) REVERT: L 106 LEU cc_start: 0.5657 (OUTLIER) cc_final: 0.4828 (mt) REVERT: L 123 GLU cc_start: 0.6699 (pm20) cc_final: 0.6400 (mp0) REVERT: M 24 ARG cc_start: 0.6079 (ttm-80) cc_final: 0.5545 (ttm-80) REVERT: M 79 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6404 (mm-30) REVERT: M 81 GLU cc_start: 0.6938 (pt0) cc_final: 0.5737 (mp0) REVERT: M 106 LEU cc_start: 0.5672 (OUTLIER) cc_final: 0.4975 (mt) REVERT: M 175 LEU cc_start: 0.7803 (tt) cc_final: 0.7599 (tt) REVERT: N 24 ARG cc_start: 0.6031 (ttm-80) cc_final: 0.5684 (tmm-80) REVERT: N 79 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6393 (mm-30) REVERT: N 81 GLU cc_start: 0.6951 (pt0) cc_final: 0.5761 (mp0) REVERT: N 106 LEU cc_start: 0.5707 (OUTLIER) cc_final: 0.4882 (mt) REVERT: N 123 GLU cc_start: 0.6786 (pm20) cc_final: 0.6403 (mp0) outliers start: 21 outliers final: 9 residues processed: 298 average time/residue: 0.3523 time to fit residues: 160.7854 Evaluate side-chains 214 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 161 optimal weight: 30.0000 chunk 250 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 216 ASN B 435 HIS C 216 ASN H 178 GLN I 178 GLN I 207 HIS J 178 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22143 Z= 0.349 Angle : 0.620 7.756 30054 Z= 0.333 Chirality : 0.047 0.184 3357 Planarity : 0.005 0.042 3882 Dihedral : 5.675 55.719 3264 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.46 % Allowed : 5.73 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -0.20 (0.15), residues: 2763 helix: 1.77 (0.24), residues: 432 sheet: -0.06 (0.16), residues: 993 loop : -0.77 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 222 HIS 0.007 0.001 HIS C 435 PHE 0.022 0.002 PHE B 338 TYR 0.031 0.002 TYR M 94 ARG 0.004 0.001 ARG J 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7372 (mm-30) REVERT: A 444 MET cc_start: 0.8811 (tpt) cc_final: 0.8503 (tpt) REVERT: A 470 TYR cc_start: 0.8374 (m-80) cc_final: 0.8012 (m-80) REVERT: B 338 PHE cc_start: 0.5925 (OUTLIER) cc_final: 0.4595 (m-80) REVERT: B 401 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7414 (mm-30) REVERT: B 444 MET cc_start: 0.8809 (tpt) cc_final: 0.8250 (tpt) REVERT: B 453 ARG cc_start: 0.7871 (mtm180) cc_final: 0.7610 (mtm180) REVERT: B 460 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6576 (tt0) REVERT: B 470 TYR cc_start: 0.8451 (m-80) cc_final: 0.7997 (m-80) REVERT: B 491 TYR cc_start: 0.8483 (m-80) cc_final: 0.8237 (m-80) REVERT: C 453 ARG cc_start: 0.7907 (mtm180) cc_final: 0.7681 (mtm180) REVERT: C 456 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7631 (mtp180) REVERT: I 35 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7898 (mt-10) REVERT: J 35 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7905 (mt-10) REVERT: L 24 ARG cc_start: 0.6282 (ttm-80) cc_final: 0.5783 (ttm-80) REVERT: L 106 LEU cc_start: 0.5672 (OUTLIER) cc_final: 0.4673 (mt) REVERT: M 24 ARG cc_start: 0.6234 (ttm-80) cc_final: 0.5819 (ttp-110) REVERT: M 79 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6297 (mm-30) REVERT: M 106 LEU cc_start: 0.5499 (OUTLIER) cc_final: 0.4615 (mt) REVERT: N 24 ARG cc_start: 0.6149 (ttm-80) cc_final: 0.5726 (ttp-110) REVERT: N 106 LEU cc_start: 0.5563 (OUTLIER) cc_final: 0.4640 (mt) REVERT: N 148 TRP cc_start: 0.6033 (m100) cc_final: 0.5476 (m-10) outliers start: 35 outliers final: 26 residues processed: 263 average time/residue: 0.3222 time to fit residues: 134.7303 Evaluate side-chains 238 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 147 GLN Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 251 optimal weight: 20.0000 chunk 271 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 HIS B 216 ASN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN H 59 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 59 ASN I 178 