Starting phenix.real_space_refine on Mon Mar 11 16:33:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/03_2024/8dzp_27804_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/03_2024/8dzp_27804.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/03_2024/8dzp_27804_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/03_2024/8dzp_27804_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/03_2024/8dzp_27804_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/03_2024/8dzp_27804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/03_2024/8dzp_27804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/03_2024/8dzp_27804_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/03_2024/8dzp_27804_updated.pdb" } resolution = 2.71 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= 0.022 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5524 2.51 5 N 1443 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 155": "OD1" <-> "OD2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B ASP 251": "OD1" <-> "OD2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8657 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2160 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1691 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2593 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 399 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'U99': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.25, per 1000 atoms: 0.61 Number of scatterers: 8657 At special positions: 0 Unit cell: (90.64, 123.2, 125.84, 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 62 16.00 O 1628 8.00 N 1443 7.00 C 5524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " 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: 3.29 Conformation dependent library (CDL) restraints added in 1.7 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 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: 25 helices and 13 sheets defined 33.8% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 59 through 86 removed outlier: 5.392A pdb=" N VAL A 69 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL A 72 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 75 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN A 77 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 78 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 86 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 120 removed outlier: 3.969A pdb=" N THR A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N MET A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 129 through 161 Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.740A pdb=" N PHE A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.588A pdb=" N SER A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 234 removed outlier: 4.014A pdb=" N ASP A 223 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 225 " --> pdb=" O TRP A 222 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE A 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 234 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 255 removed outlier: 4.082A pdb=" N SER A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 299 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 306 through 330 removed outlier: 3.711A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 335 through 338 No H-bonds generated for 'chain 'A' and resid 335 through 338' Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.800A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 212 through 215 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 296 through 310 removed outlier: 4.140A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 350 removed outlier: 3.838A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 24 Processing helix chain 'C' and resid 30 through 36 removed outlier: 5.075A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 30 through 43 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 helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing sheet with id= A, first strand: chain 'A' and resid 197 through 201 Processing sheet with id= B, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.550A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS B 195 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU B 36 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS B 197 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU B 38 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE B 199 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N GLY B 40 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.908A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.987A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.797A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.902A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.745A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.640A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.763A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.922A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 143 through 148 Processing sheet with id= M, first strand: chain 'E' and resid 214 through 219 removed outlier: 6.424A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1095 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: 2.56 Time building geometry restraints manager: 3.56 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: 1581 1.33 - 1.45: 2279 1.45 - 1.57: 4883 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 8833 Sorted by residual: bond pdb=" C20 U99 A 401 " pdb=" C22 U99 A 401 " ideal model delta sigma weight residual 0.452 1.565 -1.113 2.00e-02 2.50e+03 3.09e+03 bond pdb=" C10 U99 A 401 " pdb=" C11 U99 A 401 " ideal model delta sigma weight residual 0.683 1.528 -0.845 2.00e-02 2.50e+03 1.79e+03 bond pdb=" C10 U99 A 401 " pdb=" C8 U99 A 401 " ideal model delta sigma weight residual 0.980 1.538 -0.558 2.00e-02 2.50e+03 7.79e+02 bond pdb=" C5 U99 A 401 " pdb=" C8 U99 A 401 " ideal model delta sigma weight residual 1.134 1.564 -0.430 2.00e-02 2.50e+03 4.63e+02 bond pdb=" C12 U99 A 401 " pdb=" C20 U99 A 401 " ideal model delta sigma weight residual 1.181 1.551 -0.370 2.00e-02 2.50e+03 3.43e+02 ... (remaining 8828 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.46: 106 104.46 - 111.85: 4268 111.85 - 119.24: 3016 119.24 - 126.64: 4480 126.64 - 134.03: 123 Bond angle restraints: 11993 Sorted by residual: angle pdb=" C TYR E 223 " pdb=" CA TYR E 223 " pdb=" CB TYR E 223 " ideal model delta sigma weight residual 110.44 105.08 5.36 9.00e-01 1.23e+00 3.55e+01 angle pdb=" N PRO E 224 " pdb=" CA PRO E 224 " pdb=" CB PRO E 224 " ideal model delta sigma weight residual 103.25 99.25 4.00 1.05e+00 9.07e-01 1.45e+01 angle pdb=" N ASP B 200 " pdb=" CA ASP B 200 " pdb=" CB ASP B 200 " ideal model delta sigma weight residual 110.57 116.19 -5.62 1.57e+00 4.06e-01 1.28e+01 angle pdb=" C13 U99 A 401 " pdb=" O6 U99 A 401 " pdb=" C14 U99 A 401 " ideal model delta sigma weight residual 110.69 121.16 -10.47 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C ALA A 57 " pdb=" N ILE A 58 " pdb=" CA ILE A 58 " ideal model delta sigma weight residual 122.13 128.54 -6.41 1.85e+00 2.92e-01 1.20e+01 ... (remaining 11988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 4952 24.08 - 48.16: 240 48.16 - 72.24: 24 72.24 - 96.32: 5 96.32 - 120.40: 2 Dihedral angle restraints: 5223 sinusoidal: 1969 harmonic: 3254 Sorted by residual: dihedral pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta harmonic sigma weight residual 180.00 59.60 120.40 0 5.00e+00 4.00e-02 5.80e+02 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 167.02 -74.02 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CA ALA E 229 " pdb=" C ALA E 229 " pdb=" N GLY E 230 " pdb=" CA GLY E 230 " ideal model delta harmonic sigma weight residual -180.00 -161.14 -18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.511: 1395 0.511 - 1.022: 1 1.022 - 1.533: 1 1.533 - 2.044: 1 2.044 - 2.555: 1 Chirality restraints: 1399 Sorted by residual: chirality pdb=" C20 U99 A 401 " pdb=" C12 U99 A 401 " pdb=" C19 U99 A 401 " pdb=" C22 U99 A 401 " both_signs ideal model delta sigma weight residual False 0.50 3.05 -2.56 2.00e-01 2.50e+01 1.63e+02 chirality pdb=" C8 U99 A 401 " pdb=" C10 U99 A 401 " pdb=" C22 U99 A 401 " pdb=" C5 U99 A 401 " both_signs ideal model delta sigma weight residual False 1.13 3.00 -1.87 2.00e-01 2.50e+01 8.72e+01 chirality pdb=" C22 U99 A 401 " pdb=" C20 U99 A 401 " pdb=" C23 U99 A 401 " pdb=" C8 U99 A 401 " both_signs ideal model delta sigma weight residual False -0.67 -1.89 1.22 2.00e-01 2.50e+01 3.70e+01 ... (remaining 1396 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 222 " -0.017 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLU E 222 " 0.061 2.00e-02 2.50e+03 pdb=" O GLU E 222 