Starting phenix.real_space_refine on Wed Feb 14 21:54:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ntm_12591/02_2024/7ntm_12591.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ntm_12591/02_2024/7ntm_12591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ntm_12591/02_2024/7ntm_12591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ntm_12591/02_2024/7ntm_12591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ntm_12591/02_2024/7ntm_12591.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ntm_12591/02_2024/7ntm_12591.pdb" } resolution = 2.86 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 56 5.16 5 C 6556 2.51 5 N 1760 2.21 5 O 1956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 19": "OE1" <-> "OE2" Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A ASP 300": "OD1" <-> "OD2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 144": "OD1" <-> "OD2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 327": "OE1" <-> "OE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 300": "OD1" <-> "OD2" Residue "C PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 10336 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2582 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "B" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2582 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "D" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2582 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "C" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2582 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 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: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 340 SG CYS A 43 38.557 22.324 26.956 1.00 61.37 S ATOM 1159 SG CYS A 153 39.151 27.004 28.663 1.00 52.86 S ATOM 766 SG CYS A 100 35.384 34.553 48.913 1.00 63.83 S ATOM 793 SG CYS A 103 35.197 35.182 45.606 1.00 58.40 S ATOM 851 SG CYS A 111 33.407 32.254 46.328 1.00 56.85 S ATOM 2922 SG CYS B 43 75.521 22.601 58.159 1.00 59.45 S ATOM 3741 SG CYS B 153 75.027 26.886 56.389 1.00 52.44 S ATOM 3348 SG CYS B 100 78.374 35.166 36.250 1.00 64.62 S ATOM 3375 SG CYS B 103 79.375 34.932 39.507 1.00 56.68 S ATOM 3433 SG CYS B 111 80.669 32.247 38.640 1.00 56.55 S ATOM 5504 SG CYS D 43 75.607 62.548 27.015 1.00 59.46 S ATOM 6323 SG CYS D 153 75.027 58.119 28.612 1.00 51.08 S ATOM 5911 SG CYS D 97 81.654 50.042 47.764 1.00 61.19 S ATOM 5930 SG CYS D 100 78.101 50.395 48.840 1.00 65.41 S ATOM 5957 SG CYS D 103 79.309 49.924 45.663 1.00 57.83 S ATOM 6015 SG CYS D 111 80.737 52.740 46.512 1.00 55.09 S ATOM 8086 SG CYS C 43 38.698 62.436 58.188 1.00 59.60 S ATOM 8905 SG CYS C 153 39.118 58.117 56.393 1.00 51.26 S ATOM 8512 SG CYS C 100 35.947 50.617 36.389 1.00 74.89 S ATOM 8539 SG CYS C 103 34.816 49.669 39.226 1.00 55.83 S ATOM 8597 SG CYS C 111 33.383 52.792 38.450 1.00 55.10 S Time building chain proxies: 5.82, per 1000 atoms: 0.56 Number of scatterers: 10336 At special positions: 0 Unit cell: (114.761, 85.6152, 85.6152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 56 16.00 O 1956 8.00 N 1760 7.00 C 6556 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 B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS D 277 " - pdb=" SG CYS C 277 " distance=2.59 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: 3.87 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 153 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 66 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 111 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 100 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 103 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 66 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 153 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 43 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 103 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 100 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 111 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 66 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 153 " pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 103 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 100 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 111 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" NE2 HIS D 66 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 153 " pdb=" ZN D 402 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 97 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 103 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 111 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 100 " Number of angles added : 6 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... Secondary structure from input PDB file: 47 helices and 15 sheets defined 33.1% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.993A pdb=" N LEU A 47 " --> pdb=" O CYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 180 through 193 removed outlier: 3.970A pdb=" N LEU A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.580A pdb=" N ALA