Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 13:33:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/10_2023/7tfj_25874_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/10_2023/7tfj_25874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/10_2023/7tfj_25874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/10_2023/7tfj_25874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/10_2023/7tfj_25874_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfj_25874/10_2023/7tfj_25874_updated.pdb" } resolution = 3.3 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= -0.000 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 370 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Se 18 7.20 5 P 56 5.49 5 Mg 4 5.21 5 S 81 5.16 5 C 12880 2.51 5 N 3516 2.21 5 O 4052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 376": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E GLU 302": "OE1" <-> "OE2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 189": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 20607 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3130 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 14, 'TRANS': 381} Chain breaks: 1 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 9, 'TRANS': 310} Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2615 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "D" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2622 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2685 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "F" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2021 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2014 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "H" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "I" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 449 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.56, per 1000 atoms: 0.51 Number of scatterers: 20607 At special positions: 0 Unit cell: (119.232, 122.544, 137.448, 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) Se 18 33.99 S 81 16.00 P 56 15.00 Mg 4 11.99 O 4052 8.00 N 3516 7.00 C 12880 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: 8.49 Conformation dependent library (CDL) restraints added in 2.9 seconds 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 16 sheets defined 43.6% alpha, 13.2% beta 15 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 7.16 Creating SS restraints... Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 402 through 405 No H-bonds generated for 'chain 'A' and resid 402 through 405' Processing helix chain 'A' and resid 437 through 445 Processing helix chain 'A' and resid 462 through 466 Proline residue: A 465 - end of helix No H-bonds generated for 'chain 'A' and resid 462 through 466' Processing helix chain 'A' and resid 480 through 494 Processing helix chain 'A' and resid 502 through 510 Processing helix chain 'A' and resid 514 through 527 removed outlier: 4.363A pdb=" N THR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 543 Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.689A pdb=" N ALA A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'A' and resid 574 through 584 removed outlier: 4.186A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 3.502A pdb=" N GLN A 593 " --> pdb=" O PRO A 589 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 631 removed outlier: 3.617A pdb=" N ILE A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 648 removed outlier: 3.798A pdb=" N LEU A 641 " --> pdb=" O TRP A 638 " (cutoff:3.500A) Proline residue: A 642 - end of helix Processing helix chain 'A' and resid 650 through 654 Processing helix chain 'A' and resid 669 through 690 Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 56 through 66 Processing helix chain 'B' and resid 71 through 74 No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 86 through 98 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.538A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 168 through 181 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 215 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 282 through 301 Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 75 through 78 No H-bonds generated for 'chain 'C' and resid 75 through 78' Processing helix chain 'C' and resid 90 through 102 removed outlier: 4.090A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.991A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 256 through 270 removed outlier: 4.077A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 4.021A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 311 Processing helix chain 'C' and resid 316 through 332 Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 36 through 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 43 through 54 removed outlier: 3.914A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 82 Processing helix chain 'D' and resid 88 through 91 No H-bonds generated for 'chain 'D' and resid 88 through 91' Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.823A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 147 through 162 removed outlier: 4.339A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 161 " --> pdb=" O MET D 157 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLY D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 198 through 208 Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 