Starting phenix.real_space_refine on Fri Feb 16 10:34:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onu_13002/02_2024/7onu_13002_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onu_13002/02_2024/7onu_13002.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/7onu_13002/02_2024/7onu_13002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onu_13002/02_2024/7onu_13002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onu_13002/02_2024/7onu_13002_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onu_13002/02_2024/7onu_13002_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= 0.006 sd= 1.101 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 74 5.49 5 Mg 1 5.21 5 S 68 5.16 5 C 9272 2.51 5 N 2644 2.21 5 O 3023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15083 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "E" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3810 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 16, 'TRANS': 450} Chain: "F" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2287 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 8, 'TRANS': 267} Chain breaks: 1 Chain: "T" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1416 Classifications: {'RNA': 66} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 22} Link IDs: {'rna2p': 14, 'rna3p': 51} Chain breaks: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9296 SG CYS E 348 49.966 77.669 20.738 1.00112.31 S ATOM 9312 SG CYS E 351 47.988 79.278 18.153 1.00115.74 S ATOM 11175 SG CYS E 578 47.198 75.487 18.852 1.00107.57 S Time building chain proxies: 7.40, per 1000 atoms: 0.49 Number of scatterers: 15083 At special positions: 0 Unit cell: (93.4081, 109.254, 167.634, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 68 16.00 P 74 15.00 Mg 1 11.99 O 3023 8.00 N 2644 7.00 C 9272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 6.65 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" NE2 HIS E 557 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 351 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 348 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 578 " Number of angles added : 3 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3210 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 8 sheets defined 48.3% alpha, 9.8% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 6.47 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 68 through 82 Processing helix chain 'A' and resid 111 through 137 removed outlier: 3.775A pdb=" N GLY A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 166 through 189 removed outlier: 4.554A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 211 through 219 Processing helix chain 'A' and resid 230 through 241 Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 68 through 82 Processing helix chain 'B' and resid 111 through 138 removed outlier: 3.885A pdb=" N GLY B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 166 through 187 removed outlier: 4.616A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 230 through 241 Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 68 through 82 Processing helix chain 'C' and resid 111 through 138 removed outlier: 3.594A pdb=" N MET C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN C 138 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 166 through 187 removed outlier: 4.639A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 204 through 207 No H-bonds generated for 'chain 'C' and resid 204 through 207' Processing helix chain 'C' and resid 211 through 220 Processing helix chain 'C' and resid 230 through 242 Processing helix chain 'D' and resid 22 through 33 Processing helix chain 'D' and resid 47 through 54 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 111 through 121 Processing helix chain 'D' and resid 123 through 138 removed outlier: 4.139A pdb=" N GLN D 138 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'D' and resid 166 through 185 removed outlier: 4.629A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 204 through 207 No H-bonds generated for 'chain 'D' and resid 204 through 207' Processing helix chain 'D' and resid 211 through 220 Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'E' and resid 121 through 135 removed outlier: 4.880A pdb=" N GLU E 133 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASN E 134 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 151 Processing helix chain 'E' and resid 155 through 168 