A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 279 through 287 removed outlier: 3.700A pdb=" N GLN A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.613A pdb=" N CYS B 111 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 152 Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.913A pdb=" N LEU B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 226 through 235 removed outlier: 3.600A pdb=" N ALA B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.852A pdb=" N GLN B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 324 through 335 removed outlier: 4.090A pdb=" N GLU B 330 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 52 Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.553A pdb=" N CYS D 111 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 152 Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 180 through 193 removed outlier: 4.061A pdb=" N LEU D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 226 through 235 removed outlier: 3.549A pdb=" N ALA D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 279 through 287 removed outlier: 3.699A pdb=" N GLN D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 311 Processing helix chain 'D' and resid 324 through 335 removed outlier: 4.102A pdb=" N GLU D 330 " --> pdb=" O PRO D 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 removed outlier: 4.126A pdb=" N LEU C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.721A pdb=" N LEU C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.828A pdb=" N CYS C 111 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 152 Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 180 through 193 removed outlier: 4.044A pdb=" N LEU C 185 " --> pdb=" O GLY C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.636A pdb=" N ALA C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 258 removed outlier: 3.570A pdb=" N ILE C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 287 removed outlier: 3.828A pdb=" N GLN C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 311 Processing helix chain 'C' and resid 324 through 335 removed outlier: 4.081A pdb=" N GLU C 330 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 24 removed outlier: 3.637A pdb=" N LEU A 62 " --> pdb=" O PHE A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 132 removed outlier: 6.542A pdb=" N LEU A 33 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N MET A 75 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE A 35 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL A 73 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL A 37 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 71 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU A 67 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR A 87 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 132 removed outlier: 5.921A pdb=" N LYS A 318 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP A 344 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 320 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 220 removed outlier: 6.814A pdb=" N VAL A 197 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE A 219 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY A 199 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP A 172 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS A 240 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL A 266 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 242 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS B 240 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL B 266 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 242 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP B 172 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 197 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N ILE B 219 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY B 199 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 24 removed outlier: 3.525A pdb=" N LYS B 21 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 8 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 11 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 62 " --> pdb=" O PHE B 11 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.381A pdb=" N ASN B 36 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 72 " --> pdb=" O ASN B 36 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LYS B 38 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLY B 70 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER B 40 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY B 68 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR B 87 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 132 removed outlier: 4.774A pdb=" N TYR B 341 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LYS B 318 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP B 344 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 320 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 96 removed outlier: 5.445A pdb=" N ASP B 115 " --> pdb=" O ASN B 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.506A pdb=" N LYS