228 through 245 Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 265 through 276 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 297 through 308 Processing helix chain 'D' and resid 316 through 334 removed outlier: 3.773A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 106 through 118 removed outlier: 3.543A pdb=" N GLN E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 148 through 160 removed outlier: 4.016A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 291 Processing helix chain 'E' and resid 296 through 307 Processing helix chain 'E' and resid 315 through 333 Processing helix chain 'E' and resid 340 through 352 Processing helix chain 'F' and resid 10 through 19 removed outlier: 3.727A pdb=" N PHE F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 79 Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 191 through 193 No H-bonds generated for 'chain 'F' and resid 191 through 193' Processing helix chain 'F' and resid 209 through 220 removed outlier: 4.156A pdb=" N GLY F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER F 219 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.852A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 81 removed outlier: 4.689A pdb=" N CYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'G' and resid 191 through 193 No H-bonds generated for 'chain 'G' and resid 191 through 193' Processing helix chain 'G' and resid 210 through 218 removed outlier: 4.291A pdb=" N GLY G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 18 Processing helix chain 'H' and resid 72 through 81 Processing helix chain 'H' and resid 141 through 154 removed outlier: 3.748A pdb=" N LEU H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 220 removed outlier: 3.948A pdb=" N ILE H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY H 218 " --> pdb=" O ASP H 214 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER H 219 " --> pdb=" O ILE H 215 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N SER H 220 " --> pdb=" O ILE H 216 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 348 through 352 removed outlier: 6.061A pdb=" N LEU A 451 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU A 351 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU A 453 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.615A pdb=" N MET B 45 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 162 through 166 removed outlier: 3.871A pdb=" N GLY C 53 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 185 through 189 removed outlier: 4.008A pdb=" N GLY D 65 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 186 through 190 removed outlier: 6.280A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER E 90 " --> pdb=" O HIS E 93 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR E 97 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ASN E 86 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU E 83 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 2 through 6 removed outlier: 3.738A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 116 " --> pdb=" O ILE F 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 66 through 68 removed outlier: 4.481A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 157 through 160 Processing sheet with id= I, first strand: chain 'F' and resid 167 through 170 Processing sheet with id= J, first strand: chain 'G' and resid 66 through 68 removed outlier: 3.783A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR G 136 " --> pdb=" O GLU G 198 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 87 through 92 removed outlier: 3.766A pdb=" N LEU G 102 " --> pdb=" O THR G 89 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 167 through 172 removed outlier: 3.715A pdb=" N ILE G 167 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 3 through 5 Processing sheet with id= N, first strand: chain 'H' and resid 66 through 68 removed outlier: 3.546A pdb=" N VAL H 66 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN H 29 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE H 36 " --> pdb=" O GLN H 29 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS H 196 " --> pdb=" O SER H 138 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 157 through 160 Processing sheet with id= P, first strand: chain 'H' and resid 166 through 172 856 hydrogen bonds defined for protein. 2478 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 6.86 Time building geometry restraints manager: 9.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 6811 1.37 - 1.52: 8059 1.52 - 1.67: 5998 1.67 - 1.82: 115 1.82 - 1.97: 40 Bond restraints: 21023 Sorted by residual: bond pdb=" N GLU B 287 " pdb=" CA GLU B 287 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.94e+00 bond pdb=" CG GLU C 307 " pdb=" CD GLU C 307 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.78e+00 bond pdb=" N GLN E 110 " pdb=" CA GLN E 110 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.19e-02 7.06e+03 4.20e+00 bond pdb=" N ARG A 434 " pdb=" CA ARG A 434 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.49e-02 4.50e+03 3.69e+00 bond pdb=" C LYS A 550 " pdb=" N PRO A 551 " ideal model delta sigma weight residual 1.333 1.358 -0.025 1.44e-02 4.82e+03 3.01e+00 ... (remaining 21018 not shown) Histogram of bond angle deviations from ideal: 96.62 - 104.56: 414 104.56 - 112.50: 11287 112.50 - 120.44: 8912 120.44 - 128.39: 7854 128.39 - 136.33: 134 