Starting phenix.real_space_refine on Mon Mar 18 09:32:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6k_24280/03_2024/7r6k_24280.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6k_24280/03_2024/7r6k_24280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6k_24280/03_2024/7r6k_24280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6k_24280/03_2024/7r6k_24280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6k_24280/03_2024/7r6k_24280.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6k_24280/03_2024/7r6k_24280.pdb" } resolution = 3.17 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= 0.002 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 152 5.49 5 S 66 5.16 5 C 12382 2.51 5 N 3656 2.21 5 O 4287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20543 Number of models: 1 Model: "" Number of chains: 16 Chain: "1" Number of atoms: 3266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3266 Classifications: {'RNA': 152} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 77, 'rna3p_pyr': 54} Link IDs: {'rna2p': 21, 'rna3p': 130} Chain breaks: 13 Chain: "7" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 888 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain breaks: 1 Chain: "8" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3694 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 17, 'TRANS': 440} Chain breaks: 5 Chain: "A" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 872 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain breaks: 5 Chain: "G" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 430 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain breaks: 1 Chain: "I" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 4039 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 18, 'TRANS': 489} Chain breaks: 1 Chain: "J" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 489 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain breaks: 1 Chain: "N" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 795 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain breaks: 4 Chain: "g" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 136 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "i" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "l" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1394 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "m" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 827 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "q" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1347 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain breaks: 2 Chain: "r" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 148 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Chain: "w" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1726 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain breaks: 3 Chain: "5" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 75 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Time building chain proxies: 10.06, per 1000 atoms: 0.49 Number of scatterers: 20543 At special positions: 0 Unit cell: (164.16, 140.4, 136.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 152 15.00 O 4287 8.00 N 3656 7.00 C 12382 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: 8.03 Conformation dependent library (CDL) restraints added in 2.7 seconds 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4108 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 14 sheets defined 58.1% alpha, 6.1% beta 29 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 6.20 Creating SS restraints... Processing helix chain '7' and resid 23 through 29 Processing helix chain '7' and resid 106 through 116 Processing helix chain '7' and resid 125 through 147 removed outlier: 3.884A pdb=" N LYS 7 129 " --> pdb=" O SER 7 125 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE 7 136 " --> pdb=" O ARG 7 132 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 35 removed outlier: 3.812A pdb=" N GLY 8 35 " --> pdb=" O LYS 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 41 through 50 Processing helix chain '8' and resid 51 through 64 Processing helix chain '8' and resid 70 through 75 Processing helix chain '8' and resid 268 through 285 removed outlier: 3.754A pdb=" N ILE 8 283 " --> pdb=" O GLY 8 279 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU 8 284 " --> pdb=" O SER 8 280 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU 8 285 " --> pdb=" O LEU 8 281 " (cutoff:3.500A) Processing helix chain '8' and resid 291 through 303 removed outlier: 3.646A pdb=" N ALA 8 295 " --> pdb=" O THR 8 291 " (cutoff:3.500A) Processing helix chain '8' and resid 313 through 329 removed outlier: 3.830A pdb=" N GLU 8 317 " --> pdb=" O ARG 8 313 " (cutoff:3.500A) Processing helix chain '8' and resid 335 through 349 removed outlier: 3.691A pdb=" N PHE 8 339 " --> pdb=" O GLN 8 335 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU 8 342 " --> pdb=" O SER 8 338 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE 8 343 " --> pdb=" O PHE 8 339 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN 8 344 " --> pdb=" O ALA 8 340 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE 8 349 " --> pdb=" O THR 8 345 " (cutoff:3.500A) Processing helix chain '8' and resid 353 through 367 removed outlier: 3.605A pdb=" N THR 8 357 " --> pdb=" O MET 8 353 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS 8 367 " --> pdb=" O SER 8 363 " (cutoff:3.500A) Processing helix chain '8' and resid 376 through 391 Processing helix chain '8' and resid 396 