D 21 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 8 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 62 " --> pdb=" O PHE D 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.428A pdb=" N ASN D 36 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL D 72 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS D 38 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLY D 70 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER D 40 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY D 68 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR D 87 " --> pdb=" O ILE D 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 128 through 132 removed outlier: 4.791A pdb=" N TYR D 341 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL D 320 " --> pdb=" O ASP D 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 217 through 219 removed outlier: 6.794A pdb=" N VAL D 197 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE D 219 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY D 199 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP D 172 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N HIS D 240 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N HIS C 240 " --> pdb=" O ASN C 262 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP C 172 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL C 197 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ILE C 219 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY C 199 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 10 removed outlier: 3.530A pdb=" N GLY C 8 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 21 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 132 removed outlier: 6.440A pdb=" N ASN C 36 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C 72 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS C 38 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLY C 70 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER C 40 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY C 68 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR C 87 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 128 through 132 removed outlier: 4.817A pdb=" N TYR C 341 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS C 318 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP C 344 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 320 " --> pdb=" O ASP C 344 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1191 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: 2.99 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1984 1.33 - 1.45: 2457 1.45 - 1.57: 6023 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 10544 Sorted by residual: bond pdb=" C TYR C 102 " pdb=" N CYS C 103 " ideal model delta sigma weight residual 1.334 1.552 -0.218 1.41e-02 5.03e+03 2.40e+02 bond pdb=" C CYS C 103 " pdb=" N GLU C 104 " ideal model delta sigma weight residual 1.335 1.507 -0.172 1.35e-02 5.49e+03 1.62e+02 bond pdb=" C ALA C 99 " pdb=" N CYS C 100 " ideal model delta sigma weight residual 1.328 1.250 0.078 8.50e-03 1.38e+04 8.41e+01 bond pdb=" C MET C 98 " pdb=" N ALA C 99 " ideal model delta sigma weight residual 1.336 1.482 -0.146 1.68e-02 3.54e+03 7.56e+01 bond pdb=" C CYS D 97 " pdb=" N MET D 98 " ideal model delta sigma weight residual 1.333 1.229 0.104 1.39e-02 5.18e+03 5.55e+01 ... (remaining 10539 not shown) Histogram of bond angle deviations from ideal: 94.95 - 105.27: 250 105.27 - 115.58: 6449 115.58 - 125.89: 7466 125.89 - 136.21: 125 136.21 - 146.52: 2 Bond angle restraints: 14292 Sorted by residual: angle pdb=" O CYS D 97 " pdb=" C CYS D 97 " pdb=" N MET D 98 " ideal model delta sigma weight residual 122.36 146.52 -24.16 1.42e+00 4.96e-01 2.89e+02 angle pdb=" CA CYS D 97 " pdb=" C CYS D 97 " pdb=" N MET D 98 " ideal model delta sigma weight residual 118.14 94.95 23.19 1.56e+00 4.11e-01 2.21e+02 angle pdb=" C CYS D 97 " pdb=" N MET D 98 " pdb=" CA MET D 98 " ideal model delta sigma weight residual 122.40 101.89 20.51 1.45e+00 4.76e-01 2.00e+02 angle pdb=" C TYR C 102 " pdb=" CA TYR C 102 " pdb=" CB TYR C 102 " ideal model delta sigma weight residual 110.85 132.40 -21.55 1.70e+00 3.46e-01 1.61e+02 angle pdb=" O MET C 98 " pdb=" C MET C 98 " pdb=" N ALA C 99 " ideal model delta sigma weight residual 122.59 139.43 -16.84 1.33e+00 5.65e-01 1.60e+02 ... (remaining 14287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 5310 16.02 - 32.03: 594 32.03 - 48.05: 227 48.05 - 64.06: 45 64.06 - 80.08: 6 Dihedral angle restraints: 6182 sinusoidal: 2318 harmonic: 3864 Sorted by residual: dihedral pdb=" C TYR C 102 " pdb=" N TYR C 102 " pdb=" CA TYR C 102 " pdb=" CB TYR C 102 " ideal model delta harmonic sigma weight residual -122.60 -153.14 30.54 0 2.50e+00 1.60e-01 1.49e+02 dihedral pdb=" N TYR C 102 " pdb=" C TYR C 102 " pdb=" CA TYR C 102 " pdb=" CB TYR C 102 " ideal model delta harmonic sigma weight residual 122.80 145.00 -22.20 0 2.50e+00 1.60e-01 7.89e+01 dihedral pdb=" CB CYS D 277 " pdb=" SG CYS D 277 " pdb=" SG CYS C 277 " pdb=" CB CYS C 277 " ideal model delta