Processing helix chain 'E' and resid 175 through 187 Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 210 through 220 Processing helix chain 'E' and resid 227 through 238 removed outlier: 3.810A pdb=" N LEU E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 256 Processing helix chain 'E' and resid 260 through 272 Processing helix chain 'E' and resid 279 through 290 removed outlier: 4.020A pdb=" N LYS E 290 " --> pdb=" O PHE E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 311 Processing helix chain 'E' and resid 317 through 328 Processing helix chain 'E' and resid 362 through 376 removed outlier: 3.637A pdb=" N ASP E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 400 Processing helix chain 'E' and resid 410 through 414 Processing helix chain 'E' and resid 422 through 436 removed outlier: 4.262A pdb=" N ARG E 436 " --> pdb=" O GLN E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 448 No H-bonds generated for 'chain 'E' and resid 446 through 448' Processing helix chain 'E' and resid 457 through 466 Processing helix chain 'E' and resid 478 through 489 Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'E' and resid 511 through 524 Processing helix chain 'F' and resid 93 through 103 removed outlier: 3.567A pdb=" N GLU F 99 " --> pdb=" O ARG F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 122 Processing helix chain 'F' and resid 126 through 155 Processing helix chain 'F' and resid 183 through 201 Processing helix chain 'F' and resid 210 through 214 removed outlier: 4.448A pdb=" N ASN F 213 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 235 Processing helix chain 'F' and resid 253 through 261 Processing helix chain 'F' and resid 263 through 268 removed outlier: 3.570A pdb=" N TRP F 266 " --> pdb=" O GLN F 263 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP F 267 " --> pdb=" O GLU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 281 No H-bonds generated for 'chain 'F' and resid 278 through 281' Processing helix chain 'F' and resid 321 through 328 Processing helix chain 'F' and resid 338 through 341 No H-bonds generated for 'chain 'F' and resid 338 through 341' Processing helix chain 'F' and resid 353 through 364 Processing helix chain 'F' and resid 369 through 375 removed outlier: 4.660A pdb=" N PHE F 375 " --> pdb=" O GLU F 371 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 250 through 253 removed outlier: 9.192A pdb=" N ILE A 251 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR A 195 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU A 253 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA A 197 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY A 148 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N MET A 194 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 150 " --> pdb=" O MET A 194 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE A 196 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASN A 152 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA A 154 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER A 36 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A 15 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 38 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 250 through 253 removed outlier: 9.007A pdb=" N ILE B 251 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR B 195 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU B 253 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA B 197 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY B 148 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N MET B 194 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE B 150 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE B 196 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASN B 152 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER B 36 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE B 15 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL B 38 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 250 through 253 removed outlier: 9.016A pdb=" N ILE C 251 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR C 195 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU C 253 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA C 197 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY C 148 " --> pdb=" O ARG C 192 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N MET C 194 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE C 