Starting phenix.real_space_refine on Thu Feb 15 05:39:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2f_32966/02_2024/7x2f_32966_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2f_32966/02_2024/7x2f_32966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2f_32966/02_2024/7x2f_32966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2f_32966/02_2024/7x2f_32966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2f_32966/02_2024/7x2f_32966_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2f_32966/02_2024/7x2f_32966_updated.pdb" } resolution = 3.0 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= -0.002 sd= 0.106 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3031 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 54 5.16 5 Cl 2 4.86 5 C 5252 2.51 5 N 1429 2.21 5 O 1512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 130": "NH1" <-> "NH2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8249 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2242 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 3 Chain: "A" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1896 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2609 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 341, 2599 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 341, 2599 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 2633 Chain: "D" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 434 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 97 Unusual residues: {'CLR': 2, 'G4C': 1, 'LDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.76, per 1000 atoms: 0.82 Number of scatterers: 8249 At special positions: 0 Unit cell: (78.264, 101.091, 128.266, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 54 16.00 O 1512 8.00 N 1429 7.00 C 5252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " 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: 3.80 Conformation dependent library (CDL) restraints added in 2.3 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 10 sheets defined 40.7% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'F' and resid 22 through 50 Processing helix chain 'F' and resid 52 through 56 Processing helix chain 'F' and resid 58 through 76 removed outlier: 3.762A pdb=" N PHE F 62 " --> pdb=" O THR F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 87 Processing helix chain 'F' and resid 93 through 125 removed outlier: 3.583A pdb=" N ASN F 97 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL F 100 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP F 103 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE F 104 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET F 105 " --> pdb=" O PHE F 102 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N CYS F 106 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER F 107 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE F 111 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU F 112 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS F 115 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE F 125 " --> pdb=" O TYR F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 134 removed outlier: 3.836A pdb=" N GLU F 132 " --> pdb=" O PRO F 128 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG F 133 " --> pdb=" O PHE F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 160 removed outlier: 3.554A pdb=" N VAL F 152 " --> pdb=" O TRP F 148 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Processing helix chain 'F' and resid 192 through 202 removed outlier: 3.825A pdb=" N ILE F 196 " --> pdb=" O ARG F 192 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE F 201 " --> pdb=" O SER F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 240 removed outlier: 3.802A pdb=" N MET F 210 " --> pdb=" O PRO F 206 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 298 removed outlier: 4.042A pdb=" N PHE F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Proline residue: F 287 - end of helix Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 310 through 331 removed outlier: 3.892A pdb=" N ASN F 323 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER F 324 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER F 325 " --> pdb=" O TRP F 321 " (cutoff:3.500A) Proline residue: F 328 - end of helix Processing helix chain 'F' and resid 