Starting phenix.real_space_refine on Mon Mar 11 17:25:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2l_26314/03_2024/7u2l_26314_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2l_26314/03_2024/7u2l_26314.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2l_26314/03_2024/7u2l_26314_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2l_26314/03_2024/7u2l_26314_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2l_26314/03_2024/7u2l_26314_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2l_26314/03_2024/7u2l_26314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2l_26314/03_2024/7u2l_26314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2l_26314/03_2024/7u2l_26314_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2l_26314/03_2024/7u2l_26314_neut_updated.pdb" } resolution = 3.2 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= -0.001 sd= 0.978 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5566 2.51 5 N 1478 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "D PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E ASP 211": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8739 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1748 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "D" Number of atoms: 2191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2191 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 10, 'TRANS': 273} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "E" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'L0X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.12, per 1000 atoms: 0.59 Number of scatterers: 8739 At special positions: 0 Unit cell: (104.94, 120.84, 112.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1628 8.00 N 1478 7.00 C 5566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 3.52 Conformation dependent library (CDL) restraints added in 1.8 seconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 14 sheets defined 35.2% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.354A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.024A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.977A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'D' and resid 66 through 95 Processing helix chain 'D' and resid 102 through 130 removed outlier: 3.610A pdb=" N THR D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Proline residue: D 122 - end of helix Processing helix chain 'D' and resid 136 through 170 Processing helix chain 'D' and resid 172 through 178 removed outlier: 4.002A pdb=" N ASP D 177 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 205 removed outlier: 4.052A pdb=" N ILE D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 225 through 240 removed outlier: 3.527A pdb=" N ASN D 230 " --> pdb=" O TRP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 261 removed outlier: 4.220A pdb=" N SER D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 269 through 305 Proline residue: D 295 - end of helix Processing helix chain 'D' and resid 312 through 336 removed outlier: 3.595A pdb=" N ASN D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) Proline residue: D 333 - end of helix Processing helix chain 'D' and resid 341 through 346 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.544A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.905A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.988A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.817A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 202 removed outlier: 3.654A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.525A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.877A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.850A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 207 through 210 Processing sheet with id= J, first strand: chain 'E' and resid 17 through 23 Processing sheet with id= K, first strand: chain 'E' and resid 93 through 99 removed outlier: 5.790A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.514A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 143 through 147 Processing sheet with id= N, first strand: chain 'E' and resid 213 through 219 removed outlier: 6.278A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1146 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: 2.58 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1537 1.33 - 1.45: 2347 1.45 - 