GLN J 59 ASN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 147 GLN N 152 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 22143 Z= 0.409 Angle : 0.619 8.166 30054 Z= 0.329 Chirality : 0.047 0.178 3357 Planarity : 0.005 0.047 3882 Dihedral : 5.637 49.111 3264 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.38 % Allowed : 8.24 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -0.39 (0.15), residues: 2763 helix: 1.68 (0.24), residues: 432 sheet: -0.19 (0.16), residues: 993 loop : -0.92 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 47 HIS 0.007 0.001 HIS C 435 PHE 0.020 0.002 PHE I 105 TYR 0.030 0.002 TYR M 94 ARG 0.004 0.001 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 2.540 Fit side-chains revert: symmetry clash REVERT: A 338 PHE cc_start: 0.5718 (OUTLIER) cc_final: 0.4580 (m-80) REVERT: A 401 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7349 (mm-30) REVERT: A 470 TYR cc_start: 0.8279 (m-80) cc_final: 0.8040 (m-80) REVERT: B 338 PHE cc_start: 0.5797 (OUTLIER) cc_final: 0.4613 (m-80) REVERT: B 401 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7454 (mm-30) REVERT: B 444 MET cc_start: 0.8772 (tpt) cc_final: 0.8228 (tpt) REVERT: B 468 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7952 (ttpt) REVERT: B 470 TYR cc_start: 0.8595 (m-80) cc_final: 0.8107 (m-80) REVERT: C 338 PHE cc_start: 0.5751 (OUTLIER) cc_final: 0.4703 (m-80) REVERT: C 472 LYS cc_start: 0.8251 (mmtm) cc_final: 0.7857 (tppt) REVERT: I 39 GLN cc_start: 0.8069 (tt0) cc_final: 0.7777 (tt0) REVERT: J 152 TYR cc_start: 0.7893 (p90) cc_final: 0.7575 (p90) REVERT: L 24 ARG cc_start: 0.6304 (ttm-80) cc_final: 0.5755 (ttm-80) REVERT: L 79 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6195 (tm-30) REVERT: L 106 LEU cc_start: 0.5460 (OUTLIER) cc_final: 0.4616 (mt) REVERT: L 148 TRP cc_start: 0.6140 (m100) cc_final: 0.5766 (m-10) REVERT: M 24 ARG cc_start: 0.6350 (ttm-80) cc_final: 0.5794 (ttm-80) REVERT: M 106 LEU cc_start: 0.5476 (OUTLIER) cc_final: 0.4661 (mt) REVERT: M 148 TRP cc_start: 0.6012 (m100) cc_final: 0.5702 (m-10) REVERT: N 24 ARG cc_start: 0.6180 (ttm-80) cc_final: 0.5813 (ttm-80) REVERT: N 106 LEU cc_start: 0.5464 (OUTLIER) cc_final: 0.4560 (mt) REVERT: N 148 TRP cc_start: 0.6203 (m100) cc_final: 0.5627 (m-10) outliers start: 57 outliers final: 31 residues processed: 269 average time/residue: 0.3097 time to fit residues: 134.6866 Evaluate side-chains 240 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 93 GLU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 147 GLN Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 168 optimal weight: 9.9990 chunk 251 optimal weight: 20.0000 chunk 266 optimal weight: 0.0000 chunk 131 optimal weight: 0.1980 chunk 238 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN H 112 GLN H 178 GLN I 178 GLN J 112 GLN M 147 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22143 Z= 0.192 Angle : 0.530 8.065 30054 Z= 0.282 Chirality : 0.043 0.155 3357 Planarity : 0.004 0.048 3882 Dihedral : 5.212 45.792 3264 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.38 % Allowed : 9.20 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -0.15 (0.15), residues: 2763 helix: 2.05 (0.24), residues: 432 sheet: 0.04 (0.16), residues: 972 loop : -0.89 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS J 207 PHE 0.013 0.001 PHE I 105 TYR 0.021 0.001 TYR M 94 ARG 0.002 0.000 ARG B 452 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 231 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.5762 (OUTLIER) cc_final: 0.4829 (m-80) REVERT: A 401 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7249 (mm-30) REVERT: A 408 ASP cc_start: 0.7671 (m-30) cc_final: 0.7417 (m-30) REVERT: B 338 PHE cc_start: 0.5614 (OUTLIER) cc_final: 0.4628 (m-80) REVERT: B 378 ASN cc_start: 0.6350 (m110) cc_final: 0.6132 (m-40) REVERT: B 401 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7352 (mm-30) REVERT: B 444 MET cc_start: 0.8738 (tpt) cc_final: 0.8243 (tpt) REVERT: B 468 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7893 (ttpt) REVERT: B 469 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8057 (mm) REVERT: C 338 PHE cc_start: 0.5691 (OUTLIER) cc_final: 0.4543 (m-80) REVERT: C 468 LYS cc_start: 0.8331 (ttpt) cc_final: 0.8124 (ttpt) REVERT: C 472 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7927 (tppt) REVERT: I 39 GLN cc_start: 0.8022 (tt0) cc_final: 0.7763 (tt0) REVERT: J 152 TYR cc_start: 0.7823 (p90) cc_final: 0.7570 (p90) REVERT: L 24 ARG cc_start: 0.6210 (ttm-80) cc_final: 0.5741 (ttm-80) REVERT: L 47 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8057 (mt) REVERT: L 79 GLU cc_start: 0.6660 (mm-30) cc_final: 0.6343 (tm-30) REVERT: L 106 LEU cc_start: 0.5392 (OUTLIER) cc_final: 0.4613 (mt) REVERT: M 24 ARG cc_start: 0.6254 (ttm-80) cc_final: 0.5829 (ttp-110) REVERT: M 79 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6373 (tm-30) REVERT: M 106 LEU cc_start: 0.5328 (OUTLIER) cc_final: 0.4548 (mt) REVERT: N 24 ARG cc_start: 0.5975 (ttm-80) cc_final: 0.5613 (ttm-80) REVERT: N 79 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6414 (tm-30) REVERT: N 106 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.4553 (mt) REVERT: N 148 TRP cc_start: 0.6238 (m100) cc_final: 0.5637 (m-10) outliers start: 57 outliers final: 29 residues processed: 276 average time/residue: 0.3033 time to fit residues: 135.4479 Evaluate side-chains 248 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 10 TYR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 198 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 227 optimal weight: 30.0000 chunk 184 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 136 optimal weight: 0.9990 chunk 239 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN B 216 ASN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22143 Z= 0.314 Angle : 0.560 7.994 30054 Z= 0.298 Chirality : 0.045 0.213 3357 Planarity : 0.004 0.047 3882 Dihedral : 5.271 47.331 3264 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.43 % Allowed : 10.58 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -0.18 (0.15), residues: 2763 helix: 1.94 (0.24), residues: 432 sheet: 0.01 (0.16), residues: 972 loop : -0.87 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 148 HIS 0.006 0.001 HIS A 17 PHE 0.016 0.002 PHE J 105 TYR 0.032 0.002 TYR N 94 ARG 0.002 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.5701 (OUTLIER) cc_final: 0.4951 (m-80) REVERT: A 401 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7332 (mm-30) REVERT: A 469 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8065 (mm) REVERT: A 470 TYR cc_start: 0.8125 (m-80) cc_final: 0.7886 (m-80) REVERT: B 338 PHE cc_start: 0.5680 (OUTLIER) cc_final: 0.4720 (m-80) REVERT: B 401 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7381 (mm-30) REVERT: B 444 MET cc_start: 0.8772 (tpt) cc_final: 0.8198 (tpt) REVERT: B 468 LYS cc_start: 0.8415 (ttpt) cc_final: 0.7833 (ttpt) REVERT: B 469 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8047 (mm) REVERT: C 338 PHE cc_start: 0.5821 (OUTLIER) cc_final: 0.4769 (m-80) REVERT: C 472 LYS cc_start: 0.8268 (mmtm) cc_final: 0.7918 (tppt) REVERT: H 90 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7561 (t0) REVERT: I 39 GLN cc_start: 0.8094 (tt0) cc_final: 0.7804 (tt0) REVERT: I 152 TYR cc_start: 0.8037 (p90) cc_final: 0.7777 (p90) REVERT: J 152 TYR cc_start: 0.7863 (p90) cc_final: 0.7542 (p90) REVERT: L 24 ARG cc_start: 0.6262 (ttm-80) cc_final: 0.5765 (ttm-80) REVERT: L 47 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8156 (mt) REVERT: L 79 