Starting phenix.real_space_refine on Sun Mar 17 11:53:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z03_14403/03_2024/7z03_14403_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z03_14403/03_2024/7z03_14403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z03_14403/03_2024/7z03_14403.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z03_14403/03_2024/7z03_14403.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z03_14403/03_2024/7z03_14403_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z03_14403/03_2024/7z03_14403_updated.pdb" } resolution = 3.7 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 Anisotropic ADP refinement not supported. Converting 4287 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 82 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 8173 2.51 5 N 2365 2.21 5 O 2736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 878": "OE1" <-> "OE2" Residue "C GLU 933": "OE1" <-> "OE2" Residue "C GLU 935": "OE1" <-> "OE2" Residue "C GLU 984": "OE1" <-> "OE2" Residue "C GLU 992": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 891": "OE1" <-> "OE2" Residue "D GLU 933": "OE1" <-> "OE2" Residue "D GLU 984": "OE1" <-> "OE2" Residue "D GLU 1018": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13396 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2916 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 7, 'TRANS': 366} Chain breaks: 1 Chain: "D" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2914 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 7, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3010 Classifications: {'peptide': 381} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2897 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 20, 'TRANS': 347} Chain breaks: 2 Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 806 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "F" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 793 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 22 residue: pdb=" N GLY A 284 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY A 284 " occ=0.50 residue: pdb=" N ALA A 287 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 287 " occ=0.60 residue: pdb=" N THR A 290 " occ=0.70 ... (5 atoms not shown) pdb=" CG2 THR A 290 " occ=0.70 residue: pdb=" N ALA A 291 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 291 " occ=0.60 residue: pdb=" N GLN A 292 " occ=0.70 ... (7 atoms not shown) pdb=" NE2 GLN A 292 " occ=0.70 residue: pdb=" N LEU A 293 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU A 293 " occ=0.80 residue: pdb=" N PRO A 303 " occ=0.61 ... (5 atoms not shown) pdb=" CD PRO A 303 " occ=0.61 residue: pdb=" N PRO A 304 " occ=0.68 ... (5 atoms not shown) pdb=" CD PRO A 304 " occ=0.68 residue: pdb=" N VAL A 305 " occ=0.88 ... (5 atoms not shown) pdb=" CG2 VAL A 305 " occ=0.88 residue: pdb=" N TRP A 306 " occ=0.97 ... (12 atoms not shown) pdb=" CH2 TRP A 306 " occ=0.97 residue: pdb=" N LEU A 307 " occ=0.87 ... (6 atoms not shown) pdb=" CD2 LEU A 307 " occ=0.87 residue: pdb=" N ILE A 309 " occ=0.89 ... (6 atoms not shown) pdb=" CD1 ILE A 309 " occ=0.89 ... (remaining 10 not shown) Time building chain proxies: 7.54, per 1000 atoms: 0.56 Number of scatterers: 13396 At special positions: 0 Unit cell: (108.018, 118.608, 136.611, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 34 16.00 P 82 15.00 Mg 2 11.99 O 2736 8.00 N 2365 7.00 C 8173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.35 Conformation dependent library (CDL) restraints added in 2.2 seconds 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 15 sheets defined 38.0% alpha, 16.2% beta 39 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 6.02 Creating SS restraints... Processing helix chain 'C' and resid 43 through 55 removed outlier: 3.831A pdb=" N LEU C 47 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 144 through 150 removed outlier: 4.345A pdb=" N ARG C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 163 removed outlier: 4.458A pdb=" N PHE C 161 " --> pdb=" O PHE C 158 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 162 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 177 Processing helix chain 'C' and resid 181 through 200 Processing helix chain 'C' and resid 876 through 886 Processing helix chain 'C' and resid 890 through 918 removed outlier: 3.601A pdb=" N ASP C 893 " --> pdb=" O LYS C 890 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS C 894 " --> pdb=" O GLU C 891 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE C 895 " --> pdb=" O GLY C 892 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN C 900 " --> pdb=" O LYS C 897 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 901 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 902 