Starting phenix.real_space_refine on Wed Feb 14 20:49:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc2_22805/02_2024/7kc2_22805_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc2_22805/02_2024/7kc2_22805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc2_22805/02_2024/7kc2_22805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc2_22805/02_2024/7kc2_22805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc2_22805/02_2024/7kc2_22805_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc2_22805/02_2024/7kc2_22805_updated.pdb" } resolution = 2.67 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 8 5.49 5 S 56 5.16 5 C 6428 2.51 5 N 1732 2.21 5 O 1960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 303": "OE1" <-> "OE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10192 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2501 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2501 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2501 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2501 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 2, 'NAD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 2, 'NAD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 2, 'NAD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 2, 'NAD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 715 SG CYS A 97 28.453 49.930 34.890 1.00 44.12 S ATOM 734 SG CYS A 100 32.114 50.441 34.141 1.00 36.60 S ATOM 761 SG CYS A 103 31.274 49.062 37.415 1.00 37.10 S ATOM 819 SG CYS A 111 30.350 52.684 36.643 1.00 41.20 S ATOM 316 SG CYS A 43 35.889 60.403 55.039 1.00 46.99 S ATOM 1126 SG CYS A 153 34.886 57.151 53.195 1.00 35.09 S ATOM 3216 SG CYS B 97 76.549 34.071 34.891 1.00 44.57 S ATOM 3235 SG CYS B 100 72.889 33.560 34.141 1.00 36.92 S ATOM 3262 SG CYS B 103 73.728 34.939 37.415 1.00 37.47 S ATOM 3320 SG CYS B 111 74.653 31.318 36.643 1.00 41.01 S ATOM 2817 SG CYS B 43 69.111 23.600 55.039 1.00 47.24 S ATOM 3627 SG CYS B 153 70.115 26.852 53.195 1.00 34.69 S ATOM 5717 SG CYS C 97 28.454 34.068 44.913 1.00 44.42 S ATOM 5736 SG CYS C 100 32.115 33.557 45.663 1.00 36.74 S ATOM 5763 SG CYS C 103 31.276 34.936 42.389 1.00 37.37 S ATOM 5821 SG CYS C 111 30.351 31.315 43.161 1.00 42.01 S ATOM 5318 SG CYS C 43 35.893 23.598 24.764 1.00 47.06 S ATOM 6128 SG CYS C 153 34.890 26.850 26.608 1.00 34.58 S ATOM 8218 SG CYS D 97 76.547 49.935 44.911 1.00 44.19 S ATOM 8237 SG CYS D 100 72.886 50.445 45.660 1.00 36.84 S ATOM 8264 SG CYS D 103 73.726 49.066 42.386 1.00 37.51 S ATOM 8322 SG CYS D 111 74.650 52.688 43.158 1.00 41.31 S ATOM 7819 SG CYS D 43 69.110 60.404 24.761 1.00 47.06 S ATOM 8629 SG CYS D 153 70.114 57.152 26.605 1.00 34.68 S Time building chain proxies: 5.79, per 1000 atoms: 0.57 Number of scatterers: 10192 At special positions: 0 Unit cell: (106.05, 85.05, 80.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 56 16.00 P 8 15.00 O 1960 8.00 N 1732 7.00 C 6428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS D 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS C 277 " distance=2.03 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: 4.11 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 111 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 100 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 103 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 97 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 153 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 402 " - pdb=" NE2 HIS A 66 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 111 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 100 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 97 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 103 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 153 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 402 " - pdb=" NE2 HIS B 66 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 111 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 100 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 103 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 97 " pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 153 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 402 " - pdb=" NE2 HIS C 66 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 111 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 100 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 97 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 