150 " --> pdb=" O MET C 194 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE C 196 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN C 152 " --> pdb=" O ILE C 196 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA C 154 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER C 36 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE C 15 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL C 38 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 250 through 253 removed outlier: 9.001A pdb=" N ILE D 251 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR D 195 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU D 253 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA D 197 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY D 148 " --> pdb=" O ARG D 192 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N MET D 194 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE D 150 " --> pdb=" O MET D 194 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE D 196 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN D 152 " --> pdb=" O ILE D 196 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA D 154 " --> pdb=" O PRO D 198 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER D 36 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE D 15 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL D 38 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 336 through 341 Processing sheet with id= F, first strand: chain 'E' and resid 406 through 408 removed outlier: 6.813A pdb=" N ARG E 494 " --> pdb=" O VAL E 407 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 442 through 445 Processing sheet with id= H, first strand: chain 'F' and resid 242 through 246 removed outlier: 6.430A pdb=" N TYR F 307 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP F 208 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE F 309 " --> pdb=" O ASP F 208 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA F 332 " --> pdb=" O TYR F 289 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1779 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 7.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2497 1.32 - 1.44: 4153 1.44 - 1.56: 8601 1.56 - 1.69: 146 1.69 - 1.81: 108 Bond restraints: 15505 Sorted by residual: bond pdb=" C3N NAD B 301 " pdb=" C4N NAD B 301 " ideal model delta sigma weight residual 1.390 1.486 -0.096 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C3N NAD D 301 " pdb=" C4N NAD D 301 " ideal model delta sigma weight residual 1.390 1.486 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C3N NAD A 301 " pdb=" C4N NAD A 301 " ideal model delta sigma weight residual 1.390 1.486 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C3N NAD C 301 " pdb=" C4N NAD C 301 " ideal model delta sigma weight residual 1.390 1.486 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C4N NAD C 301 " pdb=" C5N NAD C 301 " ideal model delta sigma weight residual 1.384 1.471 -0.087 2.00e-02 2.50e+03 1.90e+01 ... (remaining 15500 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.10: 736 106.10 - 113.08: 8558 113.08 - 120.06: 5485 120.06 - 127.04: 6243 127.04 - 134.02: 310 Bond angle restraints: 21332 Sorted by residual: angle pdb=" N PHE F 97 " pdb=" CA PHE F 97 " pdb=" C PHE F 97 " ideal model delta sigma weight residual 111.07 105.72 5.35 1.07e+00 8.73e-01 2.50e+01 angle pdb=" CA PHE F 97 " pdb=" CB PHE F 97 " pdb=" CG PHE F 97 " ideal model delta sigma weight residual 113.80 117.89 -4.09 1.00e+00 1.00e+00 1.68e+01 angle pdb=" N TRP F 101 " pdb=" CA TRP F 101 " pdb=" C TRP F 101 " ideal model delta sigma weight residual 111.36 106.97 4.39 1.09e+00 8.42e-01 1.62e+01 angle pdb=" CA TRP F 101 " pdb=" C TRP F 101 " pdb=" O TRP F 101 " ideal model delta sigma weight residual 120.42 116.16 4.26 1.06e+00 8.90e-01 1.61e+01 angle pdb=" CA PHE F 97 " pdb=" C PHE F 97 " pdb=" O PHE F 97 " ideal model delta sigma weight residual 120.82 117.39 3.43 1.05e+00 9.07e-01 1.07e+01 ... (remaining 21327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.90: 9138 30.90 - 61.80: 307 61.80 - 92.71: 79 92.71 - 123.61: 0 123.61 - 154.51: 1 Dihedral angle restraints: 9525 sinusoidal: 4522 harmonic: 5003 Sorted by residual: dihedral pdb=" O4' U T 50 " pdb=" C1' U T 50 " pdb=" N1 U T 50 " pdb=" C2 U T 50 " ideal model delta sinusoidal sigma weight residual 200.00 45.49 154.51 1 1.50e+01 4.44e-03 8.12e+01 dihedral pdb=" CA GLU C 232 " pdb=" C GLU C 232 " pdb=" N TYR C 233 " pdb=" CA TYR C 233 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA LEU F 182 " pdb=" C LEU F 182 " pdb=" N TRP F 183 " pdb=" CA TRP F 183 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 9522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2008 0.044 - 0.088: 330 0.088 - 0.132: 134 0.132 - 0.176: 4 0.176 - 0.219: 5 Chirality restraints: 2481 Sorted by residual: chirality pdb=" CA PHE F 97 " pdb=" N PHE F 97 " pdb=" C PHE F 97 " pdb=" CB PHE F 97 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1D NAD D 301 " pdb=" C2D NAD D 301 " pdb=" N1N NAD D 301 " pdb=" O4D NAD D 301 " both_signs ideal model delta sigma weight residual False 2.41 2.63 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C1D NAD C 301 " pdb=" C2D NAD C 301 " pdb=" N1N NAD C 301 " pdb=" O4D NAD C 301 " both_signs ideal model delta sigma weight residual False 2.41 2.63 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2478 not shown) Planarity restraints: 2492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD A 301 " 0.046 2.00e-02 2.50e+03 4.57e-02 4.18e+01 pdb=" C2N NAD A 301 " -0.101 2.00e-02 2.50e+03 pdb=" C3N NAD A 301 " -0.013 2.00e-02 2.50e+03 pdb=" C4N NAD A 301 " -0.007 2.00e-02 2.50e+03 pdb=" C5N NAD A 301 " 0.004 2.00e-02 2.50e+03 pdb=" C6N NAD A 301 " 0.017 2.00e-02 2.50e+03 pdb=" C7N NAD A 301 " 0.062 2.00e-02 2.50e+03 pdb=" N1N NAD A 301 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD C 301 " -0.055 2.00e-02 2.50e+03 4.03e-02 3.25e+01 pdb=" C2N NAD C 301 " 0.089 2.00e-02 2.50e+03 pdb=" C3N NAD C 301 " 0.005 2.00e-02 2.50e+03 pdb=" C4N NAD C 301 " -0.025 2.00e-02 2.50e+03 pdb=" C5N NAD C 301 " 0.002 2.00e-02 2.50e+03 pdb=" C6N NAD C 301 " 0.012 2.00e-02 2.50e+03 pdb=" C7N NAD C 301 " -0.036 2.00e-02 2.50e+03 pdb=" N1N NAD C 301 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 301 " -0.028 2.00e-02 2.50e+03 2.75e-02 1.52e+01 pdb=" C2N NAD B 301 " 0.063 2.00e-02 2.50e+03 pdb=" C3N NAD B 301 " 0.005 2.00e-02 2.50e+03 pdb=" C4N NAD B 301 " 0.000 2.00e-02 2.50e+03 pdb=" C5N NAD B 301 " 0.002 2.00e-02 2.50e+03 pdb=" C6N NAD B 301 " -0.010 2.00e-02 2.50e+03 pdb=" C7N NAD B 301 " -0.035 2.00e-02 2.50e+03 pdb=" N1N NAD B 301 " 0.002 2.00e-02 2.50e+03 ... (remaining 2489 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 56 2.49 - 3.09: 10746 3.09 - 3.70: 23265 3.70 - 4.30: 36528 4.30 - 4.90: 58736 Nonbonded interactions: 129331 Sorted by model distance: nonbonded pdb=" OD2 ASP A 41 " pdb=" O3B NAD A 301 " model vdw 1.890 2.440 nonbonded pdb=" OH TYR B 168 " pdb=" O2D NAD B 301 " model vdw 1.968 2.440 nonbonded pdb=" OH TYR F 211 " pdb=" OH TYR F 289 " model vdw 2.005 2.440 nonbonded pdb=" OD2 ASP C 41 " pdb=" O3B NAD C 301 " model vdw 2.067 2.440 nonbonded pdb=" OD2 ASP A 64 " pdb=" OG1 THR A 66 " model vdw 2.083 2.440 ... (remaining 129326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.72 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: 14.630 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: 21.230 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 52.300 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 15505 Z= 0.283 Angle : 0.585 7.104 21332 Z= 0.298 Chirality : 0.040 0.219 2481 Planarity : 0.005 0.056 2492 Dihedral : 16.016 154.509 6315 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.20), residues: 1749 helix: 1.26 (0.17), residues: 893 sheet: -0.49 (0.35), residues: 198 loop : -0.54 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 101 HIS 0.004 0.001 HIS F 242 PHE 0.019 0.001 PHE F 97 TYR 0.012 0.001 TYR F 289 ARG 0.003 0.000 ARG E 541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 1.820 Fit side-chains REVERT: A 116 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8389 (ttm170) REVERT: B 212 LYS cc_start: 0.5080 (tttt) cc_final: 0.4435 (mmpt) REVERT: D 142 ASP cc_start: 0.6980 (t70) cc_final: 0.6691 (p0) REVERT: E 552 THR cc_start: 0.7539 (m) cc_final: 0.7240 (p) outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 1.5352 time to fit residues: 385.8602 Evaluate side-chains 143 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 97 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 54 optimal weight: 0.2980 chunk 85 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN B 146 GLN B 220 GLN C 260 GLN D 220 GLN E 222 HIS E 540 GLN F 147 GLN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15505 Z= 0.266 Angle : 0.552 10.410 21332 Z= 0.281 Chirality : 0.041 0.146 2481 Planarity : 0.005 0.052 2492 Dihedral : 