Starting phenix.real_space_refine (version: dev) on Thu Feb 23 16:36:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6k_24280/02_2023/7r6k_24280.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6k_24280/02_2023/7r6k_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_24280/02_2023/7r6k_24280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6k_24280/02_2023/7r6k_24280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6k_24280/02_2023/7r6k_24280.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6k_24280/02_2023/7r6k_24280.pdb" } resolution = 3.17 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 "J TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 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: 11.83, per 1000 atoms: 0.58 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: 8.49 Conformation dependent library (CDL) restraints added in 2.6 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: 5.60 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: 7.18 Time building geometry restraints manager: 9.23 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: 12332 34.08 - 68.16: 298 68.16 - 102.24: 39 102.24 - 136.32: 0 136.32 - 170.40: 1 Dihedral angle restraints: 12670 sinusoidal: 6384 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 12667 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 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. 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: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 17.590 Check model and map are aligned: 0.280 Process input model: 57.040 Find NCS groups from input model: 0.550 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:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 14.699 170.402 8562 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 % 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 *********************** 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 : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.3620 time to fit residues: 140.2389 Evaluate side-chains 218 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.241 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0175 ------------------------------------------------------------------------------- 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: 0.7916 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 21182 Z= 0.145 Angle : 0.490 8.440 29210 Z= 0.251 Chirality : 0.036 0.202 3421 Planarity : 0.004 0.067 3160 Dihedral : 10.746 168.444 4101 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 0.68 % 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: 0.88 (0.19), residues: 2077 helix: 1.84 (0.16), residues: 1156 sheet: -0.95 (0.51), residues: 103 loop : -1.08 (0.21), residues: 818 *********************** 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 241 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 228 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 234 average time/residue: 0.3525 time to fit residues: 124.7890 Evaluate side-chains 221 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 211 time to evaluate : 2.312 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1943 time to fit residues: 6.8119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 201 optimal weight: 7.9990 chunk 217 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 68 optimal weight: 0.0870 chunk 161 optimal weight: 0.4980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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: 0.7941 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 21182 Z= 0.162 Angle : 0.475 7.597 29210 Z= 0.242 Chirality : 0.036 0.167 3421 Planarity : 0.004 0.067 3160 Dihedral : 10.708 168.176 4101 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.68 % 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: 0.97 (0.19), residues: 2077 helix: 1.97 (0.16), residues: 1142 sheet: -0.85 (0.53), residues: 95 loop : -1.09 (0.21), residues: 840 *********************** 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 232 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 219 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 225 average time/residue: 0.3753 time to fit residues: 127.1391 Evaluate side-chains 215 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 207 time to evaluate : 2.091 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2434 time to fit residues: 6.4259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 104 optimal weight: 0.0020 chunk 22 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 213 optimal weight: 0.9980 chunk 105 optimal weight: 0.0970 chunk 191 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 21182 Z= 0.137 Angle : 0.455 6.473 29210 Z= 0.234 Chirality : 0.035 0.197 3421 Planarity : 0.004 0.071 3160 Dihedral : 10.729 170.429 4101 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 0.63 % 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: 1.14 (0.19), residues: 2077 helix: 2.13 (0.16), residues: 1135 sheet: -0.76 (0.54), residues: 95 loop : -1.01 (0.21), residues: 847 *********************** 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 228 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 216 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 223 average time/residue: 0.3535 time to fit residues: 119.0321 Evaluate side-chains 215 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 209 time to evaluate : 2.174 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1928 time to fit residues: 4.9849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 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: 2.0988 ------------------------------------------------------------------------------- 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 159 ASN l 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 21182 Z= 0.366 Angle : 0.599 9.729 29210 Z= 0.304 Chirality : 0.041 0.183 3421 Planarity : 0.005 0.071 3160 Dihedral : 11.079 170.300 4101 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.92 % Favored : 94.03 % Rotamer Outliers : 1.10 % 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: 0.62 (0.19), residues: 2077 helix: 1.59 (0.16), residues: 1144 sheet: -1.23 (0.51), residues: 102 loop : -1.05 (0.21), residues: 831 *********************** 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 242 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 221 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 234 average time/residue: 0.3543 time to fit residues: 124.2692 Evaluate side-chains 219 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 208 time to evaluate : 2.370 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1938 time to fit residues: 7.1507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 213 optimal weight: 0.7980 chunk 177 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** I 530 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 21182 Z= 0.181 Angle : 0.502 7.669 29210 Z= 0.256 Chirality : 0.037 0.185 3421 Planarity : 0.004 0.077 3160 Dihedral : 11.003 171.849 4101 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 1.05 % 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 (0.19), residues: 2077 helix: 1.80 (0.16), residues: 1143 sheet: -1.12 (0.52), residues: 103 loop : -0.99 (0.22), residues: 831 *********************** 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 232 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 212 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 223 average time/residue: 0.3738 time to fit residues: 125.5460 Evaluate side-chains 217 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 208 time to evaluate : 2.281 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2065 time to fit residues: 6.6567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 121 optimal weight: 0.0870 chunk 156 optimal weight: 0.7980 chunk 120 optimal weight: 0.0970 chunk 179 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 213 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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** A 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 21182 Z= 0.138 Angle : 0.475 7.190 29210 Z= 0.242 Chirality : 0.036 0.178 3421 Planarity : 0.004 0.082 3160 Dihedral : 10.864 171.985 4101 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.47 % 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: 1.04 (0.19), residues: 2077 helix: 1.99 (0.16), residues: 1143 sheet: -0.96 (0.55), residues: 95 loop : -0.96 (0.21), residues: 839 *********************** 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 218 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 209 time to evaluate : 2.244 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 214 average time/residue: 0.3682 time to fit residues: 118.3760 Evaluate side-chains 206 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 202 time to evaluate : 2.209 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1801 time to fit residues: 4.3314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 chunk 19 optimal weight: 0.0270 chunk 167 optimal weight: 0.0980 chunk 193 optimal weight: 2.9990 overall best weight: 0.3016 ------------------------------------------------------------------------------- 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** l 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 21182 Z= 0.121 Angle : 0.461 7.709 29210 Z= 0.235 Chirality : 0.035 0.181 3421 Planarity : 0.004 0.082 3160 Dihedral : 10.764 172.262 4101 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.42 % 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: 1.21 (0.19), residues: 2077 helix: 2.14 (0.16), residues: 1145 sheet: -0.81 (0.54), residues: 100 loop : -0.93 (0.22), residues: 832 *********************** 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 225 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 2.249 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 220 average time/residue: 0.3707 time to fit residues: 121.7723 Evaluate side-chains 211 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 206 time to evaluate : 2.296 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2006 time to fit residues: 4.8776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 198 optimal weight: 0.5980 chunk 119 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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** m 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1975 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= 0.152 Angle : 0.477 8.070 29210 Z= 0.244 Chirality : 0.036 0.178 3421 Planarity : 0.004 0.090 3160 Dihedral : 10.733 172.143 4101 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 0.21 % 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: 1.21 (0.19), residues: 2077 helix: 2.11 (0.16), residues: 1147 sheet: -0.77 (0.54), residues: 100 loop : -0.89 (0.22), residues: 830 *********************** 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 208 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 204 time to evaluate : 2.265 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 204 average time/residue: 0.3740 time to fit residues: 115.3679 Evaluate side-chains 203 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 2.384 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1957 time to fit residues: 3.7209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 220 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 175 optimal weight: 0.0050 chunk 18 optimal weight: 0.1980 chunk 135 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2046 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= 0.137 Angle : 0.472 7.874 29210 Z= 0.240 Chirality : 0.035 0.182 3421 Planarity : 0.004 0.086 3160 Dihedral : 10.705 172.103 4101 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.21 % 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: 1.24 (0.19), residues: 2077 helix: 2.14 (0.16), residues: 1148 sheet: -0.73 (0.54), residues: 100 loop : -0.90 (0.22), residues: 829 ********************** 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 210 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 206 time to evaluate : 2.320 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 209 average time/residue: 0.3712 time to fit residues: 117.1985 Evaluate side-chains 205 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 203 time to evaluate : 2.361 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4561 time to fit residues: 4.2333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 161 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 0.0470 chunk 175 optimal weight: 0.0870 chunk 73 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 32 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 overall best weight: 0.1852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.127528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.098699 restraints weight = 35536.898| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.01 r_work: 0.3315 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2207 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= 0.119 Angle : 0.464 8.004 29210 Z= 0.237 Chirality : 0.035 0.183 3421 Planarity : 0.004 0.088 3160 Dihedral : 10.627 172.114 4101 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.10 % 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: 1.36 (0.19), residues: 2077 helix: 2.30 (0.16), residues: 1136 sheet: -0.65 (0.55), residues: 100 loop : -0.91 (0.22), residues: 841 =============================================================================== Job complete usr+sys time: 4332.34 seconds wall clock time: 79 minutes 19.90 seconds (4759.90 seconds total)