1.57: 4936 1.57 - 1.69: 3 1.69 - 1.81: 96 Bond restraints: 8919 Sorted by residual: bond pdb=" C19 L0X D 401 " pdb=" N18 L0X D 401 " ideal model delta sigma weight residual 1.453 1.283 0.170 2.00e-02 2.50e+03 7.20e+01 bond pdb=" C17 L0X D 401 " pdb=" N18 L0X D 401 " ideal model delta sigma weight residual 1.499 1.351 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" C27 L0X D 401 " pdb=" N18 L0X D 401 " ideal model delta sigma weight residual 1.493 1.395 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C08 L0X D 401 " pdb=" C09 L0X D 401 " ideal model delta sigma weight residual 1.530 1.596 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C19 L0X D 401 " pdb=" C20 L0X D 401 " ideal model delta sigma weight residual 1.528 1.585 -0.057 2.00e-02 2.50e+03 8.03e+00 ... (remaining 8914 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.40: 184 106.40 - 113.31: 4895 113.31 - 120.22: 3180 120.22 - 127.12: 3740 127.12 - 134.03: 92 Bond angle restraints: 12091 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.15 109.45 3.70 1.19e+00 7.06e-01 9.69e+00 angle pdb=" N ASN D 328 " pdb=" CA ASN D 328 " pdb=" C ASN D 328 " ideal model delta sigma weight residual 111.07 107.87 3.20 1.07e+00 8.73e-01 8.97e+00 angle pdb=" N THR B 87 " pdb=" CA THR B 87 " pdb=" CB THR B 87 " ideal model delta sigma weight residual 113.65 109.82 3.83 1.47e+00 4.63e-01 6.80e+00 angle pdb=" O ASN D 328 " pdb=" C ASN D 328 " pdb=" N SER D 329 " ideal model delta sigma weight residual 122.07 124.70 -2.63 1.03e+00 9.43e-01 6.51e+00 angle pdb=" CA ASN D 328 " pdb=" C ASN D 328 " pdb=" O ASN D 328 " ideal model delta sigma weight residual 120.82 118.20 2.62 1.05e+00 9.07e-01 6.23e+00 ... (remaining 12086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4779 17.99 - 35.99: 419 35.99 - 53.98: 70 53.98 - 71.97: 17 71.97 - 89.97: 7 Dihedral angle restraints: 5292 sinusoidal: 2032 harmonic: 3260 Sorted by residual: dihedral pdb=" CB CYS D 140 " pdb=" SG CYS D 140 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual -86.00 -165.22 79.22 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CA MET A 53 " pdb=" C MET A 53 " pdb=" N LYS A 54 " pdb=" CA LYS A 54 " ideal model delta harmonic sigma weight residual 180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1030 0.045 - 0.090: 274 0.090 - 0.134: 78 0.134 - 0.179: 2 0.179 - 0.224: 1 Chirality restraints: 1385 Sorted by residual: chirality pdb=" CB ILE D 308 " pdb=" CA ILE D 308 " pdb=" CG1 ILE D 308 " pdb=" CG2 ILE D 308 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA LEU D 194 " pdb=" N LEU D 194 " pdb=" C LEU D 194 " pdb=" CB LEU D 194 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA ASN D 328 " pdb=" N ASN D 328 " pdb=" C ASN D 328 " pdb=" CB ASN D 328 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 1382 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 333 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.33e+00 pdb=" CG ASP B 333 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP B 333 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP B 333 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 121 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO D 122 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 122 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 122 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 180 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C MET E 180 " -0.023 2.00e-02 2.50e+03 pdb=" O MET E 180 " 0.009 2.00e-02 2.50e+03 pdb=" N SER E 181 " 0.008 2.00e-02 2.50e+03 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 782 2.74 - 3.28: 8799 3.28 - 3.82: 14380 3.82 - 4.36: 16993 4.36 - 4.90: 30870 Nonbonded interactions: 71824 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.200 2.440 nonbonded pdb=" OG SER D 329 " pdb=" N13 L0X D 401 " model vdw 2.203 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.212 2.440 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.218 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.231 2.440 ... (remaining 71819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.540 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: 2.670 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.160 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 8919 Z= 0.335 Angle : 0.578 8.445 12091 Z= 0.327 Chirality : 0.043 0.224 1385 Planarity : 0.003 0.035 1523 