335 through 345 Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.606A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.625A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.684A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 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 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.994A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 23 removed outlier: 3.578A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 removed outlier: 3.563A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.520A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= C, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.097A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.771A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.910A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.703A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.813A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.752A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.440A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.887A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1002 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: 2.54 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1326 1.26 - 1.40: 2139 1.40 - 1.54: 4786 1.54 - 1.68: 101 1.68 - 1.82: 75 Bond restraints: 8427 Sorted by residual: bond pdb=" C ARG F 130 " pdb=" O ARG F 130 " ideal model delta sigma weight residual 1.237 1.121 0.115 1.17e-02 7.31e+03 9.70e+01 bond pdb=" C05 G4C F 502 " pdb=" N04 G4C F 502 " ideal model delta sigma weight residual 1.355 1.511 -0.156 2.00e-02 2.50e+03 6.08e+01 bond pdb=" CA ARG F 130 " pdb=" C ARG F 130 " ideal model delta sigma weight residual 1.523 1.430 0.093 1.30e-02 5.92e+03 5.13e+01 bond pdb=" CA TYR B 145 " pdb=" CB TYR B 145 " ideal model delta sigma weight residual 1.527 1.431 0.096 1.44e-02 4.82e+03 4.47e+01 bond pdb=" CA ARG F 130 " pdb=" CB ARG F 130 " ideal model delta sigma weight residual 1.528 1.435 0.094 1.56e-02 4.11e+03 3.60e+01 ... (remaining 8422 not shown) Histogram of bond angle deviations from ideal: 97.10 - 104.50: 95 104.50 - 111.90: 4043 111.90 - 119.29: 2979 119.29 - 126.69: 4191 126.69 - 134.09: 126 Bond angle restraints: 11434 Sorted by residual: angle pdb=" C ARG F 130 " pdb=" CA ARG F 130 " pdb=" CB ARG F 130 " ideal model delta sigma weight residual 110.79 99.41 11.38 1.66e+00 3.63e-01 4.70e+01 angle pdb=" N GLU A 344 " pdb=" CA GLU A 344 " pdb=" CB GLU A 344 " ideal model delta sigma weight residual 110.28 119.54 -9.26 1.55e+00 4.16e-01 3.57e+01 angle pdb=" N ARG A 232 " pdb=" CA ARG A 232 " pdb=" C ARG A 232 " ideal model delta sigma weight residual 111.04 118.60 -7.56 1.55e+00 4.16e-01 2.38e+01 angle pdb=" O GLY B 144 " pdb=" C GLY B 144 " pdb=" N TYR B 145 " ideal model delta sigma weight residual 123.65 119.24 4.41 9.20e-01 1.18e+00 2.30e+01 angle pdb=" C GLY B 144 " pdb=" N TYR B 145 " pdb=" CA TYR B 145 " ideal model delta sigma weight residual 121.29 113.85 7.44 1.74e+00 3.30e-01 1.83e+01 ... (remaining 11429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4682 17.93 - 35.85: 373 35.85 - 53.78: 54 53.78 - 71.71: 10 71.71 - 89.64: 4 Dihedral angle restraints: 5123 sinusoidal: 2093 harmonic: 3030 Sorted by residual: dihedral pdb=" C ARG F 130 " pdb=" N ARG F 130 " pdb=" CA ARG F 130 " pdb=" CB ARG F 130 " ideal model delta harmonic sigma weight residual -122.60 -108.59 -14.01 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" CA ASN A 254 " pdb=" C ASN A 254 " pdb=" N ARG A 265 " pdb=" CA ARG A 265 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 55.69 37.31 1 1.00e+01 1.00e-02 1.96e+01 ... (remaining 5120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1142 0.076 - 0.152: 132 0.152 - 0.228: 10 0.228 - 0.303: 2 0.303 - 0.379: 3 Chirality restraints: 1289 Sorted by residual: chirality pdb=" CA TYR B 145 " pdb=" N TYR B 145 " pdb=" C TYR B 145 " pdb=" CB TYR B 145 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C13 CLR F 501 " pdb=" C12 CLR F 501 " pdb=" C14 CLR F 501 " pdb=" C17 CLR F 501 " both_signs ideal model delta sigma weight residual False -2.93 -2.57 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C13 CLR F 503 " pdb=" C12 CLR F 503 " pdb=" C14 CLR F 503 " pdb=" C17 CLR F 503 " both_signs ideal model delta sigma weight residual False -2.93 -2.58 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 1286 not shown) Planarity restraints: 1443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.026 2.00e-02 2.50e+03 2.18e-02 9.47e+00 pdb=" CG TYR B 59 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 145 " -0.030 2.00e-02 2.50e+03 2.05e-02 8.40e+00 pdb=" CG TYR B 145 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 145 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 145 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 145 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 145 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 145 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR B 145 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 25 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C LYS A 25 " 0.043 2.00e-02 2.50e+03 pdb=" O LYS A 25 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A 26 " -0.015 2.00e-02 2.50e+03 ... (remaining 1440 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 333 2.71 - 3.26: 8370 3.26 - 3.81: 13483 3.81 - 4.35: 17109 4.35 - 4.90: 28962 Nonbonded interactions: 68257 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.164 2.440 nonbonded pdb=" OG SER F 198 " pdb=" O2 LDP F 504 " model vdw 2.166 2.440 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.213 2.520 nonbonded pdb=" OE1 GLN A 35 " pdb=" NH2 ARG A 38 " model vdw 2.231 2.520 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.236 2.440 ... (remaining 68252 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=0.38 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 1.910 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 30.890 Find NCS groups from input model: 0.230 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:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 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 : 0.006 0.156 8427 Z= 0.412 Angle : 0.830 12.242 11434 Z= 0.456 Chirality : 0.053 0.379 1289 Planarity : 0.005 0.047 1443 Dihedral : 12.875 89.636 3148 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.11 % Allowed : 0.34 % Favored : 99.55 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.25), residues: 1021 helix: 0.04 (0.25), residues: 403 sheet: -0.60 (0.32), residues: 216 loop : -1.05 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.012 0.002 HIS A 220 PHE 0.041 0.002 PHE A 340 TYR 0.054 0.002 TYR B 59 ARG 0.005 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8258 (tp-100) cc_final: 0.7826 (tp40) REVERT: A 315 PHE cc_start: 0.7254 (t80) cc_final: 0.6856 (t80) REVERT: E 60 TYR cc_start: 0.8383 (m-80) cc_final: 0.8112 (m-80) REVERT: E 69 THR cc_start: 0.7751 (p) cc_final: 0.7543 (t) REVERT: B 259 GLN cc_start: 0.8072 (pt0) cc_final: 0.7802 (pt0) REVERT: D 38 MET cc_start: 0.6412 (mmt) cc_final: 0.5838 (mpp) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 1.0169 time to fit residues: 158.6872 Evaluate side-chains 107 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 0.0770 chunk 91 optimal weight: 0.0770 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8427 Z= 0.174 Angle : 0.541 7.468 11434 Z= 0.284 Chirality : 0.042 0.169 1289 Planarity : 0.004 0.042 1443 Dihedral : 5.984 88.045 1288 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.70 % Allowed : 11.92 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.00 (0.25), residues: 1021 helix: 0.95 (0.25), residues: 407 sheet: -0.36 (0.31), residues: 225 loop : -0.67 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.027 0.002 PHE A 340 TYR 0.009 0.001 TYR A 339 ARG 0.003 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.896 Fit side-chains REVERT: F 269 LYS cc_start: 0.7550 (tppt) cc_final: 0.7152 (tttp) REVERT: A 213 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: A 315 PHE cc_start: 0.7097 (t80) cc_final: 0.6687 (t80) REVERT: E 60 TYR cc_start: 0.8378 (m-80) cc_final: 0.8157 (m-80) REVERT: E 83 MET cc_start: 0.6655 (mtm) cc_final: 0.6270 (mtp) REVERT: B 195 ASP cc_start: 0.6515 (p0) cc_final: 0.6130 (p0) REVERT: B 259 GLN cc_start: 0.7919 (pt0) cc_final: 0.7605 (pt0) outliers start: 15 outliers final: 7 residues processed: 128 average time/residue: 0.8880 time to fit residues: 123.5745 Evaluate side-chains 116 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain B residue 269 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8427 