Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 16:40:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onu_13002/10_2023/7onu_13002_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onu_13002/10_2023/7onu_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_13002/10_2023/7onu_13002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onu_13002/10_2023/7onu_13002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onu_13002/10_2023/7onu_13002_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onu_13002/10_2023/7onu_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-1.21rc1-5097/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: 8.40, per 1000 atoms: 0.56 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: 6.06 Conformation dependent library (CDL) restraints added in 2.1 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: 6.34 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: 4.90 Time building geometry restraints manager: 6.46 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: 8866 30.90 - 61.80: 210 61.80 - 92.71: 32 92.71 - 123.61: 0 123.61 - 154.51: 1 Dihedral angle restraints: 9109 sinusoidal: 4106 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 9106 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: 2.920 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: 0.020 Extract box with map and model: 14.190 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 48.590 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 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:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.590 ------------------------------------------------------------------------------- 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 : 13.960 154.509 5899 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 *********************** 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 : 1.513 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 1.5150 time to fit residues: 381.1094 Evaluate side-chains 136 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.643 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.1775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 540 GLN F 147 GLN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15505 Z= 0.263 Angle : 0.550 10.181 21332 Z= 0.279 Chirality : 0.041 0.146 2481 Planarity : 0.005 0.052 2492 Dihedral : 10.434 153.797 2683 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.01 % Allowed : 8.05 % Favored : 89.94 % 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: 0.87 (0.20), residues: 1749 helix: 1.56 (0.18), residues: 884 sheet: -0.32 (0.35), residues: 196 loop : -0.39 (0.23), residues: 669 *********************** 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 168 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 1.615 Fit side-chains outliers start: 29 outliers final: 12 residues processed: 156 average time/residue: 1.4354 time to fit residues: 245.1720 Evaluate side-chains 152 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.962 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.4344 time to fit residues: 4.1112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0870 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 162 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 145 optimal weight: 0.0770 chunk 161 optimal weight: 0.0170 chunk 55 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.2352 ------------------------------------------------------------------------------- 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 E 540 GLN E 580 HIS ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1582 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= 0.134 Angle : 0.453 10.510 21332 Z= 0.230 Chirality : 0.038 0.130 2481 Planarity : 0.005 0.052 2492 Dihedral : 10.217 153.769 2683 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.53 % Allowed : 10.20 % Favored : 88.27 % 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: 1.34 (0.20), residues: 1749 helix: 1.97 (0.17), residues: 885 sheet: -0.10 (0.36), residues: 196 loop : -0.22 (0.23), residues: 668 *********************** 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 179 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 1.746 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 172 average time/residue: 1.4033 time to fit residues: 265.0496 Evaluate side-chains 143 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 1.699 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 3 average time/residue: 0.1896 time to fit residues: 3.1153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 3.9990 chunk 122 optimal weight: 0.0770 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 77 optimal weight: 0.0970 chunk 109 optimal weight: 0.5980 chunk 163 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN D 127 ASN D 152 ASN D 220 GLN E 437 ASN E 580 HIS F 147 GLN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15505 Z= 0.146 Angle : 0.460 14.178 21332 Z= 0.229 Chirality : 0.038 0.128 2481 Planarity : 0.005 0.051 2492 Dihedral : 10.112 153.691 2683 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.01 % Allowed : 11.17 % Favored : 86.81 % 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: 1.49 (0.20), residues: 1749 helix: 2.07 (0.17), residues: 885 sheet: 0.08 (0.36), residues: 195 loop : -0.15 (0.24), residues: 669 *********************** 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 168 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 1.550 Fit side-chains outliers start: 29 outliers final: 11 residues processed: 159 average time/residue: 1.3483 time to fit residues: 235.7068 Evaluate side-chains 147 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 1.448 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 2 average time/residue: 0.8516 time to fit residues: 4.0985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 2 optimal weight: 0.0030 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 147 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN D 152 ASN D 220 GLN E 580 HIS ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15505 Z= 0.181 Angle : 0.478 14.503 21332 Z= 0.236 Chirality : 0.038 0.127 2481 Planarity : 0.004 0.049 2492 Dihedral : 10.194 154.405 2683 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.46 % Allowed : 12.56 % Favored : 85.98 % 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: 1.45 (0.20), residues: 1749 helix: 2.00 (0.17), residues: 886 sheet: 0.09 (0.36), residues: 195 loop : -0.11 (0.24), residues: 668 *********************** 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 