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS C 909 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR C 916 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 953 through 969 Processing helix chain 'C' and resid 985 through 988 removed outlier: 3.801A pdb=" N THR C 988 " --> pdb=" O GLY C 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 985 through 988' Processing helix chain 'C' and resid 991 through 1007 removed outlier: 3.615A pdb=" N ASP C 995 " --> pdb=" O SER C 991 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER C1007 " --> pdb=" O ALA C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1023 Processing helix chain 'C' and resid 1043 through 1045 No H-bonds generated for 'chain 'C' and resid 1043 through 1045' Processing helix chain 'D' and resid 43 through 55 removed outlier: 3.865A pdb=" N LEU D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 144 through 150 removed outlier: 4.263A pdb=" N ARG D 149 " --> pdb=" O GLY D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 177 removed outlier: 3.741A pdb=" N LEU D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 199 Processing helix chain 'D' and resid 875 through 886 Processing helix chain 'D' and resid 890 through 918 removed outlier: 3.711A pdb=" N ASP D 893 " --> pdb=" O LYS D 890 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS D 894 " --> pdb=" O GLU D 891 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE D 895 " --> pdb=" O GLY D 892 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN D 900 " --> pdb=" O LYS D 897 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY D 901 " --> pdb=" O PHE D 898 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 902 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR D 916 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG D 917 " --> pdb=" O GLN D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 948 through 950 No H-bonds generated for 'chain 'D' and resid 948 through 950' Processing helix chain 'D' and resid 953 through 970 Processing helix chain 'D' and resid 991 through 1005 removed outlier: 4.528A pdb=" N THR D 996 " --> pdb=" O GLU D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1023 removed outlier: 3.639A pdb=" N ARG D1023 " --> pdb=" O ALA D1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1019 through 1023' Processing helix chain 'D' and resid 1043 through 1045 No H-bonds generated for 'chain 'D' and resid 1043 through 1045' Processing helix chain 'A' and resid 21 through 38 Processing helix chain 'A' and resid 57 through 71 removed outlier: 4.328A pdb=" N GLN A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 99 removed outlier: 4.365A pdb=" N SER A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 137 No H-bonds generated for 'chain 'A' and resid 134 through 137' Processing helix chain 'A' and resid 146 through 172 removed outlier: 3.598A pdb=" N GLN A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 286 through 296 removed outlier: 4.141A pdb=" N GLN A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TRP A 296 " --> pdb=" O GLN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 362 through 372 removed outlier: 3.582A pdb=" N LEU A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.888A pdb=" N GLN A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 38 removed outlier: 3.750A pdb=" N TRP B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 73 removed outlier: 3.634A pdb=" N GLN B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 100 removed outlier: 4.084A pdb=" N PHE B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 154 through 172 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.518A pdb=" N ALA B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N TRP B 296 " --> pdb=" O GLN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 330 removed outlier: 4.583A pdb=" N ARG B 322 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 372 removed outlier: 3.841A pdb=" N LEU B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 394 removed outlier: 4.529A pdb=" N ARG B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 17 through 21 removed outlier: 6.463A pdb=" N GLU C 84 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU C 6 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU C 82 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU C 8 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 80 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 1026 through 1029 Processing sheet with id= C, first strand: chain 'C' and resid 922 through 926 Processing sheet with id= D, first strand: chain 'D' and resid 17 through 21 removed outlier: 6.471A pdb=" N GLU D 84 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU D 6 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU D 82 