103 " pdb=" ZN D 402 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 153 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 402 " - pdb=" NE2 HIS D 66 " Number of angles added : 24 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 16 sheets defined 29.2% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 145 through 164 Proline residue: A 150 - end of helix removed outlier: 4.349A pdb=" N CYS A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 157 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 removed outlier: 4.000A pdb=" N LEU A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 249 through 256 removed outlier: 3.688A pdb=" N THR A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 323 through 333 Proline residue: A 326 - end of helix Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 101 through 104 No H-bonds generated for 'chain 'B' and resid 101 through 104' Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 145 through 164 Proline residue: B 150 - end of helix removed outlier: 4.349A pdb=" N CYS B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 157 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 removed outlier: 4.000A pdb=" N LEU B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'B' and resid 227 through 235 Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.688A pdb=" N THR B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 323 through 333 Proline residue: B 326 - end of helix Processing helix chain 'C' and resid 44 through 51 Processing helix chain 'C' and resid 101 through 104 No H-bonds generated for 'chain 'C' and resid 101 through 104' Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 145 through 164 Proline residue: C 150 - end of helix removed outlier: 4.349A pdb=" N CYS C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR C 157 " --> pdb=" O CYS C 153 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 192 removed outlier: 4.001A pdb=" N LEU C 185 " --> pdb=" O GLY C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 227 through 235 Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.688A pdb=" N THR C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 298 through 309 Processing helix chain 'C' and resid 323 through 333 Proline residue: C 326 - end of helix Processing helix chain 'D' and resid 44 through 51 Processing helix chain 'D' and resid 101 through 104 No H-bonds generated for 'chain 'D' and resid 101 through 104' Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 145 through 164 Proline residue: D 150 - end of helix removed outlier: 4.349A pdb=" N CYS D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR D 157 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 removed outlier: 4.000A pdb=" N LEU D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 213 Processing helix chain 'D' and resid 227 through 235 Processing helix chain 'D' and resid 249 through 256 removed outlier: 3.687A pdb=" N THR D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 298 through 309 Processing helix chain 'D' and resid 323 through 333 Proline residue: D 326 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 5 through 10 Processing sheet with id= B, first strand: chain 'A' and resid 128 through 132 removed outlier: 6.412A pdb=" N ASN A 36 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL A 72 " --> pdb=" O ASN A 36 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 67 through 69 removed outlier: 4.543A pdb=" N GLU A 67 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR A 341 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 265 through 267 removed outlier: 6.210A pdb=" N VAL A 242 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ARG A 196 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE A 175 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 198 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 217 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ASP A 201 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE A 219 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 5 through 10 Processing sheet with id= F, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.411A pdb=" N ASN B 36 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL B 72 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 67 through 69 removed outlier: 4.544A pdb=" N GLU B 67 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR B 341 