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR E 223 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO C 236 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 337 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C ASP B 337 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP B 337 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA B 338 " -0.014 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 983 2.75 - 3.29: 8046 3.29 - 3.83: 14584 3.83 - 4.36: 17249 4.36 - 4.90: 30220 Nonbonded interactions: 71082 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.216 2.440 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.237 2.440 nonbonded pdb=" OD1 ASP C 163 " pdb=" OG1 THR C 165 " model vdw 2.283 2.440 nonbonded pdb=" OG SER B 6 " pdb=" OD1 ASP B 9 " model vdw 2.302 2.440 nonbonded pdb=" O THR A 150 " pdb=" OG SER A 153 " model vdw 2.334 2.440 ... (remaining 71077 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: 1.550 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: 0.000 Extract box with map and model: 5.190 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.860 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 0.019 1.113 8833 Z= 1.305 Angle : 0.723 10.468 11993 Z= 0.382 Chirality : 0.104 2.555 1399 Planarity : 0.006 0.066 1503 Dihedral : 13.899 120.400 3113 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.11 % Allowed : 0.75 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.46 (0.24), residues: 1100 helix: 0.49 (0.25), residues: 371 sheet: 0.30 (0.29), residues: 285 loop : -1.35 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.011 0.001 HIS C 62 PHE 0.015 0.002 PHE A 143 TYR 0.021 0.002 TYR E 178 ARG 0.013 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.112 Fit side-chains REVERT: B 225 VAL cc_start: 0.8319 (t) cc_final: 0.8118 (t) REVERT: B 269 ASN cc_start: 0.8395 (m110) cc_final: 0.8058 (m110) REVERT: B 275 GLU cc_start: 0.7065 (tt0) cc_final: 0.6770 (tt0) REVERT: B 337 ASP cc_start: 0.7171 (m-30) cc_final: 0.6868 (m-30) REVERT: C 219 ARG cc_start: 0.7254 (mmt90) cc_final: 0.6935 (mmt90) REVERT: C 258 ASP cc_start: 0.6739 (t70) cc_final: 0.6498 (t70) REVERT: E 89 GLU cc_start: 0.7146 (mp0) cc_final: 0.6855 (mp0) outliers start: 1 outliers final: 2 residues processed: 192 average time/residue: 1.1386 time to fit residues: 234.1310 Evaluate side-chains 182 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 125 ASN C 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 8833 Z= 0.330 Angle : 0.632 17.933 11993 Z= 0.308 Chirality : 0.046 0.513 1399 Planarity : 0.004 0.056 1503 Dihedral : 5.966 79.257 1220 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.14 % Allowed : 8.33 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.24), residues: 1100 helix: 1.25 (0.27), residues: 366 sheet: 0.30 (0.29), residues: 290 loop : -1.25 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 169 HIS 0.008 0.001 HIS C 62 PHE 0.013 0.001 PHE B 189 TYR 0.024 0.002 TYR E 178 ARG 0.005 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 1.057 Fit side-chains REVERT: A 121 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6524 (ppp) REVERT: A 151 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7139 (tmm) REVERT: A 325 LEU cc_start: 0.8019 (mm) cc_final: 0.7815 (mt) REVERT: B 275 GLU cc_start: 0.7110 (tt0) cc_final: 0.6793 (tt0) REVERT: C 19 ARG cc_start: 0.7376 (ttp80) cc_final: 0.6955 (ttp80) REVERT: C 195 ASP cc_start: 0.7870 (p0) cc_final: 0.7101 (p0) REVERT: C 197 ARG cc_start: 0.7074 (mtm-85) cc_final: 0.6865 (mtm-85) REVERT: C 258 ASP cc_start: 0.6825 (t70) cc_final: 0.6544 (t70) REVERT: C 314 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7720 (ttm170) REVERT: E 89 GLU cc_start: 0.7159 (mp0) cc_final: 0.6805 (mp0) REVERT: E 93 MET cc_start: 0.7955 (tpp) cc_final: 0.7726 (tpt) outliers start: 20 outliers final: 6 residues processed: 184 average time/residue: 1.0893 time to fit residues: 215.1451 Evaluate side-chains 187 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.0270 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 8833 Z= 0.303 Angle : 0.596 17.449 11993 Z= 0.291 Chirality : 0.045 0.471 1399 Planarity : 0.004 0.054 1503 Dihedral : 5.724 72.597 1218 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.24 % Allowed : 10.90 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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 (0.25), residues: 1100 helix: 1.51 (0.27), residues: 367 sheet: 0.35 (0.29), residues: 296 loop : -1.22 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.005 0.001 HIS C 62 PHE 0.012 0.001 PHE C 151 TYR 0.022 0.002 TYR E 178 ARG 0.009 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 181 time to evaluate : 1.037 Fit side-chains REVERT: A 121 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.6448 (ppp) REVERT: A 151 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7067 (tmm) REVERT: A 192 SER cc_start: 0.7623 (OUTLIER) cc_final: 0.7325 (m) REVERT: B 275 GLU cc_start: 0.7117 (tt0) cc_final: 0.6791 (tt0) REVERT: C 197 ARG cc_start: 0.7085 (mtm-85) cc_final: 0.6758 (mtm-85) REVERT: C 217 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7027 (pmt) REVERT: C 258 ASP cc_start: 0.6838 (t70) cc_final: 0.6571 (t70) REVERT: C 290 ASP cc_start: 0.7778 (m-30) cc_final: 0.7473 (m-30) REVERT: C 314 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7745 (ttm170) REVERT: E 89 GLU cc_start: 0.7193 (mp0) cc_final: 0.6808 (mp0) REVERT: E 93 MET cc_start: 0.7887 (tpp) cc_final: 0.7680 (tpp) outliers start: 21 outliers final: 7 residues processed: 186 average time/residue: 1.0656 time to fit residues: 212.6502 Evaluate side-chains 194 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 182 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 0.0370 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN C 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 8833 Z= 0.367 Angle : 0.628 17.600 11993 Z= 0.310 Chirality : 0.046 0.485 1399 Planarity : 0.004 0.056 1503 Dihedral : 5.671 68.800 1218 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.99 % Allowed : 11.22 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.25 (0.25), residues: 1100 helix: 1.57 (0.28), residues: 367 sheet: 0.45 (0.29), residues: 290 loop : -1.24 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.002 PHE C 151 TYR 0.027 0.002 TYR E 178 ARG 0.009 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 0.995 Fit side-chains REVERT: A 121 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.6501 (ppp) REVERT: A 151 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6895 (tmm) REVERT: A 192 SER cc_start: 0.7662 (OUTLIER) cc_final: 0.7367 (m) REVERT: B 275 GLU cc_start: 0.7111 (tt0) cc_final: 0.6793 (tt0) REVERT: C 197 ARG cc_start: 0.7134 (mtm-85) cc_final: 0.6856 (mtm-85) REVERT: C 198 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7809 (pt) REVERT: C 217 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7033 (pmt) REVERT: C 258 ASP cc_start: 0.6856 (t70) cc_final: 0.6575 (t70) REVERT: C 314 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7763 (ttm170) REVERT: E 89 GLU cc_start: 0.7227 (mp0) cc_final: 0.6817 (mp0) REVERT: E 93 MET cc_start: 0.7877 (tpp) cc_final: 0.7675 (tpp) REVERT: E 223 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7732 (m-80) outliers start: 28 outliers final: 9 residues processed: 188 average time/residue: 1.0570 time to fit residues: 213.7898 Evaluate side-chains 195 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 259 GLN E 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 8833 Z= 0.314 Angle : 0.603 17.418 11993 Z= 0.295 Chirality : 0.045 0.478 1399 Planarity : 0.004 0.055 1503 Dihedral : 5.417 65.638 1218 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.67 % Allowed : 12.82 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.32 (0.25), residues: 1100 helix: 1.66 (0.28), residues: 368 sheet: 0.38 (0.28), residues: 296 loop : -1.17 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE C 151 TYR 0.022 0.002 TYR E 178 ARG 0.010 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 1.010 Fit side-chains REVERT: A 121 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.6397 (ppp) REVERT: A 151 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6934 (tmm) REVERT: A 192 SER cc_start: 0.7656 (OUTLIER) cc_final: 0.7377 (m) REVERT: B 275 GLU cc_start: 0.7107 (tt0) cc_final: 0.6791 (tt0) REVERT: C 137 ARG cc_start: 0.7925 (tpp-160) cc_final: 0.7681 (tpp80) REVERT: C 197 ARG cc_start: 0.7127 (mtm-85) cc_final: 0.6900 (mtm-85) REVERT: C 198 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7785 (pt) REVERT: C 217 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7013 (pmt) REVERT: C 258 ASP cc_start: 0.6845 (t70) cc_final: 0.6557 (t70) REVERT: C 314 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7758 (ttm170) REVERT: E 89 GLU cc_start: 0.7198 (mp0) cc_final: 0.6806 (mp0) REVERT: E 223 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7623 (m-80) outliers start: 25 outliers final: 9 residues processed: 192 average time/residue: 1.1039 time to fit residues: 226.7778 Evaluate side-chains 200 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.0670 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 8833 Z= 0.273 Angle : 0.577 17.282 11993 Z= 0.280 Chirality : 0.044 0.476 1399 Planarity : 0.004 0.054 1503 Dihedral : 5.193 63.582 1215 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.78 % Allowed : 13.57 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.44 (0.25), residues: 1100 helix: 1.83 (0.28), residues: 367 sheet: 0.40 (0.29), residues: 295 loop : -1.13 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.003 0.001 HIS C 142 PHE 0.012 0.001 PHE C 151 TYR 0.020 0.001 TYR E 178 ARG 0.008 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 1.067 Fit side-chains REVERT: A 121 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6269 (ppp) REVERT: A 151 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6955 (tmm) REVERT: A 192 SER cc_start: 0.7635 (OUTLIER) cc_final: 0.7351 (m) REVERT: A 325 LEU cc_start: 0.7947 (mm) cc_final: 0.7741 (mt) REVERT: B 275 GLU cc_start: 0.7108 (tt0) cc_final: 0.6792 (tt0) REVERT: C 137 ARG cc_start: 0.7939 (tpp-160) cc_final: 0.7699 (tpp80) REVERT: C 198 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7770 (pt) REVERT: C 217 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7011 (pmt) REVERT: C 258 ASP cc_start: 0.6833 (t70) cc_final: 0.6548 (t70) REVERT: C 314 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7757 (ttm170) REVERT: E 89 GLU cc_start: 0.7185 (mp0) cc_final: 0.6796 (mp0) REVERT: E 223 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.7547 (m-80) outliers start: 26 outliers final: 10 residues processed: 195 average time/residue: 1.0737 time to fit residues: 226.1245 Evaluate side-chains 202 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 185 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 0.0060 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 8833 Z= 0.289 Angle : 0.588 17.265 11993 Z= 0.286 Chirality : 0.044 0.480 1399 Planarity : 0.004 0.054 1503 Dihedral : 5.278 62.915 1215 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.56 % Allowed : 14.21 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.42 (0.25), residues: 1100 helix: 1.83 (0.28), residues: 368 sheet: 0.42 (0.29), residues: 286 loop : -1.15 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS C 142 PHE 0.013 0.001 PHE C 151 TYR 0.021 0.002 TYR E 178 ARG 0.007 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 188 time to evaluate : 0.980 Fit side-chains REVERT: A 121 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6283 (ppp) REVERT: A 151 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6956 (tmm) REVERT: A 192 SER cc_start: 0.7650 (OUTLIER) cc_final: 0.7371 (m) REVERT: A 325 LEU cc_start: 0.7929 (mm) cc_final: 0.7723 (mt) REVERT: B 275 GLU cc_start: 0.7114 (tt0) cc_final: 0.6796 (tt0) REVERT: C 198 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7774 (pt) REVERT: C 217 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.6995 (pmt) REVERT: C 314 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7775 (ttm170) REVERT: E 89 GLU cc_start: 0.7191 (mp0) cc_final: 0.6799 (mp0) outliers start: 24 outliers final: 11 residues processed: 194 average time/residue: 1.0787 time to fit residues: 224.1359 Evaluate side-chains 205 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 8833 Z= 0.301 Angle : 0.598 17.288 11993 Z= 0.291 Chirality : 0.044 0.473 1399 Planarity : 0.004 0.053 1503 Dihedral : 5.403 62.567 1215 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.14 % Allowed : 15.17 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.44 (0.25), residues: 1100 helix: 1.82 (0.28), residues: 367 sheet: 0.50 (0.29), residues: 289 loop : -1.16 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE C 151 TYR 0.022 0.002 TYR E 178 ARG 0.006 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 1.043 Fit side-chains REVERT: A 121 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6287 (ppp) REVERT: A 151 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6927 (tmm) REVERT: A 192 SER cc_start: 0.7617 (t) cc_final: 0.7341 (m) REVERT: B 275 GLU cc_start: 0.7114 (tt0) cc_final: 0.6799 (tt0) REVERT: B 350 ASP cc_start: 0.7139 (t0) cc_final: 0.6808 (t0) REVERT: C 198 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7785 (pt) REVERT: C 314 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7783 (ttm170) REVERT: E 89 GLU cc_start: 0.7190 (mp0) cc_final: 0.6790 (mp0) outliers start: 20 outliers final: 12 residues processed: 193 average time/residue: 1.1754 time to fit residues: 242.5280 Evaluate side-chains 204 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 0.0970 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 8833 Z= 0.309 Angle : 0.602 17.267 11993 Z= 0.293 Chirality : 0.045 0.471 1399 Planarity : 0.004 0.053 1503 Dihedral : 5.437 62.219 1215 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.14 % Allowed : 15.71 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.44 (0.25), residues: 1100 helix: 1.81 (0.28), residues: 368 sheet: 0.47 (0.29), residues: 290 loop : -1.14 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS A 291 PHE 0.014 0.001 PHE C 151 TYR 0.022 0.002 TYR E 178 ARG 0.006 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 0.999 Fit side-chains REVERT: A 118 VAL cc_start: 0.5906 (t) cc_final: 0.5360 (t) REVERT: A 121 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6308 (ppp) REVERT: A 151 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6930 (tmm) REVERT: A 192 SER cc_start: 0.7623 (t) cc_final: 0.7359 (m) REVERT: B 275 GLU cc_start: 0.7111 (tt0) cc_final: 0.6798 (tt0) REVERT: B 350 ASP cc_start: 0.7141 (t0) cc_final: 0.6832 (t0) REVERT: C 198 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7781 (pt) REVERT: C 314 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7774 (ttm170) REVERT: E 89 GLU cc_start: 0.7197 (mp0) cc_final: 0.6791 (mp0) outliers start: 20 outliers final: 13 residues processed: 192 average time/residue: 1.0965 time to fit residues: 225.3823 Evaluate side-chains 204 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.0670 chunk 100 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 8833 Z= 0.305 Angle : 0.607 17.243 11993 Z= 0.294 Chirality : 0.045 0.469 1399 Planarity : 0.004 0.052 1503 Dihedral : 5.372 61.463 1215 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.14 % Allowed : 15.60 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.46 (0.25), residues: 1100 helix: 1.83 (0.28), residues: 367 sheet: 0.43 (0.29), residues: 295 loop : -1.12 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE C 151 TYR 0.022 0.002 TYR E 178 ARG 0.006 0.000 ARG C 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 0.961 Fit side-chains REVERT: A 118 VAL cc_start: 0.5935 (t) cc_final: 0.5405 (t) REVERT: A 121 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6282 (ppp) REVERT: A 151 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6940 (tmm) REVERT: A 192 SER cc_start: 0.7658 (OUTLIER) cc_final: 0.7398 (m) REVERT: A 325 LEU cc_start: 0.7876 (mt) cc_final: 0.7672 (mp) REVERT: B 275 GLU cc_start: 0.7112 (tt0) cc_final: 0.6799 (tt0) REVERT: B 350 ASP cc_start: 0.7128 (t0) cc_final: 0.6828 (t0) REVERT: C 198 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7770 (pt) REVERT: C 314 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7790 (ttm170) REVERT: E 89 GLU cc_start: 0.7194 (mp0) cc_final: 0.6789 (mp0) outliers start: 20 outliers final: 12 residues processed: 191 average time/residue: 1.1108 time to fit residues: 227.3661 Evaluate side-chains 204 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.132814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111145 restraints weight = 12055.662| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.72 r_work: 0.3297 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 8833 Z= 0.318 Angle : 0.616 17.253 11993 Z= 0.299 Chirality : 0.045 0.470 1399 Planarity : 0.004 0.053 1503 Dihedral : 5.357 61.279 1215 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.46 % Allowed : 15.71 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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 (0.25), residues: 1100 helix: 1.79 (0.28), residues: 368 sheet: 0.43 (0.29), residues: 295 loop : -1.11 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE C 151 TYR 0.023 0.002 TYR E 178 ARG 0.006 0.000 ARG C 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4087.02 seconds wall clock time: 73 minutes 10.79 seconds (4390.79 seconds total)