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6388 (tm-30) REVERT: L 106 LEU cc_start: 0.5424 (OUTLIER) cc_final: 0.4632 (mt) REVERT: M 24 ARG cc_start: 0.6269 (ttm-80) cc_final: 0.5788 (ttp-110) REVERT: M 106 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.4625 (mt) REVERT: N 106 LEU cc_start: 0.5413 (OUTLIER) cc_final: 0.4566 (mt) REVERT: N 148 TRP cc_start: 0.6271 (m100) cc_final: 0.5641 (m-10) outliers start: 58 outliers final: 38 residues processed: 264 average time/residue: 0.3142 time to fit residues: 133.6482 Evaluate side-chains 254 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 93 GLU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 0.8980 chunk 240 optimal weight: 20.0000 chunk 52 optimal weight: 0.0980 chunk 156 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 267 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 ASN H 162 ASN H 178 GLN I 112 GLN I 162 ASN I 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22143 Z= 0.167 Angle : 0.503 7.815 30054 Z= 0.267 Chirality : 0.042 0.171 3357 Planarity : 0.004 0.052 3882 Dihedral : 4.864 44.601 3262 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.05 % Allowed : 11.50 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -0.00 (0.16), residues: 2763 helix: 2.12 (0.24), residues: 435 sheet: 0.08 (0.16), residues: 990 loop : -0.75 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 148 HIS 0.004 0.001 HIS J 207 PHE 0.015 0.001 PHE J 129 TYR 0.022 0.001 TYR N 94 ARG 0.002 0.000 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7195 (mm-30) REVERT: A 469 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7959 (mm) REVERT: B 338 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.4971 (m-80) REVERT: B 444 MET cc_start: 0.8724 (tpt) cc_final: 0.8248 (tpt) REVERT: B 468 LYS cc_start: 0.8471 (ttpt) cc_final: 0.7871 (ttpt) REVERT: B 470 TYR cc_start: 0.8302 (m-80) cc_final: 0.7818 (m-10) REVERT: C 338 PHE cc_start: 0.5744 (OUTLIER) cc_final: 0.4837 (m-80) REVERT: H 39 GLN cc_start: 0.8085 (tt0) cc_final: 0.7801 (tt0) REVERT: H 90 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7516 (t0) REVERT: H 131 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6478 (mt) REVERT: I 39 GLN cc_start: 0.8068 (tt0) cc_final: 0.7854 (tt0) REVERT: J 152 TYR cc_start: 0.7853 (p90) cc_final: 0.7496 (p90) REVERT: L 24 ARG cc_start: 0.6128 (ttm-80) cc_final: 0.5708 (ttm-80) REVERT: L 78 LEU cc_start: 0.6877 (mt) cc_final: 0.6584 (tt) REVERT: L 79 GLU cc_start: 0.6667 (mm-30) cc_final: 0.6340 (tm-30) REVERT: L 106 LEU cc_start: 0.5363 (OUTLIER) cc_final: 0.4588 (mt) REVERT: M 24 ARG cc_start: 0.6093 (ttm-80) cc_final: 0.5762 (ttp-110) REVERT: M 79 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6377 (tm-30) REVERT: M 106 LEU cc_start: 0.5320 (OUTLIER) cc_final: 0.4607 (mt) REVERT: N 78 LEU cc_start: 0.6921 (mt) cc_final: 0.6619 (tt) REVERT: N 79 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6376 (tm-30) REVERT: N 106 LEU cc_start: 0.5336 (OUTLIER) cc_final: 0.4610 (mt) REVERT: N 148 TRP cc_start: 0.6199 (m100) cc_final: 0.5602 (m-10) REVERT: N 154 LEU cc_start: 0.4102 (OUTLIER) cc_final: 0.3627 (mt) outliers start: 49 outliers final: 30 residues processed: 270 average time/residue: 0.3101 time to fit residues: 136.2708 Evaluate side-chains 245 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 224 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 178 GLN I 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22143 Z= 0.342 Angle : 0.568 7.947 30054 Z= 0.300 Chirality : 0.045 0.178 3357 Planarity : 0.004 0.047 3882 Dihedral : 5.026 47.127 3256 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.51 % Allowed : 12.17 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -0.11 (0.16), residues: 2763 helix: 2.21 (0.24), residues: 414 sheet: -0.04 (0.16), residues: 981 