through 419 removed outlier: 3.821A pdb=" N GLN 8 400 " --> pdb=" O VAL 8 396 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU 8 404 " --> pdb=" O GLN 8 400 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR 8 405 " --> pdb=" O VAL 8 401 " (cutoff:3.500A) Processing helix chain '8' and resid 427 through 435 removed outlier: 3.644A pdb=" N GLU 8 431 " --> pdb=" O ASN 8 428 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR 8 433 " --> pdb=" O ALA 8 430 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE 8 435 " --> pdb=" O ALA 8 432 " (cutoff:3.500A) Processing helix chain '8' and resid 438 through 453 removed outlier: 3.611A pdb=" N CYS 8 442 " --> pdb=" O ASN 8 438 " (cutoff:3.500A) Processing helix chain '8' and resid 471 through 484 Processing helix chain '8' and resid 491 through 508 removed outlier: 4.120A pdb=" N ARG 8 495 " --> pdb=" O PHE 8 491 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU 8 505 " --> pdb=" O SER 8 501 " (cutoff:3.500A) Processing helix chain '8' and resid 515 through 521 removed outlier: 3.802A pdb=" N LEU 8 519 " --> pdb=" O ILE 8 515 " (cutoff:3.500A) Processing helix chain '8' and resid 556 through 575 removed outlier: 3.502A pdb=" N PHE 8 575 " --> pdb=" O LEU 8 571 " (cutoff:3.500A) Processing helix chain '8' and resid 576 through 579 Processing helix chain '8' and resid 583 through 602 Proline residue: 8 590 - end of helix removed outlier: 3.533A pdb=" N LYS 8 600 " --> pdb=" O ARG 8 596 " (cutoff:3.500A) Processing helix chain '8' and resid 605 through 629 removed outlier: 3.509A pdb=" N LYS 8 609 " --> pdb=" O VAL 8 605 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG 8 610 " --> pdb=" O LYS 8 606 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG 8 629 " --> pdb=" O ILE 8 625 " (cutoff:3.500A) Processing helix chain '8' and resid 640 through 645 removed outlier: 3.940A pdb=" N PHE 8 645 " --> pdb=" O GLU 8 641 " (cutoff:3.500A) Processing helix chain '8' and resid 654 through 678 removed outlier: 3.626A pdb=" N TYR 8 659 " --> pdb=" O PRO 8 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 75 through 81 Processing helix chain 'A' and resid 199 through 206 removed outlier: 4.946A pdb=" N GLU A 204 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 53 through 69 removed outlier: 3.722A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 239 through 248 removed outlier: 3.580A pdb=" N LYS G 248 " --> pdb=" O ALA G 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 151 removed outlier: 3.541A pdb=" N GLU I 150 " --> pdb=" O THR I 146 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU I 151 " --> pdb=" O LYS I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 167 removed outlier: 3.586A pdb=" N VAL I 166 " --> pdb=" O LEU I 162 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU I 167 " --> pdb=" O CYS I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 189 removed outlier: 3.915A pdb=" N VAL I 182 " --> pdb=" O MET I 178 " (cutoff:3.500A) Proline residue: I 183 - end of helix Processing helix chain 'I' and resid 198 through 203 removed outlier: 3.798A pdb=" N LYS I 202 " --> pdb=" O THR I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 236 removed outlier: 3.646A pdb=" N LYS I 236 " --> pdb=" O GLN I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 260 Processing helix chain 'I' and resid 268 through 281 removed outlier: 3.690A pdb=" N ILE I 272 " --> pdb=" O PHE I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 304 Processing helix chain 'I' and resid 308 through 325 removed outlier: 3.544A pdb=" N GLU I 313 " --> pdb=" O SER I 309 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR I 324 " --> pdb=" O LYS I 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 335 Processing helix chain 'I' and resid 336 through 344 removed outlier: 6.225A pdb=" N ASP I 341 " --> pdb=" O LEU I 338 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL I 342 " --> pdb=" O SER I 339 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 421 Processing helix chain 'I' and resid 425 through 436 Processing helix chain 'I' and resid 437 through 440 Processing helix chain 'I' and resid 444 through 463 removed outlier: 4.257A pdb=" N ASP I 462 " --> pdb=" O ASP I 458 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN I 463 " --> pdb=" O THR I 459 " (cutoff:3.500A) Processing helix chain 'I' and resid 467 through 486 removed outlier: 4.043A pdb=" N THR I 486 " --> pdb=" O LEU I 482 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 503 Processing helix chain 'I' and resid 505 through 511 removed outlier: 3.810A pdb=" N LEU I 511 " --> pdb=" O PRO I 507 " (cutoff:3.500A) Processing helix chain 'I' and resid 541 through 556 Processing helix chain 'I' and resid 561 through 577 removed outlier: 3.802A pdb=" N ALA I 567 " --> pdb=" O GLU I 563 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS I 570 " --> pdb=" O THR I 566 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER I 577 " --> pdb=" O TYR I 573 " (cutoff:3.500A) Processing helix chain 'I' and resid 580 through 598 removed outlier: 3.719A pdb=" N ASN I 596 " --> pdb=" O ASP I 592 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG I 597 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing helix chain 'I' and resid 599 through 601 No H-bonds generated for 'chain 'I' and resid 599 through 601' Processing helix chain 'I' and resid 602 through 607 removed outlier: 3.928A pdb=" N SER I 606 " --> pdb=" O SER I 602 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER I 607 " --> pdb=" O GLY I 