15.266 153.740 3101 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.94 % Allowed : 7.77 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.20), residues: 1749 helix: 1.56 (0.18), residues: 884 sheet: -0.33 (0.35), residues: 196 loop : -0.38 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 326 HIS 0.004 0.001 HIS F 242 PHE 0.015 0.001 PHE E 518 TYR 0.015 0.001 TYR E 484 ARG 0.010 0.000 ARG E 384 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 1.785 Fit side-chains REVERT: C 143 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6562 (mm-40) REVERT: E 384 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7476 (ttp-170) REVERT: E 552 THR cc_start: 0.7584 (m) cc_final: 0.7245 (p) REVERT: F 188 ASP cc_start: 0.7355 (m-30) cc_final: 0.7011 (m-30) REVERT: F 318 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7454 (tm-30) outliers start: 28 outliers final: 10 residues processed: 160 average time/residue: 1.4386 time to fit residues: 251.5280 Evaluate side-chains 152 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 141 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 339 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 135 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 162 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN D 220 GLN E 540 GLN E 580 HIS ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 15505 Z= 0.171 Angle : 0.476 11.169 21332 Z= 0.242 Chirality : 0.038 0.130 2481 Planarity : 0.005 0.051 2492 Dihedral : 15.047 153.739 3101 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.53 % Allowed : 10.55 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.20), residues: 1749 helix: 1.84 (0.17), residues: 884 sheet: -0.18 (0.35), residues: 196 loop : -0.25 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 326 HIS 0.003 0.001 HIS E 580 PHE 0.009 0.001 PHE F 241 TYR 0.010 0.001 TYR E 484 ARG 0.006 0.000 ARG C 226 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6554 (mm-40) REVERT: E 531 ARG cc_start: 0.6540 (pmt170) cc_final: 0.5239 (mtm-85) REVERT: E 552 THR cc_start: 0.7472 (m) cc_final: 0.7219 (p) REVERT: E 571 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6722 (pt0) REVERT: F 97 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8314 (t80) REVERT: F 188 ASP cc_start: 0.7532 (m-30) cc_final: 0.7263 (m-30) outliers start: 22 outliers final: 7 residues processed: 152 average time/residue: 1.4043 time to fit residues: 234.4836 Evaluate side-chains 142 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 109 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN C 102 ASN D 127 ASN D 152 ASN D 220 GLN E 580 HIS ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15505 Z= 0.275 Angle : 0.538 12.574 21332 Z= 0.273 Chirality : 0.040 0.137 2481 Planarity : 0.005 0.052 2492 Dihedral : 15.064 154.816 3101 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.36 % Allowed : 11.45 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.20), residues: 1749 helix: 1.66 (0.17), residues: 886 sheet: -0.15 (0.35), residues: 196 loop : -0.21 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 326 HIS 0.004 0.001 HIS D 109 PHE 0.014 0.002 PHE E 518 TYR 0.016 0.001 TYR E 484 ARG 0.005 0.000 ARG C 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 1.689 Fit side-chains revert: symmetry clash REVERT: C 143 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6589 (mm-40) REVERT: D 185 ASP cc_start: 0.7854 (m-30) cc_final: 0.7630 (m-30) REVERT: E 531 ARG cc_start: 0.6562 (OUTLIER) cc_final: 0.5292 (mtm-85) REVERT: E 552 THR cc_start: 0.7327 (m) cc_final: 0.6956 (p) REVERT: E 571 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6770 (pt0) outliers start: 34 outliers final: 13 residues processed: 161 average time/residue: 1.3975 time to fit residues: 246.9224 Evaluate side-chains 153 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 531 ARG Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 2 optimal weight: 0.0770 chunk 128 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 chunk 147 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 0.0270 chunk 155 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN C 50 GLN D 220 GLN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15505 Z= 0.136 Angle : 0.453 14.262 21332 Z= 0.228 Chirality : 0.038 0.129 2481 Planarity : 0.004 0.049 2492 Dihedral : 14.757 153.703 3099 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.46 % Allowed : 12.63 