Dihedral : 14.165 89.966 3179 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.29 (0.26), residues: 1106 helix: 1.71 (0.26), residues: 383 sheet: -1.42 (0.31), residues: 272 loop : -1.00 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.005 0.001 HIS E 35 PHE 0.010 0.001 PHE A 196 TYR 0.018 0.001 TYR B 59 ARG 0.008 0.000 ARG D 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: B 160 SER cc_start: 0.8994 (p) cc_final: 0.8658 (p) REVERT: C 46 LYS cc_start: 0.8487 (mppt) cc_final: 0.8272 (mmtp) REVERT: D 95 ARG cc_start: 0.5537 (mmt180) cc_final: 0.5096 (mmt180) REVERT: D 277 ARG cc_start: 0.7489 (ttp-170) cc_final: 0.6729 (tpt-90) REVERT: E 190 ARG cc_start: 0.8137 (ptt-90) cc_final: 0.7873 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2594 time to fit residues: 52.3841 Evaluate side-chains 129 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.0770 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8919 Z= 0.170 Angle : 0.500 7.064 12091 Z= 0.265 Chirality : 0.042 0.194 1385 Planarity : 0.003 0.034 1523 Dihedral : 5.685 67.579 1227 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.74 % Allowed : 7.20 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1106 helix: 1.92 (0.26), residues: 391 sheet: -1.29 (0.30), residues: 278 loop : -0.77 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.011 0.001 TYR E 178 ARG 0.003 0.000 ARG D 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 1.042 Fit side-chains REVERT: C 46 LYS cc_start: 0.8489 (mppt) cc_final: 0.8155 (mmtm) REVERT: D 194 LEU cc_start: 0.8437 (mt) cc_final: 0.8054 (mp) REVERT: D 234 ILE cc_start: 0.8917 (mm) cc_final: 0.8717 (mm) REVERT: D 263 ARG cc_start: 0.7608 (ttt180) cc_final: 0.7395 (ttm-80) REVERT: D 277 ARG cc_start: 0.7509 (ttp-170) cc_final: 0.6755 (tpt-90) outliers start: 7 outliers final: 6 residues processed: 148 average time/residue: 0.2549 time to fit residues: 49.6707 Evaluate side-chains 139 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 301 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.0970 chunk 100 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8919 Z= 0.197 Angle : 0.497 7.752 12091 Z= 0.263 Chirality : 0.042 0.184 1385 Planarity : 0.003 0.037 1523 Dihedral : 5.581 66.383 1227 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.85 % Allowed : 11.33 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1106 helix: 2.04 (0.26), residues: 391 sheet: -1.23 (0.30), residues: 275 loop : -0.77 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.011 0.001 PHE B 199 TYR 0.015 0.001 TYR A 230 ARG 0.003 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 1.024 Fit side-chains REVERT: B 217 MET cc_start: 0.7697 (ptm) cc_final: 0.7391 (ptm) REVERT: C 46 LYS cc_start: 0.8491 (mppt) cc_final: 0.8153 (mmtm) REVERT: D 194 LEU cc_start: 0.8436 (mt) cc_final: 0.8051 (mp) REVERT: D 277 ARG cc_start: 0.7522 (ttp-170) cc_final: 0.6747 (tpt-90) REVERT: E 93 MET cc_start: 0.7717 (ttp) cc_final: 0.7339 (ttp) outliers start: 8 outliers final: 4 residues processed: 148 average time/residue: 0.2566 time to fit residues: 50.0871 Evaluate side-chains 137 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 0.0470 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8919 Z= 0.206 Angle : 0.503 7.668 12091 Z= 0.266 Chirality : 0.042 0.176 1385 Planarity : 0.003 0.037 1523 Dihedral : 5.505 65.126 1227 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.17 % Allowed : 12.50 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.21 (0.26), residues: 1106 helix: 2.09 (0.26), residues: 392 sheet: -1.07 (0.30), residues: 274 loop : -0.77 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.011 0.001 PHE B 199 TYR 0.013 0.001 TYR A 230 ARG 0.002 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.060 Fit side-chains REVERT: B 217 MET cc_start: 0.7696 (ptm) cc_final: 0.7405 (ptm) REVERT: C 46 LYS cc_start: 0.8536 (mppt) cc_final: 0.8212 (mmtm) REVERT: D 194 LEU cc_start: 0.8452 (mt) cc_final: 0.8112 (mp) REVERT: D 277 ARG cc_start: 0.7524 (ttp-170) cc_final: 0.6755 (tpt-90) REVERT: E 93 MET cc_start: 0.7692 (ttp) cc_final: 0.7268 (ttp) outliers start: 11 outliers final: 7 residues processed: 147 average time/residue: 0.2759 time to fit residues: 53.2673 Evaluate side-chains 140 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 301 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8919 