159 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 1.594 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 152 average time/residue: 1.4104 time to fit residues: 235.7726 Evaluate side-chains 145 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.577 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 4 average time/residue: 0.7641 time to fit residues: 5.7153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 220 GLN E 580 HIS F 147 GLN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15505 Z= 0.285 Angle : 0.536 14.549 21332 Z= 0.267 Chirality : 0.040 0.126 2481 Planarity : 0.005 0.048 2492 Dihedral : 10.385 155.187 2683 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.67 % Allowed : 13.25 % Favored : 85.08 % 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: 1.22 (0.20), residues: 1749 helix: 1.75 (0.17), residues: 887 sheet: 0.02 (0.36), residues: 196 loop : -0.14 (0.24), residues: 666 *********************** 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 157 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.789 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 147 average time/residue: 1.3755 time to fit residues: 222.6797 Evaluate side-chains 141 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 3 average time/residue: 0.8694 time to fit residues: 5.0754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 105 optimal weight: 0.1980 chunk 79 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN D 220 GLN E 466 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: 0.7761 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15505 Z= 0.188 Angle : 0.484 14.275 21332 Z= 0.241 Chirality : 0.038 0.128 2481 Planarity : 0.004 0.048 2492 Dihedral : 10.329 154.691 2683 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.60 % Allowed : 13.25 % Favored : 85.15 % 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: 1.31 (0.20), residues: 1749 helix: 1.84 (0.17), residues: 886 sheet: 0.00 (0.36), residues: 195 loop : -0.10 (0.24), residues: 668 *********************** 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 158 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 151 average time/residue: 1.3591 time to fit residues: 225.9282 Evaluate side-chains 143 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.572 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.1815 time to fit residues: 2.3890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN C 102 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 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: 0.7783 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15505 Z= 0.244 Angle : 0.516 14.986 21332 Z= 0.257 Chirality : 0.039 0.127 2481 Planarity : 0.004 0.048 2492 Dihedral : 10.331 154.865 2683 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.39 % Allowed : 14.09 % Favored : 84.52 % 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: 1.22 (0.20), residues: 1749 helix: 1.75 (0.17), residues: 886 sheet: -0.07 (0.35), residues: 196 loop : -0.11 (0.24), residues: 667 *********************** 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 151 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.539 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 146 average time/residue: 1.4203 time to fit residues: 228.3769 Evaluate side-chains 141 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.550 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.8801 time to fit residues: 5.1782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 160 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 170 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN C 162 GLN D 220 GLN E 466 GLN E 580 HIS ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15505 Z= 0.178 Angle : 0.481 14.432 21332 Z= 0.239 Chirality : 0.038 0.128 2481 Planarity : 0.004 0.048 2492 Dihedral : 10.256 154.528 2683 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.39 % Allowed : 14.09 % Favored : 84.52 % 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: 1.34 (0.20), residues: 1749 helix: 1.87 (0.17), residues: 886 sheet: -0.03 (0.35), residues: 195 loop : -0.07 (0.24), residues: 668 *********************** 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 154 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.562 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 151 average time/residue: 1.3920 time to fit residues: 231.0427 Evaluate side-chains 144 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.603 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.2915 time to fit residues: 2.4774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN D 152 ASN D 220 GLN E 580 HIS F 147 GLN ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15505 Z= 0.220 Angle : 0.504 14.719 21332 Z= 0.251 Chirality : 0.039 0.144 2481 Planarity : 0.004 0.048 2492 Dihedral : 10.289 154.710 2683 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.11 % Allowed : 14.50 % Favored : 84.39 % 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: 1.26 (0.20), residues: 1749 helix: 1.79 (0.17), residues: 886 sheet: -0.05 (0.35), residues: 195 loop : -0.10 (0.24), residues: 668 ********************** 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 146 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.623 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 146 average time/residue: 1.4174 time to fit residues: 227.8714 Evaluate side-chains 141 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.600 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 2.1659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 0.2980 chunk 130 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 59 optimal weight: 0.0170 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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 466 GLN E 580 HIS ** F 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.112062 restraints weight = 20709.902| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.40 r_work: 0.3161 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15505 Z= 0.144 Angle : 0.465 14.056 21332 Z= 0.231 Chirality : 0.037 0.137 2481 Planarity : 0.004 0.049 2492 Dihedral : 10.188 154.199 2683 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.32 % Allowed : 14.57 % Favored : 84.11 % 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: 1.45 (0.20), residues: 1749 helix: 1.96 (0.17), residues: 886 sheet: -0.02 (0.35), residues: 195 loop : -0.03 (0.24), residues: 668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4840.63 seconds wall clock time: 87 minutes 23.15 seconds (5243.15 seconds total)