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.20), residues: 1749 helix: 1.94 (0.17), residues: 885 sheet: -0.02 (0.36), residues: 196 loop : -0.16 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 326 HIS 0.003 0.001 HIS E 504 PHE 0.015 0.001 PHE F 97 TYR 0.009 0.001 TYR E 213 ARG 0.007 0.000 ARG C 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 107 GLN cc_start: 0.7880 (tt0) cc_final: 0.7570 (tt0) REVERT: C 123 MET cc_start: 0.7640 (tmm) cc_final: 0.7363 (ttp) REVERT: C 143 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6518 (mm-40) REVERT: D 226 ARG cc_start: 0.8278 (ptm-80) cc_final: 0.7931 (ptm160) REVERT: E 531 ARG cc_start: 0.6470 (pmt170) cc_final: 0.5344 (mtm-85) REVERT: E 571 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6792 (pt0) outliers start: 21 outliers final: 11 residues processed: 156 average time/residue: 1.4854 time to fit residues: 253.5797 Evaluate side-chains 142 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN D 220 GLN F 147 GLN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 15505 Z= 0.308 Angle : 0.546 14.126 21332 Z= 0.274 Chirality : 0.041 0.131 2481 Planarity : 0.005 0.048 2492 Dihedral : 14.930 155.132 3099 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.29 % Allowed : 12.77 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1749 helix: 1.66 (0.17), residues: 887 sheet: -0.07 (0.35), residues: 196 loop : -0.21 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 556 HIS 0.004 0.001 HIS D 109 PHE 0.020 0.002 PHE F 97 TYR 0.017 0.001 TYR E 484 ARG 0.007 0.001 ARG C 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6879 (tp30) REVERT: B 107 GLN cc_start: 0.7909 (tt0) cc_final: 0.7577 (tt0) REVERT: C 143 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6637 (mm-40) REVERT: D 185 ASP cc_start: 0.7835 (m-30) cc_final: 0.7603 (m-30) REVERT: D 206 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6422 (tt) REVERT: E 147 GLN cc_start: 0.8278 (mt0) cc_final: 0.8023 (mt0) REVERT: E 148 MET cc_start: 0.7635 (mtm) cc_final: 0.7199 (mtp) REVERT: E 531 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.5496 (mtm-85) REVERT: E 571 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6767 (pt0) REVERT: F 188 ASP cc_start: 0.7509 (m-30) cc_final: 0.7181 (m-30) outliers start: 33 outliers final: 12 residues processed: 153 average time/residue: 1.3783 time to fit residues: 232.0782 Evaluate side-chains 151 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 531 ARG Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 0.3980 chunk 19 optimal weight: 0.1980 chunk 98 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 105 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15505 Z= 0.149 Angle : 0.464 14.352 21332 Z= 0.231 Chirality : 0.038 0.129 2481 Planarity : 0.004 0.049 2492 Dihedral : 14.729 153.908 3099 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.97 % Allowed : 14.37 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1749 helix: 1.90 (0.17), residues: 887 sheet: -0.03 (0.35), residues: 196 loop : -0.16 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 326 HIS 0.004 0.001 HIS E 504 PHE 0.018 0.001 PHE F 97 TYR 0.008 0.001 TYR E 484 ARG 0.007 0.000 ARG C 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.657 Fit side-chains revert: symmetry clash REVERT: B 107 GLN cc_start: 0.7838 (tt0) cc_final: 0.7513 (tt0) REVERT: E 148 MET cc_start: 0.7513 (mtm) cc_final: 0.7042 (mtp) REVERT: E 466 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6586 (mt0) REVERT: E 531 ARG cc_start: 0.6491 (pmt170) cc_final: 0.5488 (mtm-85) REVERT: F 187 MET cc_start: 0.8558 (mtt) cc_final: 0.8179 (mtt) outliers start: 14 outliers final: 5 residues processed: 143 average time/residue: 1.4451 time to fit residues: 225.9795 Evaluate side-chains 139 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain E residue 137 LYS Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 0.0980 chunk 85 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN C 162 GLN D 152 ASN D 220 GLN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15505 Z= 0.246 Angle : 0.515 14.660 21332 Z= 0.257 Chirality : 0.039 0.127 2481 Planarity : 0.005 0.048 2492 Dihedral : 14.816 154.673 3099 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.46 % Allowed : 14.57 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1749 helix: 1.76 (0.17), residues: 887 sheet: -0.05 (0.35), residues: 196 loop : -0.15 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 326 HIS 