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU D 8 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU D 80 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 33 through 35 removed outlier: 3.860A pdb=" N PHE D 33 " --> pdb=" O ILE D1011 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 922 through 926 Processing sheet with id= G, first strand: chain 'D' and resid 1030 through 1032 Processing sheet with id= H, first strand: chain 'A' and resid 102 through 105 removed outlier: 6.429A pdb=" N LEU A 77 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL A 105 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 79 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 42 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 267 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N SER A 261 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 180 through 182 removed outlier: 6.317A pdb=" N TYR A 217 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE A 229 " --> pdb=" O MET A 232 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N HIS A 234 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 11.461A pdb=" N GLN A 227 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 279 through 284 removed outlier: 6.184A pdb=" N TRP A 306 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU A 282 " --> pdb=" O TRP A 306 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASP A 308 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N GLY A 284 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLU A 310 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE A 309 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 338 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE A 311 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG A 340 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 114 through 116 Processing sheet with id= L, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.580A pdb=" N LEU B 77 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL B 105 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL B 79 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 42 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 269 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 267 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N SER B 261 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 180 through 183 removed outlier: 6.543A pdb=" N TYR B 217 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N GLY B 183 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA B 219 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 236 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 220 " --> pdb=" O ARG B 236 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 279 through 284 removed outlier: 6.117A pdb=" N TRP B 306 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU B 282 " --> pdb=" O TRP B 306 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP B 308 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N GLY B 284 " --> pdb=" O ASP B 308 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU B 310 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 307 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE B 309 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL B 338 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE B 311 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG B 340 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 114 through 116 455 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 4.84 Time building geometry restraints manager: 6.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4039 1.34 - 1.46: 2454 1.46 - 1.57: 7091 1.57 - 1.69: 160 1.69 - 1.81: 52 Bond restraints: 13796 Sorted by residual: bond pdb=" C4 ADP D1101 " pdb=" C5 ADP D1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP C1101 " pdb=" C5 ADP C1101 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C5 ADP D1101 " pdb=" C6 ADP D1101 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C5 ADP C1101 " pdb=" C6 ADP C1101 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" N ILE A 223 " pdb=" CA ILE A 223 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.01e+01 ... (remaining 13791 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.89: 623 105.89 - 112.92: 7610 112.92 - 119.95: 4696 119.95 - 126.98: 5802 126.98 - 134.01: 318 Bond angle restraints: 19049 Sorted by residual: angle pdb=" C ASN D 12 " pdb=" CA ASN D 12 " pdb=" CB ASN D 12 " ideal model delta sigma weight residual 116.54 109.97 6.57 1.15e+00 7.56e-01 3.26e+01 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" O GLY A 221 " ideal model delta sigma weight residual 121.61 115.82 5.79 1.05e+00 9.07e-01 3.04e+01 angle pdb=" CA GLY B 221 " pdb=" C GLY B 221 " pdb=" O