Starting phenix.real_space_refine (version: dev) on Thu Feb 23 22:22:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjf_25924/02_2023/7tjf_25924_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjf_25924/02_2023/7tjf_25924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjf_25924/02_2023/7tjf_25924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjf_25924/02_2023/7tjf_25924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjf_25924/02_2023/7tjf_25924_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjf_25924/02_2023/7tjf_25924_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 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 Process input model Symmetric amino acids flipped Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 469": "OD1" <-> "OD2" Residue "C TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21125 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3897 Classifications: {'peptide': 486} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 476} Chain breaks: 4 Chain: "B" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2103 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Chain breaks: 1 Chain: "C" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4575 Classifications: {'peptide': 554} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 537} Chain breaks: 5 Chain: "D" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3536 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 3 Chain: "E" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3608 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1335 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 3, 'TRANS': 156} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 832 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 846 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Time building chain proxies: 11.51, per 1000 atoms: 0.54 Number of scatterers: 21125 At special positions: 0 Unit cell: (114.38, 127.28, 184.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 90 15.00 Mg 3 11.99 O 4341 8.00 N 3485 7.00 C 13126 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: 8.81 Conformation dependent library (CDL) restraints added in 2.6 seconds 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4520 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 121 helices and 10 sheets defined 53.1% alpha, 7.3% beta 41 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 7.09 Creating SS restraints... Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' 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 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 422 through 430 removed outlier: 4.278A pdb=" N VAL A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 Processing helix chain 'A' and resid 485 through 501 Processing helix chain 'A' and resid 521 through 533 removed outlier: 3.553A pdb=" N CYS A 524 " --> pdb=" O PRO A 521 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 528 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TRP A 529 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER A 533 " --> pdb=" O ASN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 552 Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 577 through 587 removed outlier: 3.857A pdb=" N THR A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'A' and resid 611 through 617 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 686 through 699 Processing helix chain 'A' and resid 703 through 725 Processing helix chain 'A' and resid 775 through 786 removed outlier: 3.814A pdb=" N THR A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 796 removed outlier: 3.580A pdb=" N ARG A 796 " --> pdb=" O THR A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 814 Processing helix chain 'A' and resid 822 through 835 Processing helix chain 'A' and resid 840 through 851 removed outlier: 4.943A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N THR A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 271 through 284 removed outlier: 3.634A pdb=" N GLU B 283 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 309 removed outlier: 4.254A pdb=" N LYS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 323 through 330 Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 399 through 413 removed outlier: 4.864A pdb=" N ASN B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 461 through 464 Processing helix chain 'B' and resid 467 through 473 Processing helix chain 'B' and resid 489 through 492 removed outlier: 3.877A pdb=" N PHE B 492 " --> pdb=" O GLU B 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 489 through 492' Processing helix chain 'C' and resid 17 through 19 No H-bonds generated for 'chain 'C' and resid 17 through 19' Processing helix chain 'C' and resid 51 through 91 removed outlier: 3.882A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 156 Processing helix chain 'C' and resid 186 through 189 No H-bonds generated for 'chain 'C' and resid 186 through 189' Processing helix chain 'C' and resid 191 through 194 No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.913A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS C 228 " --> pdb=" O LYS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 248 Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 272 through 