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 265 through 267 removed outlier: 6.210A pdb=" N VAL B 242 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG B 196 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE B 175 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 198 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL B 217 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ASP B 201 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE B 219 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 5 through 10 Processing sheet with id= J, first strand: chain 'C' and resid 128 through 132 removed outlier: 6.411A pdb=" N ASN C 36 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL C 72 " --> pdb=" O ASN C 36 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 67 through 69 removed outlier: 4.544A pdb=" N GLU C 67 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR C 341 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 265 through 267 removed outlier: 6.210A pdb=" N VAL C 242 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ARG C 196 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE C 175 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 198 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 217 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ASP C 201 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE C 219 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 5 through 10 Processing sheet with id= N, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.411A pdb=" N ASN D 36 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL D 72 " --> pdb=" O ASN D 36 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 67 through 69 removed outlier: 4.544A pdb=" N GLU D 67 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR D 341 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 265 through 267 removed outlier: 6.209A pdb=" N VAL D 242 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ARG D 196 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE D 175 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D 198 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL D 217 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ASP D 201 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE D 219 " --> pdb=" O ASP D 201 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 4.44 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: 3344 1.34 - 1.46: 1983 1.46 - 1.57: 4989 1.57 - 1.69: 16 1.69 - 1.81: 80 Bond restraints: 10412 Sorted by residual: bond pdb=" O3 NAD D 403 " pdb=" PA NAD D 403 " ideal model delta sigma weight residual 1.653 1.599 0.054 2.00e-02 2.50e+03 7.24e+00 bond pdb=" O3 NAD C 403 " pdb=" PA NAD C 403 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 7.06e+00 bond pdb=" O3 NAD A 403 " pdb=" PA NAD A 403 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 7.00e+00 bond pdb=" O3 NAD B 403 " pdb=" PA NAD B 403 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" C5B NAD B 403 " pdb=" O5B NAD B 403 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 3.98e+00 ... (remaining 10407 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.02: 273 106.02 - 113.02: 5724 113.02 - 120.02: 3520 120.02 - 127.02: 4555 127.02 - 134.02: 152 Bond angle restraints: 14224 Sorted by residual: angle pdb=" CA TYR C 258 " pdb=" CB TYR C 258 " pdb=" CG TYR C 258 " ideal model delta sigma weight residual 113.90 117.84 -3.94 1.80e+00 3.09e-01 4.80e+00 angle pdb=" CA TYR D 258 " pdb=" CB TYR D 258 " pdb=" CG TYR D 258 " ideal model delta sigma weight residual 113.90 117.84 -3.94 1.80e+00 3.09e-01 4.80e+00 angle pdb=" CA TYR A 258 " pdb=" CB TYR A 258 " pdb=" CG TYR A 258 " ideal model delta sigma weight residual 113.90 117.84 -3.94 1.80e+00 3.09e-01 4.80e+00 angle pdb=" CA TYR B 258 " pdb=" CB TYR B 258 " pdb=" CG TYR B 258 " ideal model delta sigma weight residual 113.90 117.84 -3.94 1.80e+00 3.09e-01 4.79e+00 angle pdb=" C2D NAD C 403 " pdb=" C1D NAD C 403 " pdb=" O4D NAD C 403 " ideal model delta sigma weight residual 105.82 99.83 5.99 3.00e+00 1.11e-01 3.99e+00 ... (remaining 14219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 5324 14.13 - 28.25: 560 28.25 - 42.38: 158 42.38 - 56.50: 40 56.50 - 70.63: 32 Dihedral angle restraints: 6114 sinusoidal: 2250 harmonic: 3864 Sorted by residual: dihedral pdb=" CB CYS B 277 " pdb=" SG CYS B 277 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual 93.00 123.35 -30.35 1 1.00e+01 1.00e-02 1.32e+01 dihedral pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " pdb=" SG CYS D 277 " pdb=" CB CYS D 277 " ideal model delta sinusoidal sigma weight residual 93.00 123.30 -30.30 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CA VAL C 197 " pdb=" C VAL C 197 " pdb=" N LEU C 198 " pdb=" CA LEU C 198 " ideal model delta harmonic sigma weight residual 180.00 162.77 17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 6111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 990 0.039 - 0.078: 458 0.078 - 0.116: 147 0.116 - 0.155: 21 0.155 - 0.194: 8 Chirality restraints: 1624 Sorted by residual: chirality pdb=" C1D NAD B 403 " pdb=" C2D NAD B 403 " pdb=" N1N NAD B 403 " pdb=" O4D NAD B 403 " both_signs ideal model delta sigma weight residual False 2.41 2.61 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" C1D NAD C 403 " pdb=" C2D NAD C 403 " pdb=" N1N NAD C 403 " pdb=" O4D NAD C 403 " both_signs ideal model delta sigma weight residual False 2.41 2.61 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" C1D NAD D 403 " pdb=" C2D NAD D 403 " pdb=" N1N NAD D 403 " pdb=" O4D NAD D 403 " both_signs ideal model delta sigma weight residual False 2.41 2.61 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 1621 not shown) Planarity restraints: 1820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD C 403 " 0.066 2.00e-02 2.50e+03 4.42e-02 3.91e+01 pdb=" C2N NAD C 403 " -0.089 2.00e-02 2.50e+03 pdb=" C3N NAD C 403 " -0.012 2.00e-02 2.50e+03 pdb=" C4N NAD C 403 " 0.020 2.00e-02 2.50e+03 pdb=" C5N NAD C 403 " 0.013 2.00e-02 2.50e+03 pdb=" C6N NAD C 403 " -0.021 2.00e-02 2.50e+03 pdb=" C7N NAD C 403 " 0.042 2.00e-02 2.50e+03 pdb=" N1N NAD C 403 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD A 403 " -0.066 2.00e-02 2.50e+03 4.42e-02 3.91e+01 pdb=" C2N NAD A 403 " 0.089 2.00e-02 2.50e+03 pdb=" C3N NAD A 403 " 0.011 2.00e-02 2.50e+03 pdb=" C4N NAD A 403 " -0.020 2.00e-02 2.50e+03 pdb=" C5N NAD A 403 " -0.013 2.00e-02 2.50e+03 pdb=" C6N NAD A 403 " 0.022 2.00e-02 2.50e+03 pdb=" C7N NAD A 403 " -0.042 2.00e-02 2.50e+03 pdb=" N1N NAD A 403 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 403 " 0.066 2.00e-02 2.50e+03 4.41e-02 3.90e+01 pdb=" C2N NAD D 403 " -0.089 2.00e-02 2.50e+03 pdb=" C3N NAD D 403 " -0.011 2.00e-02 2.50e+03 pdb=" C4N NAD D 403 " 0.020 2.00e-02 2.50e+03 pdb=" C5N NAD D 403 " 0.013 2.00e-02 2.50e+03 pdb=" C6N NAD D 403 " -0.021 2.00e-02 2.50e+03 pdb=" C7N NAD D 403 " 0.042 2.00e-02 2.50e+03 pdb=" N1N NAD D 403 " -0.020 2.00e-02 2.50e+03 ... (remaining 1817 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1657 2.75 - 3.29: 10048 3.29 - 3.83: 17624 3.83 - 4.36: 22082 4.36 - 4.90: 37910 Nonbonded interactions: 89321 Sorted by model distance: nonbonded pdb=" OD2 ASP B 201 " pdb=" O3B NAD B 403 " model vdw 2.216 2.440 nonbonded pdb=" OD2 ASP C 201 " pdb=" O3B NAD C 403 " model vdw 2.216 2.440 nonbonded pdb=" OD2 ASP A 201 " pdb=" O3B NAD A 403 " model vdw 2.216 2.440 nonbonded pdb=" OD2 ASP D 201 " pdb=" O3B NAD D 403 " model vdw 2.216 2.440 nonbonded pdb=" O VAL C 231 " pdb=" OG1 THR C 235 " model vdw 2.221 2.440 ... (remaining 89316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.780 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 32.810 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 : 0.008 0.054 10412 Z= 0.508 Angle : 0.704 6.704 14224 Z= 0.364 Chirality : 0.049 0.194 1624 Planarity : 0.005 0.044 1820 Dihedral : 14.263 70.629 3684 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.73 (0.21), residues: 1380 helix: -1.61 (0.22), residues: 464 sheet: -2.56 (0.35), residues: 220 loop : -1.60 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 92 HIS 0.006 0.001 HIS B 48 PHE 0.014 0.001 PHE C 221 TYR 0.027 0.002 TYR D 294 ARG 0.002 0.000 ARG D 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.100 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 1.0392 time to fit residues: 104.7868 Evaluate side-chains 73 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN B 51 HIS B 107 ASN C 51 HIS C 107 ASN D 107 ASN D 171 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 10412 Z= 0.346 Angle : 0.526 5.866 14224 Z= 0.269 Chirality : 0.046 0.144 1624 Planarity : 0.004 0.034 1820 Dihedral : 8.694 55.749 1696 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.40 % Allowed : 11.19 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.54 (0.21), residues: 1380 