loop : -0.77 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 222 HIS 0.006 0.001 HIS B 435 PHE 0.018 0.002 PHE J 129 TYR 0.044 0.002 TYR N 94 ARG 0.003 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 211 time to evaluate : 2.447 Fit side-chains revert: symmetry clash REVERT: A 401 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 468 LYS cc_start: 0.8461 (ttpt) cc_final: 0.7771 (ttpt) REVERT: A 469 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8055 (mm) REVERT: B 338 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.5271 (m-80) REVERT: B 444 MET cc_start: 0.8769 (tpt) cc_final: 0.8238 (tpt) REVERT: B 468 LYS cc_start: 0.8457 (ttpt) cc_final: 0.7793 (ttpt) REVERT: B 469 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8077 (mm) REVERT: B 470 TYR cc_start: 0.8352 (m-80) cc_final: 0.7804 (m-10) REVERT: C 338 PHE cc_start: 0.5858 (OUTLIER) cc_final: 0.5014 (m-80) REVERT: C 408 ASP cc_start: 0.7743 (m-30) cc_final: 0.7503 (m-30) REVERT: I 39 GLN cc_start: 0.8156 (tt0) cc_final: 0.7877 (tt0) REVERT: J 152 TYR cc_start: 0.7873 (p90) cc_final: 0.7551 (p90) REVERT: L 24 ARG cc_start: 0.6320 (ttm-80) cc_final: 0.5758 (ttp-110) REVERT: L 47 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8109 (mt) REVERT: L 79 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6362 (tm-30) REVERT: L 106 LEU cc_start: 0.5404 (OUTLIER) cc_final: 0.4621 (mt) REVERT: L 175 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7710 (tt) REVERT: M 24 ARG cc_start: 0.6134 (ttm-80) cc_final: 0.5817 (ttp-110) REVERT: M 106 LEU cc_start: 0.5383 (OUTLIER) cc_final: 0.4678 (mt) REVERT: N 78 LEU cc_start: 0.6885 (mt) cc_final: 0.6640 (tt) REVERT: N 79 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6460 (tm-30) REVERT: N 106 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.4646 (mt) REVERT: N 148 TRP cc_start: 0.6244 (m100) cc_final: 0.5779 (m100) REVERT: N 154 LEU cc_start: 0.4197 (OUTLIER) cc_final: 0.3732 (mt) outliers start: 60 outliers final: 41 residues processed: 259 average time/residue: 0.3222 time to fit residues: 134.5589 Evaluate side-chains 254 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 93 GLU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 356 GLN C 189 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN I 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22143 Z= 0.185 Angle : 0.528 9.274 30054 Z= 0.275 Chirality : 0.042 0.154 3357 Planarity : 0.004 0.049 3882 Dihedral : 4.772 44.255 3256 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.09 % Allowed : 12.46 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -0.06 (0.16), residues: 2763 helix: 2.13 (0.25), residues: 435 sheet: 0.06 (0.17), residues: 942 loop : -0.79 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 47 HIS 0.003 0.001 HIS A 17 PHE 0.022 0.001 PHE J 129 TYR 0.035 0.001 TYR N 94 ARG 0.003 0.000 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 LYS cc_start: 0.8518 (ttpt) cc_final: 0.7700 (ttpt) REVERT: A 469 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7996 (mm) REVERT: A 470 TYR cc_start: 0.8112 (m-10) cc_final: 0.7529 (m-10) REVERT: B 444 MET cc_start: 0.8726 (tpt) cc_final: 0.8204 (tpt) REVERT: B 468 LYS cc_start: 0.8486 (ttpt) cc_final: 0.7942 (ttpt) REVERT: I 39 GLN cc_start: 0.8066 (tt0) cc_final: 0.7847 (tt0) REVERT: J 35 GLU cc_start: 0.8487 (mp0) cc_final: 0.8203 (mp0) REVERT: J 152 TYR cc_start: 0.7857 (p90) cc_final: 0.7491 (p90) REVERT: L 24 ARG cc_start: 0.6262 (ttm-80) cc_final: 0.5584 (ttm-80) REVERT: L 47 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7997 (mt) REVERT: L 79 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6336 (tm-30) REVERT: L 106 LEU cc_start: 0.5344 (OUTLIER) cc_final: 0.4590 (mt) REVERT: M 24 ARG cc_start: 0.6040 (ttm-80) cc_final: 0.5765 (ttp-110) REVERT: M 