GLY B 221 " ideal model delta sigma weight residual 121.78 117.04 4.74 9.10e-01 1.21e+00 2.71e+01 angle pdb=" PA ADP C1101 " pdb=" O3A ADP C1101 " pdb=" PB ADP C1101 " ideal model delta sigma weight residual 120.50 133.94 -13.44 3.00e+00 1.11e-01 2.01e+01 angle pdb=" PA ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PB ADP D1101 " ideal model delta sigma weight residual 120.50 133.52 -13.02 3.00e+00 1.11e-01 1.88e+01 ... (remaining 19044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.46: 7608 34.46 - 68.93: 442 68.93 - 103.39: 19 103.39 - 137.85: 5 137.85 - 172.32: 2 Dihedral angle restraints: 8076 sinusoidal: 3741 harmonic: 4335 Sorted by residual: dihedral pdb=" C5' ADP D1101 " pdb=" O5' ADP D1101 " pdb=" PA ADP D1101 " pdb=" O2A ADP D1101 " ideal model delta sinusoidal sigma weight residual -60.00 66.10 -126.09 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" O2A ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PA ADP D1101 " pdb=" PB ADP D1101 " ideal model delta sinusoidal sigma weight residual -60.00 65.40 -125.40 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O1B ADP D1101 " pdb=" O3A ADP D1101 " pdb=" PB ADP D1101 " pdb=" PA ADP D1101 " ideal model delta sinusoidal sigma weight residual -60.00 57.79 -117.80 1 2.00e+01 2.50e-03 3.52e+01 ... (remaining 8073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1885 0.058 - 0.115: 277 0.115 - 0.173: 24 0.173 - 0.231: 3 0.231 - 0.288: 4 Chirality restraints: 2193 Sorted by residual: chirality pdb=" CA TYR A 237 " pdb=" N TYR A 237 " pdb=" C TYR A 237 " pdb=" CB TYR A 237 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C3' ADP C1101 " pdb=" C2' ADP C1101 " pdb=" C4' ADP C1101 " pdb=" O3' ADP C1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C3' ADP D1101 " pdb=" C2' ADP D1101 " pdb=" C4' ADP D1101 " pdb=" O3' ADP D1101 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2190 not shown) Planarity restraints: 2183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 58 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO D 59 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 47 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C GLY A 47 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY A 47 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP A 48 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 41 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C ALA D 41 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA D 41 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY D 42 " 0.008 2.00e-02 2.50e+03 ... (remaining 2180 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 12 2.18 - 2.86: 4482 2.86 - 3.54: 18950 3.54 - 4.22: 31430 4.22 - 4.90: 53782 Nonbonded interactions: 108656 Sorted by model distance: nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 501 " model vdw 1.498 2.320 nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 502 " model vdw 1.600 2.320 nonbonded pdb=" ND2 ASN A 83 " pdb=" OP2 DC F 55 " model vdw 1.761 2.520 nonbonded pdb=" OD1 ASN B 83 " pdb="MN MN B 502 " model vdw 1.806 2.320 nonbonded pdb=" O3B ADP C1101 " pdb="MG MG C1102 " model vdw 1.816 2.170 ... (remaining 108651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 137 or resid 153 through 343 or resid 356 throug \ h 395 or resid 501 through 502)) selection = (chain 'B' and (resid 1 through 189 or resid 204 through 395 or resid 501 throug \ h 502)) } ncs_group { reference = (chain 'C' and (resid 1 through 200 or resid 875 through 1047 or resid 1101 thro \ ugh 1102)) selection = (chain 'D' and (resid 1 through 200 or resid 875 through 1047 or resid 1101 thro \ ugh 1102)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 7.410 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 43.350 Find NCS groups from input model: 0.820 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: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 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 : 0.004 0.109 13796 Z= 0.256 Angle : 0.699 13.436 19049 Z= 0.396 Chirality : 0.042 0.288 2193 Planarity : 0.003 0.048 2183 Dihedral : 18.983 172.318 5264 Min Nonbonded Distance : 1.498 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.08 % Allowed : 0.31 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.23), residues: 1479 helix: 1.66 (0.23), residues: 547 sheet: 0.38 (0.34), residues: 231 loop : -0.29 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 9 HIS 0.009 0.001 HIS A 392 PHE 0.014 0.001 PHE C 895 TYR 0.014 0.001 TYR C 882 ARG 0.009 0.000 ARG D 976 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 598 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 VAL cc_start: 0.8396 (t) cc_final: 0.8010 (t) REVERT: C 1033 ILE cc_start: 0.6499 (mm) cc_final: 0.6245 (mp) REVERT: D 52 LEU