helix: -1.29 (0.22), residues: 460 sheet: -2.37 (0.30), residues: 252 loop : -1.57 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 92 HIS 0.004 0.001 HIS A 48 PHE 0.012 0.001 PHE C 221 TYR 0.018 0.001 TYR D 258 ARG 0.001 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.018 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 102 average time/residue: 0.8535 time to fit residues: 96.9747 Evaluate side-chains 75 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 58 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 0.0970 chunk 133 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 0.0050 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 262 ASN B 171 HIS B 262 ASN C 262 ASN D 262 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10412 Z= 0.163 Angle : 0.454 4.929 14224 Z= 0.231 Chirality : 0.043 0.136 1624 Planarity : 0.003 0.028 1820 Dihedral : 8.201 56.817 1696 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.60 % Allowed : 15.12 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.02 (0.21), residues: 1380 helix: -0.71 (0.24), residues: 432 sheet: -2.35 (0.33), residues: 208 loop : -1.36 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 50 HIS 0.002 0.000 HIS D 48 PHE 0.011 0.001 PHE B 221 TYR 0.014 0.001 TYR B 258 ARG 0.001 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.987 Fit side-chains REVERT: A 83 LYS cc_start: 0.7527 (mtmm) cc_final: 0.7288 (mttm) REVERT: B 83 LYS cc_start: 0.7532 (mtmm) cc_final: 0.7293 (mttm) REVERT: C 83 LYS cc_start: 0.7518 (mtmm) cc_final: 0.7275 (mttm) REVERT: D 83 LYS cc_start: 0.7525 (mtmm) cc_final: 0.7284 (mttm) outliers start: 6 outliers final: 0 residues processed: 86 average time/residue: 0.9613 time to fit residues: 91.4291 Evaluate side-chains 66 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS C 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10412 Z= 0.320 Angle : 0.487 4.814 14224 Z= 0.250 Chirality : 0.045 0.142 1624 Planarity : 0.003 0.027 1820 Dihedral : 8.571 55.321 1696 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.21 % Allowed : 17.24 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.01 (0.22), residues: 1380 helix: -0.78 (0.24), residues: 432 sheet: -2.12 (0.30), residues: 256 loop : -1.27 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 50 HIS 0.004 0.001 HIS A 48 PHE 0.010 0.001 PHE B 221 TYR 0.019 0.001 TYR C 258 ARG 0.001 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.979 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 90 average time/residue: 1.0532 time to fit residues: 103.8628 Evaluate side-chains 82 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 313 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 chunk 90 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10412 Z= 0.255 Angle : 0.462 4.833 14224 Z= 0.238 Chirality : 0.044 0.139 1624 Planarity : 0.003 0.026 1820 Dihedral : 8.474 55.894 1696 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.41 % Allowed : 18.15 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.22), residues: 1380 helix: -0.67 (0.24), residues: 432 sheet: -2.05 (0.31), residues: 256 loop : -1.20 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 50 HIS 0.003 0.001 HIS D 48 PHE 0.010 0.001 PHE D 221 TYR 0.016 0.001 TYR C 258 ARG 0.001 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 1.102 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 96 average time/residue: 0.9782 time to fit residues: 103.4719 Evaluate side-chains 81 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 313 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10412 Z= 0.363 Angle : 0.520 4.904 14224 Z= 0.262 Chirality : 0.046 0.138 1624 Planarity : 0.003 0.027 1820 Dihedral : 8.647 55.257 1696 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.61 % Allowed : 19.96 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.00 (0.22), residues: 1380 helix: -0.88 (0.23), residues: 432 sheet: -2.05 (0.31), residues: 256 loop : -1.22 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 50 HIS 0.004 0.001 HIS A 48 PHE 0.010 0.001 PHE A 221 TYR 0.019 0.001 TYR D 258 ARG 0.001 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 1.015 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 96 average time/residue: 1.1107 time to fit residues: 116.5478 Evaluate side-chains 86 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 313 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10412 Z= 0.201 Angle : 0.463 4.914 14224 Z= 0.233 Chirality : 0.043 0.137 1624 Planarity : 0.003 0.026 1820 Dihedral : 8.309 56.753 1696 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.91 % Allowed : 22.08 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.22), residues: 1380 helix: -0.65 (0.24), residues: 432 sheet: -1.93 (0.31), residues: 256 loop : -1.17 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 50 HIS 0.003 0.000 HIS A 48 PHE 0.011 0.001 PHE B 221 TYR 0.014 0.001 TYR C 258 ARG 0.001 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 1.121 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 1.1380 time to fit residues: 102.9315 Evaluate side-chains 76 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 0.0970 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 103 optimal weight: 0.0770 chunk 119 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 overall best weight: 0.9538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10412 Z= 0.172 Angle : 0.451 5.942 14224 Z= 0.225 Chirality : 0.043 0.132 1624 Planarity : 0.003 0.026 1820 Dihedral : 8.143 57.312 1696 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.60 % Allowed : 21.98 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.22), residues: 1380 helix: -0.51 (0.24), residues: 432 sheet: -1.92 (0.31), residues: 260 loop : -1.06 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 50 HIS 0.003 0.000 HIS B 48 PHE 0.011 0.001 PHE B 221 TYR 0.013 0.001 TYR C 258 ARG 0.001 0.000 ARG D 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 1.035 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 92 average time/residue: 0.9914 time to fit residues: 100.4605 Evaluate side-chains 76 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 6.9990 chunk 125 optimal weight: 0.0060 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 overall best weight: 1.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10412 Z= 0.285 Angle : 0.489 5.511 14224 Z= 0.246 Chirality : 0.045 0.139 1624 Planarity : 0.003 0.026 1820 Dihedral : 8.440 56.552 1696 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.11 % Allowed : 21.88 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.22), residues: 1380 helix: -0.59 (0.24), residues: 444 sheet: -1.95 (0.29), residues: 288 loop : -1.04 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 50 HIS 0.003 0.001 HIS D 48 PHE 0.010 0.001 PHE A 221 TYR 0.017 0.001 TYR B 258 ARG 0.001 0.000 ARG C 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 1.001 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 83 average time/residue: 1.0065 time to fit residues: 91.9684 Evaluate side-chains 79 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 83 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10412 Z= 0.313 Angle : 0.500 5.324 14224 Z= 0.251 Chirality : 0.045 0.136 1624 Planarity : 0.003 0.027 1820 Dihedral : 8.562 56.449 1696 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.41 % Allowed : 21.27 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.22), residues: 1380 helix: -0.75 (0.23), residues: 432 sheet: -1.92 (0.32), residues: 248 loop : -1.06 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 50 HIS 0.004 0.001 HIS B 48 PHE 0.010 0.001 PHE B 221 TYR 0.018 0.001 TYR A 258 ARG 0.001 0.000 ARG B 257 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 1.172 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 1.0484 time to fit residues: 101.3744 Evaluate side-chains 86 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 313 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.152138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.110716 restraints weight = 10519.645| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.44 r_work: 0.3507 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10412 Z= 0.285 Angle : 0.489 6.193 14224 Z= 0.246 Chirality : 0.045 0.137 1624 Planarity : 0.003 0.026 1820 Dihedral : 8.507 56.414 1696 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.41 % Allowed : 21.77 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.22), residues: 1380 helix: -0.72 (0.23), residues: 432 sheet: -1.93 (0.29), residues: 288 loop : -1.07 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 50 HIS 0.003 0.001 HIS D 48 PHE 0.010 0.001 PHE D 221 TYR 0.017 0.001 TYR C 258 ARG 0.001 0.000 ARG C 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2836.34 seconds wall clock time: 51 minutes 50.52 seconds (3110.52 seconds total)