0.004 0.001 HIS E 504 PHE 0.012 0.001 PHE E 397 TYR 0.015 0.001 TYR E 484 ARG 0.007 0.000 ARG C 226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 2.128 Fit side-chains revert: symmetry clash REVERT: B 107 GLN cc_start: 0.7891 (tt0) cc_final: 0.7554 (tt0) REVERT: C 143 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6636 (mm-40) REVERT: E 466 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6626 (mt0) REVERT: E 531 ARG cc_start: 0.6601 (pmt170) cc_final: 0.5607 (mtm-85) REVERT: F 187 MET cc_start: 0.8593 (mtt) cc_final: 0.8223 (mtt) REVERT: F 188 ASP cc_start: 0.7485 (m-30) cc_final: 0.7143 (m-30) outliers start: 21 outliers final: 11 residues processed: 155 average time/residue: 1.4287 time to fit residues: 242.2621 Evaluate side-chains 147 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 152 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15505 Z= 0.169 Angle : 0.478 14.227 21332 Z= 0.238 Chirality : 0.038 0.128 2481 Planarity : 0.004 0.049 2492 Dihedral : 14.733 154.090 3099 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.90 % Allowed : 15.48 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1749 helix: 1.87 (0.17), residues: 887 sheet: -0.02 (0.35), residues: 196 loop : -0.12 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 326 HIS 0.003 0.001 HIS E 504 PHE 0.020 0.001 PHE F 97 TYR 0.010 0.001 TYR E 484 ARG 0.007 0.000 ARG C 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.665 Fit side-chains revert: symmetry clash REVERT: B 107 GLN cc_start: 0.7868 (tt0) cc_final: 0.7534 (tt0) REVERT: E 148 MET cc_start: 0.7561 (mtm) cc_final: 0.7073 (mtp) REVERT: E 466 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6642 (mt0) REVERT: E 531 ARG cc_start: 0.6580 (pmt170) cc_final: 0.5601 (mtm-85) REVERT: F 188 ASP cc_start: 0.7484 (m-30) cc_final: 0.7160 (m-30) outliers start: 13 outliers final: 8 residues processed: 143 average time/residue: 1.4295 time to fit residues: 224.4223 Evaluate side-chains 147 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 142 optimal weight: 0.0870 chunk 14 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 chunk 87 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN D 220 GLN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15505 Z= 0.149 Angle : 0.464 13.873 21332 Z= 0.230 Chirality : 0.037 0.128 2481 Planarity : 0.004 0.049 2492 Dihedral : 14.623 153.721 3099 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.69 % Allowed : 15.82 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1749 helix: 1.99 (0.17), residues: 886 sheet: 0.03 (0.36), residues: 195 loop : -0.04 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 143 HIS 0.003 0.001 HIS E 504 PHE 0.017 0.001 PHE F 97 TYR 0.009 0.001 TYR E 484 ARG 0.007 0.000 ARG C 226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.750 Fit side-chains REVERT: B 107 GLN cc_start: 0.7821 (tt0) cc_final: 0.7494 (tt0) REVERT: C 143 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6631 (mm-40) REVERT: D 194 MET cc_start: 0.9118 (mmm) cc_final: 0.8880 (mmm) REVERT: E 466 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.6585 (mt0) REVERT: E 531 ARG cc_start: 0.6468 (pmt170) cc_final: 0.5576 (mtm-85) outliers start: 10 outliers final: 5 residues processed: 145 average time/residue: 1.5382 time to fit residues: 243.6057 Evaluate side-chains 137 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 0.0970 chunk 130 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 59 optimal weight: 0.2980 chunk 146 optimal weight: 0.0030 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN E 312 GLN E 412 ASN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113741 restraints weight = 20717.016| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.40 r_work: 0.3189 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15505 Z= 0.134 Angle : 0.449 13.321 21332 Z= 0.223 Chirality : 0.037 0.127 2481 Planarity : 0.004 0.049 2492 Dihedral : 14.533 153.443 3099 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.90 % Allowed : 16.38 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.20), residues: 1749 helix: 2.09 (0.17), residues: 886 sheet: 0.08 (0.36), residues: 195 loop : 0.01 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 143 HIS 0.003 0.001 HIS E 504 PHE 0.016 0.001 PHE F 97 TYR 0.008 0.001 TYR E 213 ARG 0.007 0.000 ARG C 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5120.40 seconds wall clock time: 92 minutes 57.47 seconds (5577.47 seconds total)