Z= 0.239 Angle : 0.545 9.311 11434 Z= 0.288 Chirality : 0.043 0.156 1289 Planarity : 0.004 0.042 1443 Dihedral : 5.829 85.351 1288 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.61 % Allowed : 14.07 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1021 helix: 1.16 (0.26), residues: 411 sheet: -0.20 (0.31), residues: 221 loop : -0.61 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS F 53 PHE 0.016 0.002 PHE A 212 TYR 0.010 0.001 TYR A 339 ARG 0.003 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 0.923 Fit side-chains REVERT: F 163 TRP cc_start: 0.7426 (m-10) cc_final: 0.7202 (m-10) REVERT: F 269 LYS cc_start: 0.7774 (tppt) cc_final: 0.7370 (tttp) REVERT: F 333 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7822 (m-10) REVERT: A 315 PHE cc_start: 0.7108 (t80) cc_final: 0.6753 (t80) REVERT: A 344 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: A 370 GLU cc_start: 0.7431 (mp0) cc_final: 0.7124 (mp0) REVERT: E 83 MET cc_start: 0.6663 (mtm) cc_final: 0.6313 (mtp) REVERT: B 163 ASP cc_start: 0.7291 (p0) cc_final: 0.7064 (p0) REVERT: B 184 THR cc_start: 0.8919 (p) cc_final: 0.8714 (t) REVERT: B 195 ASP cc_start: 0.6670 (p0) cc_final: 0.6354 (p0) REVERT: B 259 GLN cc_start: 0.7828 (pt0) cc_final: 0.7486 (pt0) outliers start: 23 outliers final: 13 residues processed: 124 average time/residue: 0.8697 time to fit residues: 117.7123 Evaluate side-chains 116 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8427 Z= 0.248 Angle : 0.545 8.700 11434 Z= 0.287 Chirality : 0.043 0.154 1289 Planarity : 0.004 0.042 1443 Dihedral : 5.755 83.242 1288 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.06 % Allowed : 14.87 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.39 (0.26), residues: 1021 helix: 1.32 (0.26), residues: 412 sheet: -0.19 (0.31), residues: 216 loop : -0.52 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.005 0.001 HIS F 53 PHE 0.018 0.002 PHE F 288 TYR 0.020 0.001 TYR E 60 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 0.999 Fit side-chains REVERT: F 269 LYS cc_start: 0.7852 (tppt) cc_final: 0.7425 (tttp) REVERT: F 333 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7843 (m-10) REVERT: A 315 PHE cc_start: 0.7169 (t80) cc_final: 0.6860 (t80) REVERT: A 344 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6583 (mp0) REVERT: A 370 GLU cc_start: 0.7408 (mp0) cc_final: 0.7081 (mp0) REVERT: E 83 MET cc_start: 0.6902 (mtm) cc_final: 0.6524 (mtp) REVERT: B 189 SER cc_start: 0.8537 (t) cc_final: 0.8260 (t) REVERT: B 195 ASP cc_start: 0.6640 (p0) cc_final: 0.6371 (p0) REVERT: B 259 GLN cc_start: 0.7722 (pt0) cc_final: 0.7337 (pt0) outliers start: 27 outliers final: 13 residues processed: 121 average time/residue: 0.9413 time to fit residues: 123.5014 Evaluate side-chains 114 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 329 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8427 Z= 0.242 Angle : 0.530 6.284 11434 Z= 0.281 Chirality : 0.042 0.146 1289 Planarity : 0.004 0.041 1443 Dihedral : 5.618 80.169 1288 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.29 % Allowed : 16.23 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.40 (0.26), residues: 1021 helix: 1.37 (0.26), residues: 410 sheet: -0.30 (0.31), residues: 219 loop : -0.48 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.005 0.001 HIS F 53 PHE 0.016 0.002 PHE F 288 TYR 0.011 0.001 TYR A 339 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 0.984 Fit side-chains REVERT: F 269 LYS cc_start: 0.7849 (tppt) cc_final: 0.7458 (tttp) REVERT: F 333 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7826 (m-10) REVERT: A 29 GLN cc_start: 0.8353 (tp-100) cc_final: 0.7938 (tm-30) REVERT: A 31 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7651 (tp40) REVERT: A 315 PHE cc_start: 0.7221 (t80) cc_final: 0.6946 (t80) REVERT: A 344 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: E 83 MET cc_start: 0.6907 (mtm) cc_final: 0.6578 (mtp) REVERT: B 59 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: B 189 SER cc_start: 0.8556 (t) cc_final: 0.8281 (t) REVERT: B 195 ASP cc_start: 0.6723 (p0) cc_final: 0.6500 (p0) REVERT: B 259 GLN cc_start: 0.7477 (pt0) cc_final: 0.7234 (pt0) outliers start: 29 outliers final: 18 residues processed: 123 average time/residue: 0.9323 time to fit residues: 124.4744 Evaluate side-chains 124 