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 602 through 607' Processing helix chain 'I' and resid 627 through 631 removed outlier: 3.693A pdb=" N ALA I 630 " --> pdb=" O ASN I 627 " (cutoff:3.500A) Processing helix chain 'I' and resid 633 through 642 removed outlier: 3.922A pdb=" N ASN I 636 " --> pdb=" O LEU I 633 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU I 639 " --> pdb=" O ASN I 636 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLU I 640 " --> pdb=" O ALA I 637 " (cutoff:3.500A) Processing helix chain 'I' and resid 644 through 662 removed outlier: 3.881A pdb=" N LYS I 659 " --> pdb=" O SER I 655 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU I 660 " --> pdb=" O SER I 656 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 220 removed outlier: 3.566A pdb=" N GLU J 219 " --> pdb=" O SER J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 264 Processing helix chain 'J' and resid 281 through 294 Processing helix chain 'N' and resid 9 through 14 removed outlier: 3.882A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 9 through 14' Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.626A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 108 Processing helix chain 'N' and resid 165 through 173 removed outlier: 3.569A pdb=" N GLY N 173 " --> pdb=" O LYS N 169 " (cutoff:3.500A) Processing helix chain 'g' and resid 98 through 111 Processing helix chain 'i' and resid 45 through 49 removed outlier: 3.793A pdb=" N GLY i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 45 through 49' Processing helix chain 'i' and resid 51 through 63 Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 95 Processing helix chain 'l' and resid 5 through 18 Processing helix chain 'l' and resid 22 through 26 removed outlier: 3.858A pdb=" N SER l 25 " --> pdb=" O ARG l 22 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 54 removed outlier: 3.654A pdb=" N LEU l 54 " --> pdb=" O HIS l 50 " (cutoff:3.500A) Processing helix chain 'l' and resid 55 through 58 Processing helix chain 'l' and resid 59 through 61 No H-bonds generated for 'chain 'l' and resid 59 through 61' Processing helix chain 'l' and resid 85 through 92 removed outlier: 3.744A pdb=" N LYS l 91 " --> pdb=" O THR l 87 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS l 92 " --> pdb=" O VAL l 88 " (cutoff:3.500A) Processing helix chain 'l' and resid 100 through 108 removed outlier: 3.972A pdb=" N MET l 105 " --> pdb=" O PRO l 101 " (cutoff:3.500A) Proline residue: l 106 - end of helix Processing helix chain 'l' and resid 169 through 176 removed outlier: 4.026A pdb=" N LEU l 173 " --> pdb=" O ILE l 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP l 175 " --> pdb=" O GLU l 171 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU l 176 " --> pdb=" O TYR l 172 " (cutoff:3.500A) Processing helix chain 'm' and resid 161 through 166 removed outlier: 3.535A pdb=" N ALA m 164 " --> pdb=" O PRO m 161 " (cutoff:3.500A) Processing helix chain 'm' and resid 187 through 197 Processing helix chain 'm' and resid 217 through 229 Processing helix chain 'q' and resid 281 through 293 Processing helix chain 'q' and resid 319 through 324 Processing helix chain 'q' and resid 331 through 333 No H-bonds generated for 'chain 'q' and resid 331 through 333' Processing helix chain 'q' and resid 334 through 342 removed outlier: 4.589A pdb=" N VAL q 338 " --> pdb=" O SER q 334 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU q 341 " --> pdb=" O PRO q 337 " (cutoff:3.500A) Processing helix chain 'q' and resid 359 through 368 Processing helix chain 'q' and resid 379 through 381 No H-bonds generated for 'chain 'q' and resid 379 through 381' Processing helix chain 'q' and resid 382 through 393 removed outlier: 3.890A pdb=" N LEU q 386 " --> pdb=" O ARG q 382 " (cutoff:3.500A) Processing helix chain 'q' and resid 404 through 408 Processing helix chain 'q' and resid 455 through 462 Processing helix chain 'r' and resid 165 through 169 removed outlier: 3.565A pdb=" N MET r 168 " --> pdb=" O PRO r 165 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU r 169 " --> pdb=" O VAL r 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 165 through 169' Processing helix chain 'w' and resid 409 through 416 removed outlier: 3.758A pdb=" N THR w 416 " --> pdb=" O THR w 412 " (cutoff:3.500A) Processing helix chain 'w' and resid 457 through 479 Processing helix chain 'w' and resid 481 through 490 removed outlier: 3.695A pdb=" N ARG w 485 " --> pdb=" O ASP w 481 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG w 490 " --> pdb=" O ALA w 486 " (cutoff:3.500A) Processing helix chain 'w' and resid 552 through 560 Processing helix chain 'w' and resid 638 through 656 removed outlier: 3.648A pdb=" N GLU w 642 " --> pdb=" O ASP w 638 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP w 654 " --> pdb=" O LYS w 650 " (cutoff:3.500A) Processing helix chain 'w' and resid 659 through 671 Processing helix chain 'w' and resid 675 through 683 Processing helix chain 'w' and resid 696 through 704 removed outlier: 4.058A pdb=" N ASP w 702 " --> pdb=" O TRP w 698 " (cutoff:3.500A) Processing helix chain 'w' and resid 715 through 725 Processing helix chain 'w' and resid 732 through 759 Processing helix chain '5' and resid 217 through 222 Processing sheet with id=AA1, first strand: chain '7' and resid 12 through 15 removed outlier: 3.591A pdb=" N ARG N 71 " --> pdb=" O GLU 7 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '7' and resid 20 through 21 Processing sheet with id=AA3, first strand: chain '7' and resid 89 through 90 Processing sheet