sinusoidal sigma weight residual -86.00 -35.08 -50.92 1 1.00e+01 1.00e-02 3.55e+01 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 1574 0.223 - 0.446: 15 0.446 - 0.670: 2 0.670 - 0.893: 0 0.893 - 1.116: 1 Chirality restraints: 1592 Sorted by residual: chirality pdb=" CA TYR C 102 " pdb=" N TYR C 102 " pdb=" C TYR C 102 " pdb=" CB TYR C 102 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.11e+01 chirality pdb=" CA ALA D 99 " pdb=" N ALA D 99 " pdb=" C ALA D 99 " pdb=" CB ALA D 99 " both_signs ideal model delta sigma weight residual False 2.48 3.06 -0.58 2.00e-01 2.50e+01 8.27e+00 chirality pdb=" CA ALA C 99 " pdb=" N ALA C 99 " pdb=" C ALA C 99 " pdb=" CB ALA C 99 " both_signs ideal model delta sigma weight residual False 2.48 1.99 0.50 2.00e-01 2.50e+01 6.20e+00 ... (remaining 1589 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 99 " -0.036 2.00e-02 2.50e+03 6.88e-02 4.73e+01 pdb=" C ALA C 99 " 0.119 2.00e-02 2.50e+03 pdb=" O ALA C 99 " -0.040 2.00e-02 2.50e+03 pdb=" N CYS C 100 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 210 " -0.021 2.00e-02 2.50e+03 4.31e-02 1.85e+01 pdb=" C PHE D 210 " 0.074 2.00e-02 2.50e+03 pdb=" O PHE D 210 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG D 211 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 98 " -0.015 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C MET C 98 " 0.065 2.00e-02 2.50e+03 pdb=" O MET C 98 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA C 99 " -0.021 2.00e-02 2.50e+03 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 57 2.55 - 3.14: 7304 3.14 - 3.72: 15370 3.72 - 4.31: 23133 4.31 - 4.90: 37616 Nonbonded interactions: 83480 Sorted by model distance: nonbonded pdb=" OE1 GLU D 108 " pdb=" NE2 GLN D 135 " model vdw 1.962 2.520 nonbonded pdb=" OE1 GLU B 108 " pdb=" NE2 GLN B 135 " model vdw 1.974 2.520 nonbonded pdb=" O LEU B 232 " pdb=" O ASP B 236 " model vdw 1.986 3.040 nonbonded pdb=" O SER C 176 " pdb=" CG2 VAL C 245 " model vdw 2.033 3.460 nonbonded pdb=" O SER D 176 " pdb=" CG2 VAL D 245 " model vdw 2.039 3.460 ... (remaining 83475 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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 15.540 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.960 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9375 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 : 0.013 0.218 10544 Z= 0.856 Angle : 1.609 24.160 14292 Z= 1.209 Chirality : 0.105 1.116 1592 Planarity : 0.003 0.069 1844 Dihedral : 15.613 80.079 3752 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.77 % Allowed : 16.14 % Favored : 82.09 % Cbeta Deviations : 0.58 % 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: -3.56 (0.17), residues: 1380 helix: -2.61 (0.17), residues: 464 sheet: -1.10 (0.28), residues: 268 loop : -2.69 (0.18), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 172 HIS 0.003 0.001 HIS D 66 PHE 0.010 0.001 PHE D 11 TYR 0.009 0.001 TYR A 329 ARG 0.001 0.000 ARG A 340 *********************** 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 59 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 40 time to evaluate : 1.247 Fit side-chains REVERT: B 27 LYS cc_start: 0.9596 (OUTLIER) cc_final: 0.9024 (mttt) outliers start: 19 outliers final: 5 residues processed: 58 average time/residue: 1.5011 time to fit residues: 94.0077 Evaluate side-chains 32 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain C residue 182 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN A 166 ASN A 244 ASN B 126 GLN D 126 GLN D 138 HIS C 138 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9404 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10544 Z= 0.151 Angle : 0.482 6.908 14292 Z= 0.261 Chirality : 0.044 0.131 1592 Planarity : 0.003 0.038 1844 Dihedral : 5.671 62.167 1491 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.24 % Allowed : 16.70 % Favored : 81.06 % 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: -1.72 (0.20), residues: 1380 helix: -0.60 (0.24), residues: 464 sheet: -0.13 (0.31), residues: 260 loop : -1.96 (0.19), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 92 HIS 0.003 0.001 HIS D 66 PHE 0.014 0.002 PHE D 11 TYR 0.033 0.001 TYR A 258 ARG 0.003 0.000 ARG A 211 *********************** 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 49 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 25 time to evaluate : 1.210 Fit side-chains REVERT: B 182 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8529 (mp) REVERT: C 182 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8675 (mp) outliers start: 24 outliers final: 6 residues processed: 49 average time/residue: 1.0863 time to fit residues: 59.0796 Evaluate side-chains 33 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 213 ILE 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: 3.9990 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 107 ASN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN C 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9479 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10544 Z= 0.213 Angle : 0.475 5.208 