cc_start: 0.7449 (tp) cc_final: 0.7076 (tp) REVERT: A 93 SER cc_start: 0.7256 (m) cc_final: 0.6498 (p) REVERT: B 246 PHE cc_start: 0.6214 (m-80) cc_final: 0.5736 (m-10) outliers start: 1 outliers final: 1 residues processed: 598 average time/residue: 0.2770 time to fit residues: 229.2716 Evaluate side-chains 394 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 139 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN B 234 HIS ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13796 Z= 0.247 Angle : 0.828 16.557 19049 Z= 0.397 Chirality : 0.046 0.232 2193 Planarity : 0.005 0.038 2183 Dihedral : 21.158 174.822 2467 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.14 % Allowed : 18.84 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.33 (0.22), residues: 1479 helix: 1.10 (0.22), residues: 522 sheet: 0.23 (0.32), residues: 265 loop : -0.39 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 880 HIS 0.005 0.001 HIS B 24 PHE 0.047 0.003 PHE C 895 TYR 0.024 0.003 TYR D 55 ARG 0.008 0.001 ARG C 926 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 456 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.6205 (t80) REVERT: C 182 TYR cc_start: 0.5154 (m-80) cc_final: 0.4901 (m-80) REVERT: C 189 VAL cc_start: 0.8608 (t) cc_final: 0.8122 (t) REVERT: C 883 LEU cc_start: 0.7954 (mt) cc_final: 0.7233 (mt) REVERT: C 976 ARG cc_start: 0.6221 (OUTLIER) cc_final: 0.5932 (ptp90) REVERT: A 16 TYR cc_start: 0.6397 (m-10) cc_final: 0.5942 (m-10) REVERT: B 15 PHE cc_start: 0.6459 (t80) cc_final: 0.5506 (t80) REVERT: B 62 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7617 (mm) REVERT: B 207 PHE cc_start: 0.6848 (t80) cc_final: 0.5639 (t80) REVERT: B 306 TRP cc_start: 0.7533 (m-10) cc_final: 0.6776 (m-10) REVERT: B 394 LEU cc_start: 0.8459 (mm) cc_final: 0.8169 (mp) outliers start: 40 outliers final: 22 residues processed: 472 average time/residue: 0.2427 time to fit residues: 165.9643 Evaluate side-chains 413 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 388 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 169 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 95 optimal weight: 0.0770 chunk 38 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 124 optimal weight: 0.1980 chunk 138 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 914 GLN A 10 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13796 Z= 0.232 Angle : 0.805 15.045 19049 Z= 0.384 Chirality : 0.046 0.293 2193 Planarity : 0.004 0.039 2183 Dihedral : 21.212 177.159 2467 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.69 % Allowed : 24.80 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.12 (0.22), residues: 1479 helix: 0.59 (0.22), residues: 526 sheet: 0.47 (0.32), residues: 251 loop : -0.37 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 880 HIS 0.015 0.001 HIS A 385 PHE 0.041 0.003 PHE C 895 TYR 0.030 0.003 TYR D 55 ARG 0.004 0.000 ARG C 926 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 388 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 189 VAL cc_start: 0.8625 (t) cc_final: 0.8178 (t) REVERT: D 983 ASP cc_start: 0.5565 (t70) cc_final: 0.4778 (t0) REVERT: D 1036 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.6995 (pp) REVERT: B 246 PHE cc_start: 0.6283 (m-10) cc_final: 0.5898 (m-10) outliers start: 47 outliers final: 29 residues processed: 405 average time/residue: 0.2249 time to fit residues: 135.6117 Evaluate side-chains 390 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 360 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 1013 VAL Chi-restraints excluded: chain D residue 1036 LEU Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 386 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 chunk 148 optimal weight: 20.0000 chunk 73 optimal weight: 0.8980 chunk 133 optimal weight: 0.0970 chunk 40 optimal weight: 4.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN B 224 HIS B 234 HIS ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13796 Z= 0.287 Angle : 0.783 13.025 19049 Z= 0.384 Chirality : 0.045 0.334 2193 Planarity : 0.004 0.041 2183 Dihedral : 21.260 178.778 2467 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.71 % Allowed : 25.20 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.03 (0.22), residues: 1479 helix: 0.38 (0.22), residues: 533 sheet: 0.27 (0.32), residues: 247 loop : -0.22 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 880 HIS 0.012 0.001 HIS A 385 PHE 0.034 0.003 PHE C 895 TYR 0.029 0.003 TYR D 55 ARG 0.004 0.001 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 368 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 LEU cc_start: 0.7316 (pp) cc_final: 0.6951 (pp) REVERT: C 151 MET cc_start: 0.5732 (ppp) cc_final: 0.5215 (ppp) REVERT: C 193 HIS cc_start: 0.6911 (t-90) cc_final: 0.5242 (t-90) REVERT: C 994 