with id=AA4, first strand: chain '7' and resid 89 through 90 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 61 removed outlier: 7.275A pdb=" N THR A 33 " --> pdb=" O ARG A 60 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 34 " --> pdb=" O LEU A 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'N' and resid 64 through 67 removed outlier: 7.123A pdb=" N TYR N 127 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLN N 123 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'l' and resid 2 through 3 removed outlier: 6.961A pdb=" N VAL l 44 " --> pdb=" O LEU l 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'l' and resid 63 through 66 removed outlier: 6.708A pdb=" N VAL q 373 " --> pdb=" O ILE q 399 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N CYS q 401 " --> pdb=" O VAL q 373 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA q 375 " --> pdb=" O CYS q 401 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE q 349 " --> pdb=" O PHE q 374 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ASN q 376 " --> pdb=" O ILE q 349 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'l' and resid 95 through 99 removed outlier: 6.674A pdb=" N TYR l 95 " --> pdb=" O ILE l 132 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE l 134 " --> pdb=" O TYR l 95 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE l 97 " --> pdb=" O PHE l 134 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ALA l 135 " --> pdb=" O PRO l 140 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N LEU l 141 " --> pdb=" O ASP l 168 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ASP l 168 " --> pdb=" O LEU l 141 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE l 143 " --> pdb=" O GLN l 166 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL l 113 " --> pdb=" O VAL l 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'm' and resid 170 through 173 removed outlier: 6.795A pdb=" N ILE m 180 " --> pdb=" O ILE m 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 202 through 206 removed outlier: 5.221A pdb=" N LEU m 205 " --> pdb=" O LEU m 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'q' and resid 294 through 298 removed outlier: 7.017A pdb=" N ASN q 295 " --> pdb=" O PHE q 310 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'q' and resid 417 through 420 removed outlier: 6.747A pdb=" N ILE q 418 " --> pdb=" O VAL q 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 814 hydrogen bonds defined for protein. 2337 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 6.81 Time building geometry restraints manager: 8.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5711 1.34 - 1.45: 4064 1.45 - 1.57: 11006 1.57 - 1.69: 290 1.69 - 1.81: 111 Bond restraints: 21182 Sorted by residual: bond pdb=" O5' U 12604 " pdb=" C5' U 12604 " ideal model delta sigma weight residual 1.420 1.441 -0.021 1.50e-02 4.44e+03 1.87e+00 bond pdb=" O5' G 12603 " pdb=" C5' G 12603 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.85e+00 bond pdb=" O5' C 1 918 " pdb=" C5' C 1 918 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.81e+00 bond pdb=" O5' G 12605 " pdb=" C5' G 12605 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.74e+00 bond pdb=" O5' G 1 908 " pdb=" C5' G 1 908 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.65e+00 ... (remaining 21177 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.85: 1298 106.85 - 113.64: 12075 113.64 - 120.43: 7900 120.43 - 127.21: 7479 127.21 - 134.00: 458 Bond angle restraints: 29210 Sorted by residual: angle pdb=" C VAL 7 85 " pdb=" N PRO 7 86 " pdb=" CA PRO 7 86 " ideal model delta sigma weight residual 119.98 124.61 -4.63 1.16e+00 7.43e-01 1.59e+01 angle pdb=" C ILE 7 77 " pdb=" N PRO 7 78 " pdb=" CA PRO 7 78 " ideal model delta sigma weight residual 120.03 123.75 -3.72 9.90e-01 1.02e+00 1.41e+01 angle pdb=" O4' G 12603 " pdb=" C1' G 12603 " pdb=" C2' G 12603 " ideal model delta sigma weight residual 107.60 104.19 3.41 1.00e+00 1.00e+00 1.16e+01 angle pdb=" C ARG 7 43 " pdb=" N LYS 7 44 " pdb=" CA LYS 7 44 " ideal model delta sigma weight residual 120.68 115.56 5.12 1.52e+00 4.33e-01 1.14e+01 angle pdb=" C3' G 1 908 " pdb=" C2' G 1 908 " pdb=" O2' G 1 908 " ideal model delta sigma weight residual 110.70 115.75 -5.05 1.50e+00 4.44e-01 1.14e+01 ... (remaining 29205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 12573 34.08 - 68.16: 571 68.16 - 102.24: 65 102.24 - 136.32: 0 136.32 - 170.40: 1 Dihedral angle restraints: 13210 sinusoidal: 6924 harmonic: 6286 Sorted by residual: dihedral pdb=" CA PHE q 408 " pdb=" C PHE q 408 " pdb=" N PRO q 409 " pdb=" CA PRO q 409 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" C3' G 12603 " pdb=" C4' G 12603 " pdb=" O4' G 12603 " pdb=" C1' G 12603 " ideal model delta sinusoidal sigma weight residual 20.00 -10.76 30.76 1 8.00e+00 1.56e-02 2.11e+01 dihedral pdb=" C4' G 12603 " pdb=" O4' G 12603 " pdb=" C1' G 12603 " pdb=" C2' G 12603 " ideal model delta sinusoidal sigma weight residual 3.00 32.36 -29.36 1 8.00e+00 1.56e-02 1.93e+01 ... (remaining 13207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2734 0.043 - 0.087: 530 0.087 - 0.130: 130 0.130 - 0.174: 25 0.174 - 0.217: 2 Chirality restraints: 3421 Sorted by residual: chirality pdb=" CB THR 8 550 " pdb=" CA THR 8 550 " pdb=" OG1 THR 8 550 " pdb=" CG2 THR 8 550 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C2' G 1 908 " pdb=" C3' G 1 908 " pdb=" O2' G 1 908 " pdb=" C1' G 1 908 " both_signs ideal model delta sigma weight residual False -2.75 -2.55 -0.20 2.00e-01 2.50e+01 9.84e-01 chirality