14292 Z= 0.255 Chirality : 0.044 0.137 1592 Planarity : 0.003 0.041 1844 Dihedral : 4.955 54.806 1485 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.49 % Allowed : 16.51 % Favored : 82.00 % 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: -0.86 (0.21), residues: 1380 helix: 0.20 (0.25), residues: 440 sheet: 0.11 (0.30), residues: 292 loop : -1.41 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 92 HIS 0.003 0.001 HIS B 138 PHE 0.015 0.002 PHE D 11 TYR 0.023 0.001 TYR A 258 ARG 0.003 0.000 ARG A 211 *********************** 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 41 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 25 time to evaluate : 1.083 Fit side-chains outliers start: 16 outliers final: 3 residues processed: 41 average time/residue: 1.1159 time to fit residues: 50.8402 Evaluate side-chains 28 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.9468 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10544 Z= 0.171 Angle : 0.443 5.208 14292 Z= 0.236 Chirality : 0.043 0.133 1592 Planarity : 0.003 0.042 1844 Dihedral : 4.209 49.467 1476 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.84 % Allowed : 17.16 % Favored : 82.00 % 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: -0.41 (0.22), residues: 1380 helix: 0.57 (0.25), residues: 440 sheet: 0.28 (0.30), residues: 292 loop : -1.10 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 92 HIS 0.003 0.001 HIS B 138 PHE 0.014 0.001 PHE D 11 TYR 0.020 0.001 TYR A 258 ARG 0.002 0.000 ARG A 211 *********************** 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 34 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 1.097 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 34 average time/residue: 1.1636 time to fit residues: 44.0925 Evaluate side-chains 28 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain D residue 96 SER 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: 4.9990 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 0.0870 chunk 117 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9491 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10544 Z= 0.234 Angle : 0.464 5.259 14292 Z= 0.247 Chirality : 0.044 0.137 1592 Planarity : 0.003 0.041 1844 Dihedral : 4.261 46.630 1476 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.49 % Allowed : 17.16 % Favored : 81.34 % 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: -0.38 (0.22), residues: 1380 helix: 0.42 (0.25), residues: 464 sheet: 0.34 (0.30), residues: 292 loop : -1.00 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 92 HIS 0.003 0.001 HIS B 138 PHE 0.014 0.002 PHE D 11 TYR 0.017 0.001 TYR A 258 ARG 0.001 0.000 ARG A 211 *********************** 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 41 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 25 time to evaluate : 1.223 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 41 average time/residue: 1.0389 time to fit residues: 47.7921 Evaluate side-chains 32 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9486 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10544 Z= 0.204 Angle : 0.452 5.203 14292 Z= 0.240 Chirality : 0.044 0.134 1592 Planarity : 0.003 0.040 1844 Dihedral : 4.198 43.756 1476 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.12 % Allowed : 17.35 % Favored : 81.53 % 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: -0.24 (0.22), residues: 1380 helix: 0.54 (0.25), residues: 464 sheet: 0.37 (0.30), residues: 292 loop : -0.89 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 92 HIS 0.003 0.001 HIS B 138 PHE 0.014 0.002 PHE D 11 TYR 0.017 0.001 TYR A 258 ARG 0.001 0.000 ARG C 340 *********************** 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 37 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 25 time to evaluate : 1.177 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 37 average time/residue: 1.1856 time to fit residues: 48.8699 Evaluate side-chains 31 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 110 optimal weight: 0.0770 chunk 73 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 overall best weight: 3.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9512 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10544 Z= 0.323 Angle : 0.497 5.301 14292 Z= 0.264 Chirality : 0.046 0.137 1592 Planarity : 0.003 0.040 1844 Dihedral : 4.414 44.685 1476 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.03 % Allowed : 18.00 % Favored : 80.97 % 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: -0.36 (0.22), residues: 1380 helix: 0.40 (0.25), residues: 464 sheet: 0.40 (0.30), residues: 292 loop : -0.99 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 92 HIS 0.003 0.001 HIS B 138 PHE 0.016 0.002 PHE C 221 TYR 0.014 0.001 TYR A 258 ARG 0.001 0.000 ARG C 340 *********************** 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 35 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 24 time to evaluate : 1.202 Fit side-chains REVERT: D 317 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8833 (pp) outliers start: 11 outliers final: 7 