LEU cc_start: 0.7866 (pp) cc_final: 0.7023 (tt) outliers start: 60 outliers final: 45 residues processed: 391 average time/residue: 0.2229 time to fit residues: 129.5869 Evaluate side-chains 375 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 330 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1028 ILE Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13796 Z= 0.312 Angle : 0.772 12.518 19049 Z= 0.387 Chirality : 0.046 0.248 2193 Planarity : 0.004 0.041 2183 Dihedral : 21.257 179.598 2467 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.81 % Allowed : 26.53 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.02 (0.22), residues: 1479 helix: 0.37 (0.22), residues: 525 sheet: 0.13 (0.32), residues: 254 loop : -0.16 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 296 HIS 0.009 0.001 HIS A 385 PHE 0.026 0.003 PHE C 895 TYR 0.022 0.002 TYR B 217 ARG 0.004 0.000 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 340 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 LEU cc_start: 0.7244 (pp) cc_final: 0.6929 (pp) REVERT: C 151 MET cc_start: 0.5942 (ppp) cc_final: 0.5589 (ppp) REVERT: C 994 LEU cc_start: 0.7981 (pp) cc_final: 0.7176 (tt) REVERT: A 244 LEU cc_start: 0.8032 (mt) cc_final: 0.7750 (mm) outliers start: 74 outliers final: 52 residues processed: 375 average time/residue: 0.2321 time to fit residues: 127.8437 Evaluate side-chains 381 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 329 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 984 GLU Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 904 LEU Chi-restraints excluded: chain D residue 906 ASN Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 906 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13796 Z= 0.226 Angle : 0.792 14.045 19049 Z= 0.379 Chirality : 0.046 0.292 2193 Planarity : 0.004 0.042 2183 Dihedral : 21.213 178.279 2467 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.77 % Allowed : 30.69 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 0.01 (0.22), residues: 1479 helix: 0.37 (0.22), residues: 524 sheet: 0.11 (0.32), residues: 262 loop : -0.17 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 296 HIS 0.008 0.001 HIS A 385 PHE 0.028 0.003 PHE C 895 TYR 0.025 0.002 TYR D 92 ARG 0.005 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 353 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.5806 (ppp) cc_final: 0.5560 (ppp) REVERT: A 131 PHE cc_start: 0.7967 (t80) cc_final: 0.7643 (t80) outliers start: 48 outliers final: 38 residues processed: 372 average time/residue: 0.2353 time to fit residues: 130.9071 Evaluate side-chains 370 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 332 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 893 ASP Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 970 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13796 Z= 0.268 Angle : 0.819 16.897 19049 Z= 0.392 Chirality : 0.046 0.274 2193 Planarity : 0.004 0.042 2183 Dihedral : 21.199 177.674 2467 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.47 % Allowed : 30.69 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.08 (0.22), residues: 1479 helix: 0.27 (0.22), residues: 525 sheet: -0.07 (0.31), residues: 261 loop : -0.14 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 296 HIS 0.007 0.001 HIS A 385 PHE 0.024 0.003 PHE C 895 TYR 0.021 0.002 TYR B 217 ARG 0.005 0.000 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 338 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 LEU cc_start: 0.7205 (pp) cc_final: 0.6747 (pp) REVERT: C 151 MET cc_start: 0.6179 (ppp) cc_final: 0.5848 (ppp) REVERT: C 1036 LEU cc_start: 0.7834 (mp) cc_final: 0.7624 (mt) REVERT: D 896 ARG cc_start: 0.6653 (ttp-110) cc_final: 0.6413 (ttp-110) REVERT: A 131 PHE cc_start: 0.8102 (t80) cc_final: 0.7826 (t80) outliers start: 57 outliers final: 45 residues processed: 366 average time/residue: 0.2264 time to fit residues: 123.4096 Evaluate side-chains 353 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 308 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 904 LEU Chi-restraints excluded: chain D residue 908 VAL Chi-restraints excluded: chain D residue 919 HIS Chi-restraints excluded: chain D residue 993 THR Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1030 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 73 optimal weight: 0.0470 chunk 13 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 0.3980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 HIS ** B 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13796 Z= 0.209 Angle : 0.852 15.134 19049 Z= 0.397 Chirality : 0.047 0.337 2193 Planarity : 0.004 0.067 2183 Dihedral : 21.187 177.251 2467 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.77 % Allowed : 31.79 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.05 (0.22), residues: 1479 helix: 0.28 (0.23), residues: 516 sheet: -0.07 (0.31), residues: 268 loop : -0.09 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 296 HIS 0.007 0.001 HIS A 385 PHE 0.022 0.002 PHE A 387 TYR 0.023 0.002 TYR B 217 ARG 0.005 0.000 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 338 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.6432 (ppp) cc_final: 0.6128 (ppp) REVERT: A 131 PHE cc_start: 0.7996 (t80) cc_final: 0.7731 (t80) REVERT: B 260 PHE cc_start: 0.6785 (m-80) cc_final: 0.6559 (m-80) outliers start: 48 outliers final: 40 residues processed: 361 average time/residue: 0.2326 time to fit residues: 125.0251 Evaluate side-chains 354 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 314 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 138 optimal weight: 0.0370 chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 0.0060 chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13796 Z= 0.223 Angle : 0.871 16.299 19049 Z= 0.403 Chirality : 0.047 0.422 2193 Planarity : 0.004 0.047 2183 Dihedral : 21.163 177.896 2467 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.98 % Allowed : 32.57 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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 (0.22), residues: 1479 helix: 0.20 (0.23), residues: 514 sheet: -0.23 (0.30), residues: 271 loop : -0.10 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP C 880 HIS 0.029 0.002 HIS A 164 PHE 0.035 0.003 PHE C 190 TYR 0.021 0.002 TYR B 217 ARG 0.016 0.001 ARG C 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 317 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 LEU cc_start: 0.7153 (pp) cc_final: 0.6775 (pp) REVERT: C 151 MET cc_start: 0.6435 (ppp) cc_final: 0.6179 (ppp) REVERT: C 172 LEU cc_start: 0.7709 (pp) cc_final: 0.7437 (pp) REVERT: A 43 ILE cc_start: 0.8767 (mp) cc_final: 0.8564 (mm) outliers start: 38 outliers final: 37 residues processed: 337 average time/residue: 0.2262 time to fit residues: 114.0390 Evaluate side-chains 352 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 315 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 HIS ** B 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13796 Z= 0.249 Angle : 0.857 15.680 19049 Z= 0.406 Chirality : 0.047 0.410 2193 Planarity : 0.004 0.046 2183 Dihedral : 21.163 179.196 2467 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.06 % Allowed : 33.12 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.22 (0.22), residues: 1479 helix: 0.09 (0.22), residues: 514 sheet: -0.29 (0.30), residues: 275 loop : -0.09 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A 296 HIS 0.019 0.002 HIS B 164 PHE 0.036 0.002 PHE C 190 TYR 0.022 0.002 TYR A 160 ARG 0.006 0.000 ARG B 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 311 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.6573 (ppp) cc_final: 0.6284 (ppp) REVERT: C 172 LEU cc_start: 0.7764 (pp) cc_final: 0.7514 (pp) outliers start: 39 outliers final: 37 residues processed: 333 average time/residue: 0.2324 time to fit residues: 114.4006 Evaluate side-chains 342 residues out of total 1274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 305 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 976 ARG Chi-restraints excluded: chain C residue 1017 VAL Chi-restraints excluded: chain C residue 1030 VAL Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 887 ILE Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 1017 VAL Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 309 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 125 optimal weight: 0.0070 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1016 HIS ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 HIS ** B 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.085327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.058541 restraints weight = 46670.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060922 restraints weight = 27899.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.062603 restraints weight = 19451.528| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13796 Z= 0.238 Angle : 0.860 15.966 19049 Z= 0.406 Chirality : 0.047 0.441 2193 Planarity : 0.004 0.047 2183 Dihedral : 21.162 179.737 2467 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.06 % Allowed : 33.05 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -0.19 (0.22), residues: 1479 helix: 0.15 (0.23), residues: 512 sheet: -0.31 (0.31), residues: 275 loop : -0.07 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 296 HIS 0.009 0.001 HIS B 385 PHE 0.036 0.002 PHE C 190 TYR 0.025 0.002 TYR A 160 ARG 0.006 0.000 ARG B 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3296.79 seconds wall clock time: 60 minutes 10.68 seconds (3610.68 seconds total)