pdb=" C3' C 1 918 " pdb=" C4' C 1 918 " pdb=" O3' C 1 918 " pdb=" C2' C 1 918 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.17 2.00e-01 2.50e+01 7.48e-01 ... (remaining 3418 not shown) Planarity restraints: 3160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE q 408 " -0.058 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO q 409 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO q 409 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO q 409 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER 8 535 " 0.036 5.00e-02 4.00e+02 5.55e-02 4.94e+00 pdb=" N PRO 8 536 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO 8 536 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO 8 536 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 8 513 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.14e+00 pdb=" N PRO 8 514 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO 8 514 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO 8 514 " -0.028 5.00e-02 4.00e+02 ... (remaining 3157 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1776 2.74 - 3.28: 20118 3.28 - 3.82: 34209 3.82 - 4.36: 41049 4.36 - 4.90: 66974 Nonbonded interactions: 164126 Sorted by model distance: nonbonded pdb=" NH1 ARG N 31 " pdb=" OD2 ASP N 124 " model vdw 2.200 2.520 nonbonded pdb=" OG SER q 312 " pdb=" O VAL q 314 " model vdw 2.210 2.440 nonbonded pdb=" OH TYR l 19 " pdb=" OE1 GLN l 166 " model vdw 2.225 2.440 nonbonded pdb=" ND2 ASN 7 28 " pdb=" OD1 ASN m 159 " model vdw 2.248 2.520 nonbonded pdb=" OE2 GLU J 260 " pdb=" NH2 ARG J 263 " model vdw 2.251 2.520 ... (remaining 164121 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.300 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: 0.010 Extract box with map and model: 16.950 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 54.180 Find NCS groups from input model: 0.560 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 0.042 21182 Z= 0.164 Angle : 0.524 7.458 29210 Z= 0.284 Chirality : 0.038 0.217 3421 Planarity : 0.004 0.088 3160 Dihedral : 17.703 170.402 9102 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 0.58 (0.19), residues: 2077 helix: 1.56 (0.16), residues: 1136 sheet: -1.01 (0.53), residues: 93 loop : -1.10 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 52 HIS 0.005 0.001 HIS A 175 PHE 0.014 0.001 PHE 8 645 TYR 0.018 0.001 TYR I 224 ARG 0.004 0.000 ARG 7 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 262 LYS cc_start: 0.8177 (mttp) cc_final: 0.7908 (mttm) REVERT: q 359 LYS cc_start: 0.8202 (mttp) cc_final: 0.8000 (mttp) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.3196 time to fit residues: 123.0107 Evaluate side-chains 218 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 4.9990 chunk 167 optimal weight: 0.4980 chunk 92 optimal weight: 0.0980 chunk 57 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 0.0870 chunk 128 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN ** I 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 284 HIS l 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21182 Z= 0.140 Angle : 0.492 8.492 29210 Z= 0.251 Chirality : 0.036 0.205 3421 Planarity : 0.004 0.066 3160 Dihedral : 17.507 167.309 4641 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.63 % Allowed : 6.69 % Favored : 92.68 % 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: 0.87 (0.19), residues: 2077 helix: 1.83 (0.16), residues: 1156 sheet: -0.95 (0.51), residues: 103 loop : -1.07 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 120 HIS 0.006 0.001 HIS 8 299 PHE 0.014 0.001 PHE 8 645 TYR 0.018 0.001 TYR q 322 ARG 0.003 0.000 ARG 8 629 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 230 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 220 HIS cc_start: 0.7821 (p90) cc_final: 0.7562 (p90) REVERT: J 262 LYS cc_start: 0.8172 (mttp) cc_final: 0.7885 (mttm) outliers start: 12 outliers final: 9 residues processed: 236 average time/residue: 0.3378 time to fit residues: 120.7300 Evaluate side-chains 223 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 214 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 8 residue 303 GLU Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 489 MET Chi-restraints excluded: chain l residue 28 VAL Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 691 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 217 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 68 optimal weight: 0.4980 chunk 161 optimal weight: 0.4980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 284 HIS q 402 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21182 Z= 0.192 Angle : 0.495 7.345 29210 Z= 0.252 Chirality : 0.037 0.166 3421 Planarity : 0.004 0.068 3160 Dihedral : 17.421 167.077 4641 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.15 % Allowed : 8.42 % Favored : 90.43 % 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: 0.90 (0.19), residues: 2077 helix: 1.91 (0.16), residues: 1143 sheet: -0.95 (0.55), residues: 90 loop : -1.10 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 120 HIS 0.005 0.001 HIS 8 299 PHE 0.015 0.001 PHE 8 645 TYR 0.012 0.001 TYR 8 516 ARG 0.005 0.000 ARG q 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 211 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 397 LEU cc_start: 0.7616 (tt) cc_final: 0.7301 (mm) REVERT: J 262 LYS cc_start: 0.8148 (mttp) cc_final: 0.7897 (mttm) outliers start: 22 outliers final: 17 residues processed: 222 average time/residue: 0.3522 time to fit residues: 116.7539 Evaluate side-chains 223 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 