Z= 0.183 Angle : 0.489 7.060 12091 Z= 0.259 Chirality : 0.041 0.171 1385 Planarity : 0.003 0.039 1523 Dihedral : 5.392 63.805 1227 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.38 % Allowed : 14.09 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1106 helix: 2.29 (0.26), residues: 386 sheet: -0.92 (0.30), residues: 278 loop : -0.74 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.010 0.001 PHE B 199 TYR 0.012 0.001 TYR A 230 ARG 0.003 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 1.035 Fit side-chains REVERT: B 217 MET cc_start: 0.7653 (ptm) cc_final: 0.7357 (ptm) REVERT: C 46 LYS cc_start: 0.8531 (mppt) cc_final: 0.8199 (mmtm) REVERT: D 194 LEU cc_start: 0.8442 (mt) cc_final: 0.8088 (mp) REVERT: D 277 ARG cc_start: 0.7515 (ttp-170) cc_final: 0.6752 (tpt-90) REVERT: E 93 MET cc_start: 0.7686 (ttp) cc_final: 0.7285 (ttp) REVERT: E 190 ARG cc_start: 0.8099 (ptt-90) cc_final: 0.7816 (ptt-90) REVERT: E 211 ASP cc_start: 0.7378 (m-30) cc_final: 0.7140 (m-30) outliers start: 13 outliers final: 8 residues processed: 146 average time/residue: 0.2675 time to fit residues: 50.9346 Evaluate side-chains 145 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 0.2980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8919 Z= 0.166 Angle : 0.481 7.174 12091 Z= 0.255 Chirality : 0.041 0.172 1385 Planarity : 0.003 0.039 1523 Dihedral : 5.276 61.918 1227 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.27 % Allowed : 14.83 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.45 (0.26), residues: 1106 helix: 2.35 (0.26), residues: 387 sheet: -0.89 (0.30), residues: 278 loop : -0.71 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR A 230 ARG 0.006 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.089 Fit side-chains REVERT: A 51 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8269 (pttp) REVERT: B 59 TYR cc_start: 0.8850 (m-80) cc_final: 0.8616 (m-80) REVERT: B 217 MET cc_start: 0.7582 (ptm) cc_final: 0.7312 (ptm) REVERT: D 133 TRP cc_start: 0.6840 (t-100) cc_final: 0.6247 (t-100) REVERT: D 194 LEU cc_start: 0.8410 (mt) cc_final: 0.8039 (mp) REVERT: E 93 MET cc_start: 0.7743 (ttp) cc_final: 0.7339 (ttp) outliers start: 12 outliers final: 8 residues processed: 141 average time/residue: 0.2625 time to fit residues: 48.8762 Evaluate side-chains 139 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 66 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN D 328 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8919 Z= 0.247 Angle : 0.515 7.382 12091 Z= 0.272 Chirality : 0.042 0.170 1385 Planarity : 0.003 0.041 1523 Dihedral : 5.310 59.468 1227 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.17 % Allowed : 15.78 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.37 (0.26), residues: 1106 helix: 2.18 (0.26), residues: 393 sheet: -0.94 (0.30), residues: 275 loop : -0.67 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.001 PHE B 199 TYR 0.012 0.001 TYR E 178 ARG 0.005 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.040 Fit side-chains REVERT: A 51 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8339 (pttp) REVERT: B 217 MET cc_start: 0.7581 (ptm) cc_final: 0.7293 (ptm) REVERT: B 234 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: D 194 LEU cc_start: 0.8441 (mt) cc_final: 0.8111 (mp) REVERT: D 277 ARG cc_start: 0.7535 (ttp-170) cc_final: 0.6769 (tpt-90) REVERT: E 93 MET cc_start: 0.7700 (ttp) cc_final: 0.7283 (ttp) outliers start: 11 outliers final: 8 residues processed: 145 average time/residue: 0.2775 time to fit residues: 51.9594 Evaluate side-chains 145 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8919 Z= 0.180 Angle : 0.490 7.665 12091 Z= 0.259 Chirality : 0.041 0.166 1385 Planarity : 0.003 0.040 1523 Dihedral : 5.251 58.577 1227 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.48 % Allowed : 16.00 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.49 (0.26), residues: 1106 helix: 2.35 (0.26), residues: 387 sheet: -0.89 (0.30), residues: 278 loop : -0.62 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.010 0.001 PHE E 27 TYR 0.021 0.001 TYR A 230 ARG 0.005 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 0.999 Fit side-chains REVERT: A 51 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8357 (pttp) REVERT: B 59 TYR cc_start: 0.8864 (m-80) cc_final: 0.8632 (m-80) REVERT: B 217 MET cc_start: 0.7566 (ptm) cc_final: 0.7275 (ptm) REVERT: B 234 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8266 (m-80) REVERT: D 133 TRP cc_start: 0.6768 (t-100) cc_final: 0.6200 (t-100) REVERT: D 194 LEU cc_start: 0.8429 (mt) cc_final: 0.8123 (mp) REVERT: D 277 ARG cc_start: 0.7519 (ttp-170) cc_final: 0.6755 (tpt-90) REVERT: E 93 MET cc_start: 0.7664 (ttp) cc_final: 0.7260 (ttp) outliers start: 14 outliers final: 9 residues processed: 145 average time/residue: 0.2724 time to fit residues: 51.4224 Evaluate side-chains 142 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 218 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8919 Z= 0.192 Angle : 0.499 7.800 12091 Z= 0.261 Chirality : 0.041 0.166 1385 Planarity : 0.003 0.040 1523 Dihedral : 5.177 58.820 1227 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.27 % Allowed : 16.21 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.53 (0.26), residues: 1106 helix: 2.37 (0.26), residues: 387 sheet: -0.86 (0.30), residues: 278 loop : -0.58 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.010 0.001 PHE B 199 TYR 0.020 0.001 TYR A 230 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.049 Fit side-chains REVERT: A 51 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8355 (pttp) REVERT: B 59 TYR cc_start: 0.8866 (m-80) cc_final: 0.8623 (m-80) REVERT: B 217 MET cc_start: 0.7563 (ptm) cc_final: 0.7270 (ptm) REVERT: B 234 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8270 (m-80) REVERT: D 133 TRP cc_start: 0.6781 (t-100) cc_final: 0.6141 (t-100) REVERT: D 194 LEU cc_start: 0.8447 (mt) cc_final: 0.8145 (mp) REVERT: D 277 ARG cc_start: 0.7523 (ttp-170) cc_final: 0.6755 (tpt-90) REVERT: E 93 MET cc_start: 0.7688 (ttp) cc_final: 0.7280 (ttp) outliers start: 12 outliers final: 9 residues processed: 142 average time/residue: 0.2803 time to fit residues: 51.9002 Evaluate side-chains 142 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.3980 chunk 72 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8919 Z= 0.153 Angle : 0.484 7.904 12091 Z= 0.254 Chirality : 0.041 0.180 1385 Planarity : 0.003 0.040 1523 Dihedral : 5.072 58.212 1227 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.17 % Allowed : 16.63 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.66 (0.26), residues: 1106 helix: 2.47 (0.26), residues: 385 sheet: -0.77 (0.30), residues: 275 loop : -0.52 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.010 0.001 PHE E 27 TYR 0.020 0.001 TYR A 230 ARG 0.002 0.000 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 1.063 Fit side-chains REVERT: A 51 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8368 (pttp) REVERT: B 59 TYR cc_start: 0.8838 (m-80) cc_final: 0.8589 (m-80) REVERT: B 217 MET cc_start: 0.7569 (ptm) cc_final: 0.7295 (ptm) REVERT: B 234 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8335 (m-80) REVERT: C 47 GLU cc_start: 0.7499 (mp0) cc_final: 0.7251 (pt0) REVERT: D 133 TRP cc_start: 0.6765 (t-100) cc_final: 0.6119 (t-100) REVERT: D 194 LEU cc_start: 0.8464 (mt) cc_final: 0.8142 (mp) REVERT: E 93 MET cc_start: 0.7732 (ttp) cc_final: 0.7310 (ttp) outliers start: 11 outliers final: 8 residues processed: 141 average time/residue: 0.2574 time to fit residues: 48.0070 Evaluate side-chains 142 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 87 optimal weight: 0.0770 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 0.0060 chunk 4 optimal weight: 0.0040 chunk 63 optimal weight: 0.8980 overall best weight: 0.1966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.151633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118796 restraints weight = 11122.482| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.04 r_work: 0.3178 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8919 Z= 0.115 Angle : 0.463 7.888 12091 Z= 0.244 Chirality : 0.040 0.171 1385 Planarity : 0.003 0.041 1523 Dihedral : 4.806 57.524 1227 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.95 % Allowed : 17.16 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.81 (0.26), residues: 1106 helix: 2.62 (0.26), residues: 384 sheet: -0.67 (0.30), residues: 275 loop : -0.47 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.000 HIS E 35 PHE 0.009 0.001 PHE E 27 TYR 0.020 0.001 TYR A 230 ARG 0.004 0.000 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.83 seconds wall clock time: 40 minutes 52.69 seconds (2452.69 seconds total)