79 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6441 (tm-30) REVERT: M 106 LEU cc_start: 0.5293 (OUTLIER) cc_final: 0.4582 (mt) REVERT: N 79 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6387 (tm-30) REVERT: N 106 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.4726 (mt) REVERT: N 148 TRP cc_start: 0.6169 (m100) cc_final: 0.5602 (m-10) REVERT: N 154 LEU cc_start: 0.4086 (OUTLIER) cc_final: 0.3631 (mt) REVERT: N 175 LEU cc_start: 0.7790 (tt) cc_final: 0.7570 (tt) outliers start: 50 outliers final: 36 residues processed: 267 average time/residue: 0.3054 time to fit residues: 133.8570 Evaluate side-chains 256 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 93 GLU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 232 optimal weight: 30.0000 chunk 247 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 224 optimal weight: 0.2980 chunk 234 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN I 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22143 Z= 0.254 Angle : 0.546 9.206 30054 Z= 0.284 Chirality : 0.043 0.164 3357 Planarity : 0.004 0.050 3882 Dihedral : 4.809 44.874 3252 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.01 % Allowed : 12.51 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -0.09 (0.16), residues: 2763 helix: 2.11 (0.24), residues: 432 sheet: 0.01 (0.17), residues: 948 loop : -0.77 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 222 HIS 0.005 0.001 HIS B 435 PHE 0.016 0.002 PHE J 153 TYR 0.040 0.002 TYR N 94 ARG 0.003 0.000 ARG I 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 2.424 Fit side-chains REVERT: A 320 MET cc_start: 0.7532 (ptt) cc_final: 0.7237 (ptt) REVERT: A 468 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8187 (ttmt) REVERT: A 469 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8040 (mm) REVERT: B 277 CYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7176 (t) REVERT: B 444 MET cc_start: 0.8752 (tpt) cc_final: 0.8175 (tpt) REVERT: B 468 LYS cc_start: 0.8453 (ttpt) cc_final: 0.7825 (ttpt) REVERT: B 470 TYR cc_start: 0.8226 (m-80) cc_final: 0.7733 (m-10) REVERT: C 408 ASP cc_start: 0.7744 (m-30) cc_final: 0.7508 (m-30) REVERT: H 90 ASP cc_start: 0.7700 (t0) cc_final: 0.7499 (t0) REVERT: I 39 GLN cc_start: 0.8114 (tt0) cc_final: 0.7869 (tt0) REVERT: J 35 GLU cc_start: 0.8556 (mp0) cc_final: 0.8271 (mp0) REVERT: J 152 TYR cc_start: 0.7877 (p90) cc_final: 0.7514 (p90) REVERT: L 24 ARG cc_start: 0.6121 (ttm-80) cc_final: 0.5500 (ttp-110) REVERT: L 47 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8062 (mt) REVERT: L 79 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6171 (tm-30) REVERT: L 106 LEU cc_start: 0.5420 (OUTLIER) cc_final: 0.4629 (mt) REVERT: M 24 ARG cc_start: 0.6087 (ttm-80) cc_final: 0.5822 (ttp-110) REVERT: M 79 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6429 (tm-30) REVERT: M 106 LEU cc_start: 0.5325 (OUTLIER) cc_final: 0.4640 (mt) REVERT: N 79 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6422 (tm-30) REVERT: N 106 LEU cc_start: 0.5536 (OUTLIER) cc_final: 0.4747 (mt) REVERT: N 148 TRP cc_start: 0.6202 (m100) cc_final: 0.5684 (m-10) REVERT: N 154 LEU cc_start: 0.4156 (OUTLIER) cc_final: 0.3698 (mt) REVERT: N 175 LEU cc_start: 0.7882 (tt) cc_final: 0.7660 (tt) outliers start: 48 outliers final: 36 residues processed: 247 average time/residue: 0.2963 time to fit residues: 120.6850 Evaluate side-chains 246 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 93 GLU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 124 optimal weight: 0.0000 chunk 182 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 253 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 169 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22143 Z= 0.347 Angle : 0.586 8.930 30054 Z= 0.305 Chirality : 0.045 0.176 3357 