residues processed: 35 average time/residue: 1.2303 time to fit residues: 47.7960 Evaluate side-chains 32 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 24 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9491 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10544 Z= 0.205 Angle : 0.454 5.180 14292 Z= 0.242 Chirality : 0.044 0.135 1592 Planarity : 0.003 0.040 1844 Dihedral : 4.257 42.671 1476 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.03 % Allowed : 18.00 % Favored : 80.97 % 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: -0.20 (0.22), residues: 1380 helix: 0.55 (0.25), residues: 464 sheet: 0.43 (0.30), residues: 292 loop : -0.89 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 92 HIS 0.003 0.001 HIS B 138 PHE 0.014 0.002 PHE D 11 TYR 0.016 0.001 TYR A 258 ARG 0.001 0.000 ARG C 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 36 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 25 time to evaluate : 1.262 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 36 average time/residue: 1.2015 time to fit residues: 48.3152 Evaluate side-chains 31 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain C residue 213 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 73 optimal weight: 0.0010 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.3792 ------------------------------------------------------------------------------- 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: 0.9471 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10544 Z= 0.161 Angle : 0.431 5.134 14292 Z= 0.229 Chirality : 0.043 0.135 1592 Planarity : 0.003 0.040 1844 Dihedral : 4.057 38.477 1476 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.56 % Allowed : 18.38 % Favored : 81.06 % 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: -0.05 (0.22), residues: 1380 helix: 0.70 (0.25), residues: 464 sheet: 0.42 (0.30), residues: 292 loop : -0.76 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 92 HIS 0.003 0.000 HIS B 138 PHE 0.013 0.001 PHE A 11 TYR 0.017 0.001 TYR A 258 ARG 0.001 0.000 ARG C 340 *********************** 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 31 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 1.150 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 31 average time/residue: 1.2772 time to fit residues: 43.9512 Evaluate side-chains 30 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 SER Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain D residue 1 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 124 optimal weight: 0.2980 chunk 107 optimal weight: 8.9990 chunk 11 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 114 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.9443 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10544 Z= 0.123 Angle : 0.410 5.072 14292 Z= 0.217 Chirality : 0.043 0.135 1592 Planarity : 0.003 0.040 1844 Dihedral : 3.804 32.398 1476 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.47 % Allowed : 18.47 % Favored : 81.06 % 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: 0.13 (0.22), residues: 1380 helix: 0.88 (0.25), residues: 464 sheet: 0.44 (0.30), residues: 292 loop : -0.62 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 92 HIS 0.002 0.000 HIS B 138 PHE 0.012 0.001 PHE A 11 TYR 0.017 0.001 TYR A 258 ARG 0.001 0.000 ARG C 340 ********************** 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 32 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 1.205 Fit side-chains REVERT: D 247 VAL cc_start: 0.9042 (t) cc_final: 0.8740 (m) REVERT: C 247 VAL cc_start: 0.8904 (t) cc_final: 0.8597 (m) outliers start: 5 outliers final: 5 residues processed: 32 average time/residue: 1.3283 time to fit residues: 47.0534 Evaluate side-chains 32 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain D residue 1 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.1933 r_free = 0.1933 target = 0.023336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.1763 r_free = 0.1763 target = 0.019901 restraints weight = 29829.743| |-----------------------------------------------------------------------------| r_work (start): 0.1761 rms_B_bonded: 0.92 r_work: 0.1701 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.1626 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.1626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9508 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10544 Z= 0.239 Angle : 0.465 5.246 14292 Z= 0.247 Chirality : 0.045 0.139 1592 Planarity : 0.003 0.040 1844 Dihedral : 4.121 35.789 1476 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.84 % Allowed : 18.38 % Favored : 80.78 % 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: -0.02 (0.22), residues: 1380 helix: 0.70 (0.25), residues: 464 sheet: 0.44 (0.30), residues: 292 loop : -0.72 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 92 HIS 0.003 0.001 HIS B 138 PHE 0.014 0.002 PHE D 11 TYR 0.015 0.001 TYR A 258 ARG 0.001 0.000 ARG C 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2273.47 seconds wall clock time: 42 minutes 18.52 seconds (2538.52 seconds total)