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8427 Z= 0.155 Angle : 0.499 9.372 11434 Z= 0.261 Chirality : 0.040 0.144 1289 Planarity : 0.003 0.040 1443 Dihedral : 5.333 78.473 1288 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.82 % Allowed : 18.96 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.59 (0.26), residues: 1021 helix: 1.54 (0.26), residues: 408 sheet: -0.23 (0.31), residues: 219 loop : -0.36 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 82 HIS 0.005 0.001 HIS F 53 PHE 0.014 0.001 PHE A 212 TYR 0.008 0.001 TYR A 339 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.009 Fit side-chains REVERT: F 269 LYS cc_start: 0.7881 (tppt) cc_final: 0.7499 (tttp) REVERT: F 333 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7633 (m-10) REVERT: A 29 GLN cc_start: 0.8325 (tp-100) cc_final: 0.7916 (tp40) REVERT: A 31 GLN cc_start: 0.7881 (tp-100) cc_final: 0.7595 (tp40) REVERT: A 35 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7469 (mm-40) REVERT: A 284 THR cc_start: 0.8671 (p) cc_final: 0.8268 (t) REVERT: A 315 PHE cc_start: 0.7222 (t80) cc_final: 0.6929 (t80) REVERT: A 370 GLU cc_start: 0.7401 (mp0) cc_final: 0.7138 (mp0) REVERT: E 83 MET cc_start: 0.6834 (mtm) cc_final: 0.6527 (mtp) REVERT: B 189 SER cc_start: 0.8462 (t) cc_final: 0.8192 (t) REVERT: B 195 ASP cc_start: 0.6565 (p0) cc_final: 0.6338 (p0) REVERT: B 220 GLN cc_start: 0.7808 (mt0) cc_final: 0.7608 (mt0) REVERT: B 262 MET cc_start: 0.6007 (ttt) cc_final: 0.5801 (ttt) outliers start: 16 outliers final: 11 residues processed: 124 average time/residue: 0.9390 time to fit residues: 125.9854 Evaluate side-chains 119 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 59 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN B 75 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8427 Z= 0.174 Angle : 0.493 6.805 11434 Z= 0.262 Chirality : 0.041 0.139 1289 Planarity : 0.004 0.040 1443 Dihedral : 5.218 76.492 1288 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.84 % Allowed : 18.27 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.62 (0.26), residues: 1021 helix: 1.56 (0.26), residues: 408 sheet: -0.22 (0.32), residues: 219 loop : -0.34 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.007 0.001 HIS F 53 PHE 0.013 0.001 PHE A 212 TYR 0.007 0.001 TYR A 339 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 0.972 Fit side-chains REVERT: F 269 LYS cc_start: 0.7901 (tppt) cc_final: 0.7535 (tttp) REVERT: F 333 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7620 (m-10) REVERT: A 28 LYS cc_start: 0.7406 (ttmt) cc_final: 0.7137 (ttmm) REVERT: A 29 GLN cc_start: 0.8353 (tp-100) cc_final: 0.7933 (tp40) REVERT: A 31 GLN cc_start: 0.7901 (tp-100) cc_final: 0.7593 (tp40) REVERT: A 284 THR cc_start: 0.8674 (p) cc_final: 0.8314 (t) REVERT: A 315 PHE cc_start: 0.7152 (t80) cc_final: 0.6885 (t80) REVERT: E 83 MET cc_start: 0.6828 (mtm) cc_final: 0.6511 (mtp) REVERT: B 189 SER cc_start: 0.8524 (t) cc_final: 0.8261 (t) outliers start: 25 outliers final: 16 residues processed: 127 average time/residue: 0.9167 time to fit residues: 126.2536 Evaluate side-chains 126 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN B 75 GLN B 220 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8427 Z= 0.281 Angle : 0.554 9.414 11434 Z= 0.291 Chirality : 0.043 0.157 1289 Planarity : 0.004 0.040 1443 Dihedral : 5.423 75.527 1288 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.06 % Allowed : 18.73 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 1021 helix: 1.48 (0.26), residues: 410 sheet: -0.31 (0.31), residues: 219 loop : -0.43 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.008 0.001 HIS F 53 PHE 0.015 0.002 PHE B 235 TYR 0.011 0.001 TYR A 339 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 0.991 Fit side-chains REVERT: F 269 LYS cc_start: 0.7869 (tppt) cc_final: 0.7479 (tttm) REVERT: F 333 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7694 (m-10) REVERT: A 28 LYS cc_start: 0.7399 (ttmt) cc_final: 0.7143 (ttmm) REVERT: A 31 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7631 (tp40) REVERT: A 284 THR cc_start: 0.8710 (p) cc_final: 0.8370 (t) REVERT: A 315 PHE cc_start: 0.7298 (t80) cc_final: 0.7076 (t80) REVERT: A 356 ARG cc_start: 0.7703 (ttp-170) cc_final: 0.7474 (ttp-170) REVERT: A 370 GLU cc_start: 0.7548 (mp0) cc_final: 0.7068 (mp0) REVERT: E 83 MET cc_start: 0.6849 (mtm) cc_final: 0.6550 (mtp) REVERT: B 82 TRP cc_start: 0.8019 (OUTLIER) cc_final: 0.6905 (m-10) REVERT: B 189 SER cc_start: 0.8556 (t) cc_final: 0.8281 (t) REVERT: B 220 GLN cc_start: 0.7885 (mt0) cc_final: 0.7685 (mt0) REVERT: B 325 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7113 (mmm) outliers start: 27 outliers final: 20 residues processed: 123 average time/residue: 0.8891 time to fit residues: 119.8701 Evaluate side-chains 130 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 54 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN B 75 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8427 Z= 0.183 Angle : 0.505 7.880 11434 Z= 0.267 Chirality : 0.041 0.153 1289 Planarity : 0.004 0.039 1443 Dihedral : 5.284 74.279 1288 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.38 % Allowed : 19.75 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.57 (0.26), residues: 1021 helix: 1.57 (0.26), residues: 407 sheet: -0.31 (0.31), residues: 219 loop : -0.37 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.007 0.001 HIS F 53 PHE 0.014 0.001 PHE F 288 TYR 0.012 0.001 TYR B 289 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: F 269 LYS cc_start: 0.7833 (tppt) cc_final: 0.7438 (tttm) REVERT: F 333 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7615 (m-10) REVERT: A 28 LYS cc_start: 0.7392 (ttmt) cc_final: 0.7132 (ttmm) REVERT: A 29 GLN cc_start: 0.8358 (tp-100) cc_final: 0.7944 (tp40) REVERT: A 31 GLN cc_start: 0.7869 (tp-100) cc_final: 0.7584 (tp40) REVERT: A 284 THR cc_start: 0.8696 (p) cc_final: 0.8375 (t) REVERT: A 315 PHE cc_start: 0.7276 (t80) cc_final: 0.7074 (t80) REVERT: A 370 GLU cc_start: 0.7549 (mp0) cc_final: 0.7084 (mp0) REVERT: E 83 MET cc_start: 0.6759 (mtm) cc_final: 0.6463 (mtp) REVERT: B 189 SER cc_start: 0.8538 (t) cc_final: 0.8251 (t) outliers start: 21 outliers final: 14 residues processed: 125 average time/residue: 0.9240 time to fit residues: 125.4729 Evaluate side-chains 123 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 8 optimal weight: 0.0770 chunk 61 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8427 Z= 0.205 Angle : 0.534 9.688 11434 Z= 0.278 Chirality : 0.042 0.151 1289 Planarity : 0.004 0.039 1443 Dihedral : 5.267 73.640 1288 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.93 % Allowed : 20.66 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 1021 helix: 1.56 (0.26), residues: 410 sheet: -0.34 (0.31), residues: 219 loop : -0.42 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.008 0.001 HIS F 53 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR B 289 ARG 0.002 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: F 269 LYS cc_start: 0.7842 (tppt) cc_final: 0.7455 (tttm) REVERT: F 333 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7618 (m-10) REVERT: A 28 LYS cc_start: 0.7388 (ttmt) cc_final: 0.7146 (ttmm) REVERT: A 31 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7583 (tp40) REVERT: A 284 THR cc_start: 0.8705 (p) cc_final: 0.8391 (t) REVERT: A 315 PHE cc_start: 0.7297 (t80) cc_final: 0.7086 (t80) REVERT: A 370 GLU cc_start: 0.7552 (mp0) cc_final: 0.7088 (mp0) REVERT: E 83 MET cc_start: 0.6813 (mtm) cc_final: 0.6517 (mtp) REVERT: B 189 SER cc_start: 0.8553 (t) cc_final: 0.8268 (t) outliers start: 17 outliers final: 14 residues processed: 121 average time/residue: 0.9060 time to fit residues: 119.1948 Evaluate side-chains 124 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.178981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128070 restraints weight = 22485.842| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 4.45 r_work: 0.3402 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8427 Z= 0.175 Angle : 0.508 7.985 11434 Z= 0.269 Chirality : 0.041 0.154 1289 Planarity : 0.004 0.039 1443 Dihedral : 5.174 72.237 1288 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.04 % Allowed : 20.43 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.60 (0.26), residues: 1021 helix: 1.60 (0.26), residues: 407 sheet: -0.30 (0.32), residues: 219 loop : -0.35 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.007 0.001 HIS F 53 PHE 0.013 0.001 PHE A 212 TYR 0.014 0.001 TYR B 289 ARG 0.003 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2930.37 seconds wall clock time: 53 minutes 17.47 seconds (3197.47 seconds total)