287 removed outlier: 4.160A pdb=" N LYS C 275 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR C 276 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY C 277 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN C 278 " --> pdb=" O LYS C 275 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 279 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE C 281 " --> pdb=" O ASN C 278 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C 282 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 314 through 331 Processing helix chain 'C' and resid 333 through 338 removed outlier: 4.001A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 348 through 356 removed outlier: 4.068A pdb=" N ARG C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 Processing helix chain 'C' and resid 375 through 380 removed outlier: 3.518A pdb=" N SER C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 375 through 380' Processing helix chain 'C' and resid 389 through 395 removed outlier: 3.653A pdb=" N VAL C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 389 through 395' Processing helix chain 'C' and resid 402 through 415 Processing helix chain 'C' and resid 424 through 433 Processing helix chain 'C' and resid 436 through 440 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 483 through 492 Processing helix chain 'C' and resid 511 through 516 Processing helix chain 'C' and resid 520 through 529 removed outlier: 3.516A pdb=" N LEU C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 547 removed outlier: 3.846A pdb=" N THR C 547 " --> pdb=" O ALA C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.980A pdb=" N LEU C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 558 " --> pdb=" O LEU C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 570 Processing helix chain 'C' and resid 575 through 594 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 73 through 90 removed outlier: 4.510A pdb=" N ASP D 77 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N CYS D 78 " --> pdb=" O TYR D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 removed outlier: 3.800A pdb=" N GLN D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 155 Processing helix chain 'D' and resid 177 through 187 Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 229 through 240 Processing helix chain 'D' and resid 256 through 259 No H-bonds generated for 'chain 'D' and resid 256 through 259' Processing helix chain 'D' and resid 262 through 267 Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 302 through 314 Processing helix chain 'D' and resid 319 through 330 Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.565A pdb=" N SER D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 351 through 360 Processing helix chain 'D' and resid 362 through 371 Processing helix chain 'D' and resid 376 through 382 removed outlier: 3.540A pdb=" N LEU D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 382 " --> pdb=" O GLY D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 408 through 424 Processing helix chain 'D' and resid 453 through 465 removed outlier: 4.164A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 488 Processing helix chain 'D' and resid 493 through 495 No H-bonds generated for 'chain 'D' and resid 493 through 495' Processing helix chain 'D' and resid 499 through 501 No H-bonds generated for 'chain 'D' and resid 499 through 501' Processing helix chain 'D' and resid 510 through 516 Processing helix chain 'D' and resid 524 through 527 Processing helix chain 'E' and resid 12 through 21 Processing helix chain 'E' and resid 26 through 28 No H-bonds generated for 'chain 'E' and resid 26 through 28' Processing helix chain 'E' and resid 43 through 53 Processing helix chain 'E' and resid 70 through 88 Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 105 through 119 removed outlier: 4.246A pdb=" N GLN E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR E 119 " --> pdb=" O ILE E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.541A pdb=" N TYR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASN E 153 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 182 removed outlier: 4.135A pdb=" N TYR E 179 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N THR E 181 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 210 removed outlier: 5.685A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 221 removed outlier: 3.662A pdb=" N ILE E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 251 removed outlier: 6.031A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 272 Proline residue: E 267 - end of helix removed outlier: 3.894A pdb=" N ARG E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 278 No H-bonds generated for 'chain 'E' and resid 275 through 278' Processing helix chain 'E' and resid 281 through 287 Processing helix chain 'E' and resid 289 through 292 Processing helix chain 'E' and resid 326 through 340 Processing helix chain 'E' and resid 346 through 349 No H-bonds generated for 'chain 'E' and resid 346 through 349' Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 383 through 393 Processing helix chain 'E' and resid 418 through 429 Processing helix chain 'E' and resid 456 through 465 Processing helix chain 'E' and resid 471 through 475 removed outlier: 4.027A pdb=" N SER E 475 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 290 Processing helix chain 'F' and resid 296 through 312 removed outlier: 3.623A pdb=" N ASN F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N SER F 311 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG F 312 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 331 removed outlier: 3.507A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 Processing helix chain 'F' and resid 340 through 353 removed outlier: 4.362A pdb=" N VAL F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER F 348 " --> pdb=" O HIS F 344 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER F 352 " --> pdb=" O SER F 348 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 373 removed outlier: 3.659A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 385 Processing helix chain 'F' and resid 394 through 401 removed outlier: 4.228A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 429 Processing sheet with id= A, first strand: chain 'A' and resid 620 through 624 removed outlier: 6.355A pdb=" N ILE A 561 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE A 596 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL A 563 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL A 598 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 565 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 657 through 659 removed outlier: 3.637A pdb=" N SER A 646 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 879 through 881 Processing sheet with id= D, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.232A pdb=" N SER B 313 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS B 478 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 315 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 420 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL B 453 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B 422 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER B 455 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 424 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 263 through 267 removed outlier: 6.826A pdb=" N THR C 104 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU C 266 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE C 106 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 199 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N SER C 235 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET C 201 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE C 237 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE C 203 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN C 239 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE C 205 " --> pdb=" O ASN C 239 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 534 through 536 Processing sheet with id= G, first strand: chain 'D' and resid 271 through 274 removed outlier: 4.474A pdb=" N ARG D 271 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL D 212 " --> pdb=" O CYS D 246 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE D 248 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE D 214 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N CYS D 250 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE D 216 " --> pdb=" O CYS D 250 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 469 through 471 Processing sheet with id= I, first strand: chain 'E' and resid 185 through 189 removed outlier: 8.945A pdb=" N LEU E 33 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE E 166 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU E 35 " --> pdb=" O PHE E 166 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TYR E 168 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLY E 37 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N MET E 170 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR E 126 " --> pdb=" O ASN E 163 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LYS E 165 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU E 128 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE E 167 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU E 130 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR E 169 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU E 132 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 433 through 435 773 hydrogen bonds defined for protein. 2253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 7.83 Time building geometry restraints manager: 9.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3241 1.31 - 1.44: 6093 1.44 - 1.57: 11768 1.57 - 1.70: 177 1.70 - 1.83: 132 Bond restraints: 21411 Sorted by residual: bond pdb=" C PRO C 27 " pdb=" O PRO C 27 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.21e-02 6.83e+03 1.88e+01 bond pdb=" C LEU A 568 " pdb=" O LEU A 568 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.28e-02 6.10e+03 1.64e+01 bond pdb=" C ASP A 569 " pdb=" O ASP A 569 " ideal model delta sigma weight residual 1.236 1.186 0.051 1.26e-02 6.30e+03 1.62e+01 bond pdb=" C ARG D 227 " pdb=" O ARG D 227 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.26e-02 6.30e+03 1.38e+01 bond pdb=" C ARG D 227 " pdb=" N GLN D 228 " ideal model delta sigma weight residual 1.334 1.289 0.045 1.25e-02 6.40e+03 1.28e+01 ... (remaining 21406 not shown) Histogram of bond angle deviations from ideal: 95.24 - 104.18: 501 104.18 - 113.12: 11701 113.12 - 122.05: 13097 122.05 - 130.99: 3888 130.99 - 139.93: 111 Bond angle restraints: 29298 Sorted by residual: angle pdb=" CB MET A 779 " pdb=" CG MET A 779 " pdb=" SD MET A 779 " ideal model delta sigma weight residual 112.70 129.59 -16.89 3.00e+00 1.11e-01 3.17e+01 angle pdb=" C PRO C 27 " pdb=" CA PRO C 27 " pdb=" CB PRO C 27 " ideal model delta sigma weight residual 111.12 118.02 -6.90 1.29e+00 6.01e-01 2.86e+01 angle pdb=" C TYR C 26 " pdb=" CA TYR C 26 " pdb=" CB TYR C 26 " ideal model delta sigma weight residual 110.17 119.92 -9.75 1.97e+00 2.58e-01 2.45e+01 angle pdb=" CA GLU C 59 " pdb=" CB GLU C 59 " pdb=" CG GLU C 59 " ideal model delta sigma weight residual 114.10 123.80 -9.70 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CA LEU A 461 " pdb=" CB LEU A 461 " pdb=" CG LEU A 461 " ideal model delta sigma weight residual 116.30 133.25 -16.95 3.50e+00 8.16e-02 2.34e+01 ... (remaining 29293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 10551 18.16 - 36.32: 1348 36.32 - 54.48: 571 54.48 - 72.64: 109 72.64 - 90.80: 35 Dihedral angle restraints: 12614 sinusoidal: 5692 harmonic: 6922 Sorted by residual: dihedral pdb=" CA VAL E 8 " pdb=" C VAL E 8 " pdb=" N ALA E 9 " pdb=" CA ALA E 9 " ideal model delta harmonic sigma weight residual -180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LYS E 431 " pdb=" C LYS E 431 " pdb=" N LEU E 432 " pdb=" CA LEU E 432 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE B 475 " pdb=" C PHE B 475 " pdb=" N VAL B 476 " pdb=" CA VAL B 476 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 12611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2655 0.060 - 0.121: 577 0.121 - 0.181: 75 0.181 - 0.242: 12 0.242 - 0.302: 3 Chirality restraints: 3322 Sorted by residual: chirality pdb=" CB THR A 474 " pdb=" CA THR A 474 " pdb=" OG1 THR A 474 " pdb=" CG2 THR A 474 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB ILE E 326 " pdb=" CA ILE E 326 " pdb=" CG1 ILE E 326 " pdb=" CG2 ILE E 326 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB THR E 87 " pdb=" CA THR E 87 " pdb=" OG1 THR E 87 " pdb=" CG2 THR E 87 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 3319 not shown) Planarity restraints: 3392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 25 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C VAL C 25 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL C 25 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR C 26 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 332 " 0.022 2.00e-02 2.50e+03 2.44e-02 1.04e+01 pdb=" CG PHE F 332 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE F 332 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE F 332 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE F 332 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 332 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 484 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO B 485 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.041 5.00e-02 4.00e+02 ... (remaining 3389 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 115 2.42 - 3.04: 10978 3.04 - 3.66: 34312 3.66 - 4.28: 53253 4.28 - 4.90: 82399 Nonbonded interactions: 181057 Sorted by model distance: nonbonded pdb=" OD1 ASP E 136 " pdb=" O HOH E1101 " model vdw 1.795 2.440 nonbonded pdb=" O PRO B 415 " pdb=" O HOH B 701 " model vdw 1.811 2.440 nonbonded pdb=" OD1 ASP A 867 " pdb=" O HOH A1101 " model vdw 1.879 2.440 nonbonded pdb=" O ILE E 184 " pdb=" O HOH E1102 " model vdw 1.948 2.440 nonbonded pdb=" OD2 ASP B 479 " pdb=" O HOH B 702 " model vdw 1.996 2.440 ... (remaining 181052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 90 5.49 5 Mg 3 5.21 5 S 80 5.16 5 C 13126 2.51 5 N 3485 2.21 5 O 4341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.030 Extract box with map and model: 8.090 Check model and map are aligned: 0.280 Process input model: 58.310 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 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 0.073 21411 Z= 0.301 Angle : 0.868 16.948 29298 Z= 0.478 Chirality : 0.051 0.302 3322 Planarity : 0.006 0.084 3392 Dihedral : 19.490 90.804 8094 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 1.87 % 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: -1.60 (0.15), residues: 2283 helix: -1.12 (0.12), residues: 1279 sheet: 0.14 (0.32), residues: 222 loop : -1.00 (0.19), residues: 782 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 352 time to evaluate : 2.382 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 13 residues processed: 384 average time/residue: 1.6509 time to fit residues: 704.4638 Evaluate side-chains 236 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 223 time to evaluate : 2.485 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 2 average time/residue: 0.3178 time to fit residues: 4.2578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 201 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 405 GLN B 493 GLN C 253 GLN C 271 ASN C 312 HIS C 370 GLN C 532 ASN D 96 HIS D 155 GLN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 241 HIS F 307 ASN F 318 GLN F 344 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 21411 Z= 0.280 Angle : 0.571 8.814 29298 Z= 0.307 Chirality : 0.042 0.145 3322 Planarity : 0.004 0.066 3392 Dihedral : 17.932 74.625 3339 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 2.94 % 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: -0.15 (0.16), residues: 2283 helix: 0.24 (0.14), residues: 1272 sheet: 0.37 (0.32), residues: 212 loop : -0.59 (0.20), residues: 799 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 222 time to evaluate : 2.530 Fit side-chains outliers start: 63 outliers final: 26 residues processed: 266 average time/residue: 1.5776 time to fit residues: 470.6561 Evaluate side-chains 220 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 194 time to evaluate : 2.591 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 25 residues processed: 3 average time/residue: 0.3069 time to fit residues: 4.7189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 GLN D 493 GLN E 2 ASN F 307 ASN F 344 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 21411 Z= 0.259 Angle : 0.535 6.694 29298 Z= 0.289 Chirality : 0.041 0.185 3322 Planarity : 0.003 0.058 3392 Dihedral : 17.918 75.033 3339 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 3.54 % 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: 0.38 (0.17), residues: 2283 helix: 0.75 (0.14), residues: 1274 sheet: 0.33 (0.33), residues: 205 loop : -0.41 (0.21), residues: 804 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 203 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 34 residues processed: 262 average time/residue: 1.5363 time to fit residues: 453.2787 Evaluate side-chains 223 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 189 time to evaluate : 2.440 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 31 residues processed: 4 average time/residue: 0.5870 time to fit residues: 6.5286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 214 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 231 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN B 342 GLN C 271 ASN C 313 ASN C 371 HIS D 155 GLN E 2 ASN F 307 ASN F 318 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 21411 Z= 0.391 Angle : 0.585 7.733 29298 Z= 0.315 Chirality : 0.044 0.155 3322 Planarity : 0.004 0.058 3392 Dihedral : 18.071 77.490 3339 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 3.45 % 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: 2283 helix: 0.84 (0.15), residues: 1276 sheet: 0.26 (0.33), residues: 200 loop : -0.34 (0.21), residues: 807 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 200 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 40 residues processed: 257 average time/residue: 1.5277 time to fit residues: 441.6331 Evaluate side-chains 229 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 189 time to evaluate : 2.666 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 36 residues processed: 5 average time/residue: 0.4363 time to fit residues: 6.3924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 192 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 3 optimal weight: 0.0040 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 197 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN A 725 HIS C 271 ASN C 370 GLN D 155 GLN E 2 ASN F 307 ASN F 318 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 21411 Z= 0.145 Angle : 0.479 7.503 29298 Z= 0.262 Chirality : 0.038 0.141 3322 Planarity : 0.003 0.053 3392 Dihedral : 17.737 75.087 3339 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 3.03 % 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: 0.92 (0.17), residues: 2283 helix: 1.26 (0.15), residues: 1271 sheet: 0.28 (0.34), residues: 191 loop : -0.21 (0.21), residues: 821 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 200 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 39 residues processed: 252 average time/residue: 1.5075 time to fit residues: 428.7468 Evaluate side-chains 220 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 2.524 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 36 residues processed: 4 average time/residue: 1.2395 time to fit residues: 9.3369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 77 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN C 271 ASN C 313 ASN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN F 307 ASN F 318 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 21411 Z= 0.373 Angle : 0.572 7.861 29298 Z= 0.307 Chirality : 0.043 0.158 3322 Planarity : 0.003 0.056 3392 Dihedral : 17.994 75.874 3339 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 2.85 % 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: 0.84 (0.17), residues: 2283 helix: 1.17 (0.15), residues: 1277 sheet: 0.28 (0.33), residues: 200 loop : -0.23 (0.21), residues: 806 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 190 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 35 residues processed: 242 average time/residue: 1.5051 time to fit residues: 410.4481 Evaluate side-chains 217 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 182 time to evaluate : 2.400 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 34 residues processed: 1 average time/residue: 2.2942 time to fit residues: 5.7035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 222 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 144 optimal weight: 0.0980 chunk 140 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 ASN C 470 ASN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN F 307 ASN F 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 21411 Z= 0.162 Angle : 0.496 8.276 29298 Z= 0.270 Chirality : 0.039 0.184 3322 Planarity : 0.003 0.052 3392 Dihedral : 17.736 74.882 3339 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 2.80 % 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: 1.10 (0.18), residues: 2283 helix: 1.42 (0.15), residues: 1279 sheet: 0.40 (0.33), residues: 190 loop : -0.19 (0.21), residues: 814 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 191 time to evaluate : 2.432 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 36 residues processed: 238 average time/residue: 1.4461 time to fit residues: 389.0079 Evaluate side-chains 219 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 2.423 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 34 residues processed: 2 average time/residue: 0.8111 time to fit residues: 5.1265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 142 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 2 ASN E 82 GLN F 307 ASN F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 21411 Z= 0.236 Angle : 0.526 8.721 29298 Z= 0.284 Chirality : 0.040 0.169 3322 Planarity : 0.003 0.053 3392 Dihedral : 17.781 74.308 3339 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 2.33 % 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: 1.13 (0.18), residues: 2283 helix: 1.44 (0.15), residues: 1280 sheet: 0.33 (0.33), residues: 200 loop : -0.15 (0.22), residues: 803 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 189 time to evaluate : 2.533 Fit side-chains outliers start: 50 outliers final: 37 residues processed: 231 average time/residue: 1.4873 time to fit residues: 388.4459 Evaluate side-chains 218 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 181 time to evaluate : 2.197 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 36 residues processed: 1 average time/residue: 0.1828 time to fit residues: 3.3980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 209 optimal weight: 1.9990 chunk 220 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 193 optimal weight: 0.2980 chunk 203 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN F 307 ASN F 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 21411 Z= 0.232 Angle : 0.529 9.019 29298 Z= 0.285 Chirality : 0.040 0.162 3322 Planarity : 0.003 0.052 3392 Dihedral : 17.767 74.202 3339 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.18), residues: 2283 helix: 1.45 (0.15), residues: 1280 sheet: 0.36 (0.33), residues: 200 loop : -0.13 (0.22), residues: 803 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 188 time to evaluate : 2.627 Fit side-chains outliers start: 51 outliers final: 37 residues processed: 231 average time/residue: 1.4775 time to fit residues: 386.3566 Evaluate side-chains 219 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 2.548 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 35 residues processed: 2 average time/residue: 0.2618 time to fit residues: 4.0809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 140 optimal weight: 3.9990 chunk 226 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 219 optimal weight: 0.0010 chunk 189 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN F 307 ASN F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 21411 Z= 0.239 Angle : 0.553 11.705 29298 Z= 0.294 Chirality : 0.041 0.173 3322 Planarity : 0.003 0.078 3392 Dihedral : 17.766 74.023 3339 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 1.82 % 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: 1.17 (0.18), residues: 2283 helix: 1.46 (0.15), residues: 1280 sheet: 0.39 (0.33), residues: 200 loop : -0.12 (0.22), residues: 803 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 190 time to evaluate : 2.381 Fit side-chains outliers start: 39 outliers final: 35 residues processed: 227 average time/residue: 1.5514 time to fit residues: 398.8194 Evaluate side-chains 219 residues out of total 2144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 2.581 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 34 residues processed: 1 average time/residue: 0.4459 time to fit residues: 4.0601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 239 random chunks: chunk 150 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 195 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN F 307 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.071957 restraints weight = 37279.076| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.04 r_work: 0.2872 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 21411 Z= 0.165 Angle : 0.520 10.095 29298 Z= 0.278 Chirality : 0.039 0.180 3322 Planarity : 0.003 0.052 3392 Dihedral : 17.623 74.515 3339 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 1.77 % 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: 1.25 (0.18), residues: 2283 helix: 1.55 (0.15), residues: 1281 sheet: 0.48 (0.34), residues: 191 loop : -0.13 (0.21), residues: 811 =============================================================================== Job complete usr+sys time: 7370.30 seconds wall clock time: 131 minutes 42.76 seconds (7902.76 seconds total)