Bond angle restraints: 28601 Sorted by residual: angle pdb=" N GLU C 307 " pdb=" CA GLU C 307 " pdb=" CB GLU C 307 " ideal model delta sigma weight residual 110.28 118.10 -7.82 1.55e+00 4.16e-01 2.54e+01 angle pdb=" CA ARG E 106 " pdb=" CB ARG E 106 " pdb=" CG ARG E 106 " ideal model delta sigma weight residual 114.10 122.74 -8.64 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA GLU C 307 " pdb=" CB GLU C 307 " pdb=" CG GLU C 307 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" N VAL A 401 " pdb=" CA VAL A 401 " pdb=" C VAL A 401 " ideal model delta sigma weight residual 112.96 109.23 3.73 1.00e+00 1.00e+00 1.39e+01 angle pdb=" C GLU A 293 " pdb=" N GLU A 294 " pdb=" CA GLU A 294 " ideal model delta sigma weight residual 122.61 128.22 -5.61 1.56e+00 4.11e-01 1.29e+01 ... (remaining 28596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.79: 12253 30.79 - 61.58: 458 61.58 - 92.37: 22 92.37 - 123.17: 1 123.17 - 153.96: 2 Dihedral angle restraints: 12736 sinusoidal: 5472 harmonic: 7264 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 -178.91 118.91 1 2.00e+01 2.50e-03 3.56e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 86.23 -153.96 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C4' DT J 19 " pdb=" C3' DT J 19 " pdb=" O3' DT J 19 " pdb=" P DA J 20 " ideal model delta sinusoidal sigma weight residual 220.00 85.93 134.07 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 12733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2314 0.037 - 0.075: 759 0.075 - 0.112: 204 0.112 - 0.150: 48 0.150 - 0.187: 5 Chirality restraints: 3330 Sorted by residual: chirality pdb=" CA ASP D 178 " pdb=" N ASP D 178 " pdb=" C ASP D 178 " pdb=" CB ASP D 178 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA PHE H 19 " pdb=" N PHE H 19 " pdb=" C PHE H 19 " pdb=" CB PHE H 19 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" CB THR H 193 " pdb=" CA THR H 193 " pdb=" OG1 THR H 193 " pdb=" CG2 THR H 193 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 3327 not shown) Planarity restraints: 3483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA H 251 " 0.088 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO H 252 " -0.228 5.00e-02 4.00e+02 pdb=" CA PRO H 252 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO H 252 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " 0.061 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO E 63 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 680 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C TYR A 680 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR A 680 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 681 " 0.014 2.00e-02 2.50e+03 ... (remaining 3480 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 304 2.65 - 3.21: 19017 3.21 - 3.78: 32119 3.78 - 4.34: 44249 4.34 - 4.90: 72632 Nonbonded interactions: 168321 Sorted by model distance: nonbonded pdb=" OG1 THR D 72 " pdb="MG MG D 402 " model vdw 2.088 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.105 2.170 nonbonded pdb=" OG1 THR A 360 " pdb="MG MG A 902 " model vdw 2.142 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.151 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.164 2.170 ... (remaining 168316 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 'F' and resid 1 through 254) selection = (chain 'G' and resid 1 through 254) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 14.150 Check model and map are aligned: 0.370 Set scattering table: 0.180 Process input model: 56.720 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.070 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 0.003 0.079 21023 Z= 0.208 Angle : 0.623 10.361 28601 Z= 0.330 Chirality : 0.041 0.187 3330 Planarity : 0.005 0.132 3483 Dihedral : 14.872 153.957 8008 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.09 % Allowed : 0.50 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2466 helix: 1.09 (0.16), residues: 1127 sheet: -0.35 (0.25), residues: 469 loop : -0.77 (0.21), residues: 870 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 367 time to evaluate : 2.419 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 368 average time/residue: 0.3428 time to fit residues: 192.1467 Evaluate side-chains 282 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 281 time to evaluate : 2.475 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2281 time to fit residues: 3.7337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 119 optimal weight: 0.0060 chunk 145 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21023 Z= 0.169 Angle : 0.534 11.121 28601 Z= 0.275 Chirality : 0.039 0.147 3330 Planarity : 0.004 0.079 3483 Dihedral : 13.514 154.335 3117 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.95 % Allowed : 7.93 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2466 helix: 1.41 (0.16), residues: 1124 sheet: -0.22 (0.26), residues: 449 loop : -0.73 (0.20), residues: 893 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 318 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 330 average time/residue: 0.3595 time to fit residues: 177.7149 Evaluate side-chains 298 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 283 time to evaluate : 2.372 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1919 time to fit residues: 8.5619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 126 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 