Planarity : 0.004 0.048 3882 Dihedral : 5.060 46.953 3252 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.01 % Allowed : 12.55 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -0.18 (0.16), residues: 2763 helix: 2.18 (0.24), residues: 414 sheet: -0.11 (0.17), residues: 945 loop : -0.81 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 222 HIS 0.006 0.001 HIS B 435 PHE 0.025 0.002 PHE N 118 TYR 0.051 0.002 TYR N 94 ARG 0.004 0.000 ARG C 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 2.518 Fit side-chains REVERT: A 320 MET cc_start: 0.7848 (ptt) cc_final: 0.7598 (ptt) REVERT: A 469 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8073 (mm) REVERT: B 444 MET cc_start: 0.8756 (tpt) cc_final: 0.8246 (tpt) REVERT: B 468 LYS cc_start: 0.8454 (ttpt) cc_final: 0.7808 (ttpt) REVERT: B 470 TYR cc_start: 0.8288 (m-80) cc_final: 0.7757 (m-10) REVERT: C 408 ASP cc_start: 0.7751 (m-30) cc_final: 0.7507 (m-30) REVERT: C 462 MET cc_start: 0.7926 (mmm) cc_final: 0.7713 (mmm) REVERT: C 468 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8053 (ttpt) REVERT: I 39 GLN cc_start: 0.8155 (tt0) cc_final: 0.7858 (tt0) REVERT: J 35 GLU cc_start: 0.8561 (mp0) cc_final: 0.8282 (mp0) REVERT: J 152 TYR cc_start: 0.7919 (p90) cc_final: 0.7597 (p90) REVERT: L 24 ARG cc_start: 0.6210 (ttm-80) cc_final: 0.5689 (ttm-80) REVERT: L 47 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8162 (mt) REVERT: L 106 LEU cc_start: 0.5323 (OUTLIER) cc_final: 0.4569 (mt) REVERT: L 148 TRP cc_start: 0.6119 (m100) cc_final: 0.5771 (m-10) REVERT: M 24 ARG cc_start: 0.6159 (ttm-80) cc_final: 0.5847 (ttp-110) REVERT: M 106 LEU cc_start: 0.5260 (OUTLIER) cc_final: 0.4682 (mt) REVERT: M 137 ASN cc_start: 0.7474 (t0) cc_final: 0.7259 (t0) REVERT: M 148 TRP cc_start: 0.6042 (m100) cc_final: 0.5691 (m-10) REVERT: N 106 LEU cc_start: 0.5460 (OUTLIER) cc_final: 0.4764 (mt) REVERT: N 148 TRP cc_start: 0.6311 (m100) cc_final: 0.5776 (m-10) REVERT: N 154 LEU cc_start: 0.4049 (OUTLIER) cc_final: 0.3627 (mt) REVERT: N 175 LEU cc_start: 0.7859 (tt) cc_final: 0.7640 (tt) outliers start: 48 outliers final: 40 residues processed: 241 average time/residue: 0.2912 time to fit residues: 116.4992 Evaluate side-chains 240 residues out of total 2391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 388 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 202 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 93 GLU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 83 PHE Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 83 PHE Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 chunk 32 optimal weight: 0.0020 chunk 60 optimal weight: 2.9990 chunk 219 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 192 optimal weight: 8.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN ** M 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.141664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098327 restraints weight = 36681.178| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.90 r_work: 0.3064 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22143 Z= 0.174 Angle : 0.525 9.143 30054 Z= 0.272 Chirality : 0.042 0.209 3357 Planarity : 0.004 0.051 3882 Dihedral : 4.699 43.861 3252 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.05 % Allowed : 12.55 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.90 % 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: -0.10 (0.16), residues: 2763 helix: 2.19 (0.25), residues: 435 sheet: -0.01 (0.16), residues: 990 loop : -0.85 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 47 HIS 0.003 0.001 HIS J 207 PHE 0.014 0.001 PHE L 118 TYR 0.029 0.001 TYR N 94 ARG 0.002 0.000 ARG C 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4666.81 seconds wall clock time: 87 minutes 0.99 seconds (5220.99 seconds total)