206 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 8 residue 303 GLU Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain 8 residue 522 ILE Chi-restraints excluded: chain 8 residue 631 ASP Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 489 MET Chi-restraints excluded: chain l residue 28 VAL Chi-restraints excluded: chain l residue 173 LEU Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain q residue 314 VAL Chi-restraints excluded: chain q residue 334 SER Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 691 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 104 optimal weight: 0.0970 chunk 22 optimal weight: 0.0570 chunk 95 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 201 optimal weight: 0.4980 chunk 213 optimal weight: 0.5980 chunk 105 optimal weight: 0.0070 chunk 191 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21182 Z= 0.118 Angle : 0.456 6.723 29210 Z= 0.233 Chirality : 0.035 0.188 3421 Planarity : 0.004 0.070 3160 Dihedral : 17.390 169.325 4641 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.05 % Allowed : 10.25 % Favored : 88.71 % 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 (0.19), residues: 2077 helix: 2.16 (0.16), residues: 1136 sheet: -0.72 (0.55), residues: 95 loop : -1.01 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 120 HIS 0.019 0.001 HIS 8 299 PHE 0.014 0.001 PHE J 217 TYR 0.019 0.001 TYR q 322 ARG 0.004 0.000 ARG q 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 220 HIS cc_start: 0.7846 (p90) cc_final: 0.7623 (p90) REVERT: J 262 LYS cc_start: 0.8086 (mttp) cc_final: 0.7871 (mttm) outliers start: 20 outliers final: 15 residues processed: 234 average time/residue: 0.3741 time to fit residues: 132.1361 Evaluate side-chains 223 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 208 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 8 residue 303 GLU Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain 8 residue 522 ILE Chi-restraints excluded: chain 8 residue 631 ASP Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain I residue 212 LYS Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 489 MET Chi-restraints excluded: chain l residue 28 VAL Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 691 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 0.9980 chunk 121 optimal weight: 0.2980 chunk 3 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 22 GLN ** 8 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 545 HIS 8 621 ASN A 26 GLN A 158 HIS l 62 ASN m 191 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21182 Z= 0.297 Angle : 0.554 8.835 29210 Z= 0.280 Chirality : 0.039 0.179 3421 Planarity : 0.005 0.068 3160 Dihedral : 17.431 168.914 4641 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.44 % Favored : 94.51 % Rotamer: Outliers : 1.57 % Allowed : 11.50 % Favored : 86.93 % 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: 0.86 (0.19), residues: 2077 helix: 1.82 (0.16), residues: 1143 sheet: -1.08 (0.52), residues: 103 loop : -1.01 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP m 202 HIS 0.016 0.001 HIS 8 299 PHE 0.018 0.002 PHE l 143 TYR 0.013 0.002 TYR 8 516 ARG 0.006 0.000 ARG q 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 2.271 Fit side-chains revert: symmetry clash REVERT: J 220 HIS cc_start: 0.7893 (p90) cc_final: 0.7607 (p90) REVERT: J 262 LYS cc_start: 0.8191 (mttp) cc_final: 0.7971 (mttp) outliers start: 30 outliers final: 22 residues processed: 234 average time/residue: 0.3517 time to fit residues: 123.9960 Evaluate side-chains 225 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 203 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 8 residue 303 GLU Chi-restraints excluded: chain 8 residue 341 PHE Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain 8 residue 631 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain I residue 212 LYS Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 489 MET Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain g residue 101 VAL Chi-restraints excluded: chain l residue 28 VAL Chi-restraints excluded: chain l residue 173 LEU Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain q residue 314 VAL Chi-restraints excluded: chain q residue 334 SER Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 691 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 213 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 299 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21182 Z= 0.174 Angle : 0.489 7.390 29210 Z= 0.250 Chirality : 0.036 0.181 3421 Planarity : 0.004 0.076 3160 Dihedral : 17.438 170.773 4641 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.83 % Allowed : 12.08 % Favored : 86.10 % 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: 0.97 (0.19), residues: 2077 helix: 1.92 (0.16), residues: 1143 sheet: -1.09 (0.52), residues: 103 loop : -0.96 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 120 HIS 0.014 0.001 HIS 8 299 PHE 0.015 0.001 PHE J 217 TYR 0.020 0.001 TYR q 322 ARG 0.005 0.000 ARG q 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 209 time to evaluate : 2.215 Fit side-chains revert: symmetry clash REVERT: 8 573 ASP cc_start: 0.7587 (t0) cc_final: 0.7354 (t0) REVERT: I 511 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8668 (mp) REVERT: J 220 HIS cc_start: 0.7855 (p90) cc_final: 0.7610 (p90) REVERT: J 262 LYS cc_start: 0.8117 (mttp) cc_final: 0.7916 (mttm) REVERT: w 675 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7474 (p0) outliers start: 35 outliers final: 24 residues processed: 230 average time/residue: 0.3436 time to fit residues: 118.8488 Evaluate side-chains 232 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 206 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 8 residue 42 ASP Chi-restraints excluded: chain 8 residue 303 GLU Chi-restraints excluded: chain 8 residue 341 PHE Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain 8 residue 522 ILE Chi-restraints excluded: chain 8 residue 631 ASP Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain I residue 212 LYS Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 489 MET Chi-restraints excluded: chain I residue 511 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain l residue 28 VAL Chi-restraints excluded: chain l residue 150 THR Chi-restraints excluded: chain l residue 173 LEU Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain m residue 231 GLU Chi-restraints excluded: chain q residue 334 SER Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 675 ASN Chi-restraints excluded: chain w residue 691 ASP Chi-restraints excluded: chain w residue 733 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 119 optimal weight: 0.2980 chunk 213 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 477 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21182 Z= 0.162 Angle : 0.482 7.462 29210 Z= 0.245 Chirality : 0.036 0.175 3421 Planarity : 0.004 0.084 3160 Dihedral : 17.391 171.008 4641 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.57 % Allowed : 12.75 % Favored : 85.68 % 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: 1.05 (0.19), residues: 2077 helix: 2.01 (0.16), residues: 1144 sheet: -0.96 (0.55), residues: 95 loop : -0.99 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 120 HIS 0.005 0.001 HIS 8 299 PHE 0.016 0.001 PHE J 217 TYR 0.014 0.001 TYR 8 516 ARG 0.005 0.000 ARG q 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 2.233 Fit side-chains revert: symmetry clash REVERT: 8 573 ASP cc_start: 0.7572 (t0) cc_final: 0.7337 (t0) REVERT: I 511 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8692 (mp) REVERT: J 220 HIS cc_start: 0.7805 (p90) cc_final: 0.7555 (p90) REVERT: w 675 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7498 (p0) outliers start: 30 outliers final: 23 residues processed: 232 average time/residue: 0.3587 time to fit residues: 124.2043 Evaluate side-chains 230 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 205 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 8 residue 303 GLU Chi-restraints excluded: chain 8 residue 341 PHE Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain 8 residue 522 ILE Chi-restraints excluded: chain 8 residue 631 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain I residue 212 LYS Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 489 MET Chi-restraints excluded: chain I residue 511 LEU Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain l residue 28 VAL Chi-restraints excluded: chain l residue 150 THR Chi-restraints excluded: chain l residue 173 LEU Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain q residue 334 SER Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 675 ASN Chi-restraints excluded: chain w residue 691 ASP Chi-restraints excluded: chain w residue 733 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 167 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 299 HIS A 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21182 Z= 0.174 Angle : 0.487 8.121 29210 Z= 0.248 Chirality : 0.036 0.180 3421 Planarity : 0.004 0.082 3160 Dihedral : 17.371 171.202 4641 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.57 % Allowed : 13.75 % Favored : 84.68 % 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: 1.07 (0.19), residues: 2077 helix: 2.01 (0.16), residues: 1144 sheet: -0.96 (0.55), residues: 95 loop : -0.95 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 120 HIS 0.022 0.001 HIS 8 299 PHE 0.015 0.001 PHE J 217 TYR 0.023 0.001 TYR q 322 ARG 0.005 0.000 ARG q 406 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 2.012 Fit side-chains revert: symmetry clash REVERT: I 511 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8682 (mp) REVERT: J 220 HIS cc_start: 0.7837 (p90) cc_final: 0.7596 (p90) REVERT: w 675 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7516 (p0) outliers start: 30 outliers final: 23 residues processed: 224 average time/residue: 0.3527 time to fit residues: 118.0145 Evaluate side-chains 224 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 8 residue 42 ASP Chi-restraints excluded: chain 8 residue 303 GLU Chi-restraints excluded: chain 8 residue 341 PHE Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain 8 residue 631 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain I residue 212 LYS Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 489 MET Chi-restraints excluded: chain I residue 511 LEU Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain l residue 28 VAL Chi-restraints excluded: chain l residue 150 THR Chi-restraints excluded: chain l residue 173 LEU Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain q residue 334 SER Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 675 ASN Chi-restraints excluded: chain w residue 691 ASP Chi-restraints excluded: chain w residue 733 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 0.9980 chunk 186 optimal weight: 0.0060 chunk 198 optimal weight: 1.9990 chunk 119 optimal weight: 0.0570 chunk 86 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 187 optimal weight: 0.6980 chunk 197 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 overall best weight: 0.4714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21182 Z= 0.136 Angle : 0.472 7.882 29210 Z= 0.241 Chirality : 0.035 0.182 3421 Planarity : 0.004 0.090 3160 Dihedral : 17.340 171.515 4641 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.46 % Allowed : 14.01 % Favored : 84.53 % 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: 1.18 (0.19), residues: 2077 helix: 2.10 (0.16), residues: 1145 sheet: -0.85 (0.54), residues: 100 loop : -0.91 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 120 HIS 0.010 0.001 HIS 8 299 PHE 0.016 0.001 PHE J 217 TYR 0.014 0.001 TYR 8 516 ARG 0.005 0.000 ARG q 406 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 207 time to evaluate : 2.097 Fit side-chains revert: symmetry clash REVERT: 8 397 LEU cc_start: 0.7535 (tt) cc_final: 0.7259 (mm) REVERT: I 511 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8660 (mp) REVERT: J 220 HIS cc_start: 0.7790 (p90) cc_final: 0.7575 (p90) REVERT: q 403 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.6741 (m-10) outliers start: 28 outliers final: 24 residues processed: 222 average time/residue: 0.3391 time to fit residues: 113.0190 Evaluate side-chains 225 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 8 residue 42 ASP Chi-restraints excluded: chain 8 residue 303 GLU Chi-restraints excluded: chain 8 residue 341 PHE Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain 8 residue 631 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 158 HIS Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain I residue 212 LYS Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 489 MET Chi-restraints excluded: chain I residue 511 LEU Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain l residue 28 VAL Chi-restraints excluded: chain l residue 150 THR Chi-restraints excluded: chain l residue 173 LEU Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain q residue 334 SER Chi-restraints excluded: chain q residue 403 TYR Chi-restraints excluded: chain r residue 164 ARG Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 691 ASP Chi-restraints excluded: chain w residue 733 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 175 optimal weight: 0.3980 chunk 18 optimal weight: 0.0970 chunk 135 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21182 Z= 0.141 Angle : 0.473 8.022 29210 Z= 0.241 Chirality : 0.035 0.185 3421 Planarity : 0.004 0.086 3160 Dihedral : 17.287 171.507 4641 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.57 % Allowed : 13.96 % Favored : 84.47 % 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 (0.19), residues: 2077 helix: 2.16 (0.16), residues: 1145 sheet: -0.77 (0.54), residues: 100 loop : -0.89 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 120 HIS 0.006 0.001 HIS 8 299 PHE 0.015 0.001 PHE J 217 TYR 0.028 0.001 TYR q 322 ARG 0.005 0.000 ARG w 653 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 206 time to evaluate : 2.008 Fit side-chains revert: symmetry clash REVERT: 8 397 LEU cc_start: 0.7543 (tt) cc_final: 0.7263 (mm) REVERT: A 159 ASN cc_start: 0.7649 (t0) cc_final: 0.7395 (t0) REVERT: I 511 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8650 (mp) REVERT: q 403 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.6732 (m-10) outliers start: 30 outliers final: 26 residues processed: 222 average time/residue: 0.3554 time to fit residues: 118.4044 Evaluate side-chains 230 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 8 residue 42 ASP Chi-restraints excluded: chain 8 residue 303 GLU Chi-restraints excluded: chain 8 residue 341 PHE Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain 8 residue 603 THR Chi-restraints excluded: chain 8 residue 631 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain I residue 212 LYS Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 489 MET Chi-restraints excluded: chain I residue 511 LEU Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain l residue 28 VAL Chi-restraints excluded: chain l residue 150 THR Chi-restraints excluded: chain l residue 173 LEU Chi-restraints excluded: chain m residue 217 THR Chi-restraints excluded: chain q residue 334 SER Chi-restraints excluded: chain q residue 403 TYR Chi-restraints excluded: chain r residue 164 ARG Chi-restraints excluded: chain r residue 172 ILE Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 691 ASP Chi-restraints excluded: chain w residue 733 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 161 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 0.0470 chunk 175 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 22 optimal weight: 0.0870 chunk 32 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.126205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097163 restraints weight = 35731.759| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.03 r_work: 0.3292 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21182 Z= 0.121 Angle : 0.467 7.845 29210 Z= 0.238 Chirality : 0.035 0.186 3421 Planarity : 0.004 0.090 3160 Dihedral : 17.260 171.672 4641 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.31 % Allowed : 14.53 % Favored : 84.16 % 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: 1.31 (0.19), residues: 2077 helix: 2.20 (0.16), residues: 1148 sheet: -0.73 (0.54), residues: 100 loop : -0.88 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 120 HIS 0.006 0.001 HIS 8 299 PHE 0.017 0.001 PHE J 217 TYR 0.014 0.001 TYR 8 516 ARG 0.004 0.000 ARG J 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4447.45 seconds wall clock time: 81 minutes 41.47 seconds (4901.47 seconds total)