245 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 225 optimal weight: 20.0000 chunk 77 optimal weight: 0.5980 chunk 182 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN D 124 HIS ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN G 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21023 Z= 0.338 Angle : 0.592 8.325 28601 Z= 0.304 Chirality : 0.042 0.169 3330 Planarity : 0.004 0.062 3483 Dihedral : 13.989 163.372 3117 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.50 % Allowed : 11.51 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2466 helix: 1.18 (0.16), residues: 1134 sheet: -0.41 (0.24), residues: 489 loop : -0.71 (0.21), residues: 843 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 288 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 22 residues processed: 308 average time/residue: 0.3583 time to fit residues: 165.0567 Evaluate side-chains 290 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 268 time to evaluate : 2.405 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1854 time to fit residues: 10.9583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 224 optimal weight: 7.9990 chunk 170 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 216 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21023 Z= 0.177 Angle : 0.516 9.030 28601 Z= 0.265 Chirality : 0.039 0.152 3330 Planarity : 0.004 0.053 3483 Dihedral : 13.826 157.182 3117 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.13 % Allowed : 12.74 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2466 helix: 1.47 (0.16), residues: 1125 sheet: -0.40 (0.23), residues: 497 loop : -0.61 (0.21), residues: 844 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 295 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 309 average time/residue: 0.3576 time to fit residues: 166.8890 Evaluate side-chains 278 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 265 time to evaluate : 2.425 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1934 time to fit residues: 8.0200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 201 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 206 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS E 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 21023 Z= 0.414 Angle : 0.632 7.870 28601 Z= 0.323 Chirality : 0.043 0.214 3330 Planarity : 0.004 0.049 3483 Dihedral : 14.170 164.039 3117 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.63 % Allowed : 14.60 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2466 helix: 1.06 (0.16), residues: 1138 sheet: -0.53 (0.23), residues: 507 loop : -0.74 (0.21), residues: 821 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 282 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 24 residues processed: 302 average time/residue: 0.3666 time to fit residues: 167.5344 Evaluate side-chains 292 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 268 time to evaluate : 2.661 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2328 time to fit residues: 14.1383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 81 optimal weight: 1.9990 chunk 217 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 241 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 126 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS B 146 GLN ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN D 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21023 Z= 0.181 Angle : 0.530 8.198 28601 Z= 0.272 Chirality : 0.039 0.172 3330 Planarity : 0.004 0.046 3483 Dihedral : 13.957 156.116 3117 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.82 % Allowed : 16.09 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2466 helix: 1.39 (0.16), residues: 1117 sheet: -0.50 (0.23), residues: 500 loop : -0.65 (0.21), residues: 849 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 286 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 298 average time/residue: 0.3570 time to fit residues: 159.3793 Evaluate side-chains 272 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 265 time to evaluate : 2.491 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1898 time to fit residues: 5.5433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 233 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 136 optimal weight: 0.0970 chunk 203 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 111 optimal weight: 0.0870 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 21023 Z= 0.150 Angle : 0.508 8.389 28601 Z= 0.261 Chirality : 0.038 0.157 3330 Planarity : 0.003 0.046 3483 Dihedral : 13.771 155.595 3117 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.82 % Allowed : 17.00 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2466 helix: 1.55 (0.16), residues: 1116 sheet: -0.34 (0.23), residues: 491 loop : -0.60 (0.21), residues: 859 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 287 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 297 average time/residue: 0.3586 time to fit residues: 159.0822 Evaluate side-chains 275 residues out of total 2207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 265 time to evaluate : 2.079 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1951 time to fit residues: 6.7761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 149 optimal weight: 0.0270 chunk 96 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 153 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: