Starting phenix.real_space_refine on Sun Sep 13 04:04:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r6k_24280/09_2026/7r6k_24280.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r6k_24280/09_2026/7r6k_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/cci-nas-00/data/ceres_data/7r6k_24280/09_2026/7r6k_24280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r6k_24280/09_2026/7r6k_24280.map" model { file = "/net/cci-nas-00/data/ceres_data/7r6k_24280/09_2026/7r6k_24280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r6k_24280/09_2026/7r6k_24280.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7r6k_24280/09_2026/7r6k_24280.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r6k_24280/09_2026/7r6k_24280.cif" } 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 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. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'RNAv2': 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: 4.48, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 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: 1.87 Conformation dependent library (CDL) restraints added in 876.0 milliseconds 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: 2.37 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: 3.34 Time building geometry restraints manager: 2.38 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=" CG1 ILE G 64 " pdb=" CD1 ILE G 64 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.18e+00 bond pdb=" CB ASP l 42 " pdb=" CG ASP l 42 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 bond pdb=" C1' G 1 908 " pdb=" N9 G 1 908 " ideal model delta sigma weight residual 1.478 1.458 0.020 2.00e-02 2.50e+03 1.00e+00 bond pdb=" C1' G 1 909 " pdb=" N9 G 1 909 " ideal model delta sigma weight residual 1.478 1.458 0.020 2.00e-02 2.50e+03 9.85e-01 bond pdb=" C VAL 7 85 " pdb=" N PRO 7 86 " ideal model delta sigma weight residual 1.332 1.343 -0.011 1.12e-02 7.97e+03 9.66e-01 ... (remaining 21177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 28132 1.49 - 2.98: 824 2.98 - 4.47: 187 4.47 - 5.97: 60 5.97 - 7.46: 7 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=" 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=" CA ARG G 48 " pdb=" CB ARG G 48 " pdb=" CG ARG G 48 " ideal model delta sigma weight residual 114.10 120.71 -6.61 2.00e+00 2.50e-01 1.09e+01 angle pdb=" C LYS N 13 " pdb=" N LYS N 14 " pdb=" CA LYS N 14 " ideal model delta sigma weight residual 121.54 127.77 -6.23 1.91e+00 2.74e-01 1.06e+01 ... (remaining 29205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 12154 34.08 - 68.16: 459 68.16 - 102.24: 56 102.24 - 136.32: 0 136.32 - 170.40: 1 Dihedral angle restraints: 12670 sinusoidal: 6384 harmonic: 6286 Sorted by residual: dihedral pdb=" C4' A 12967 " pdb=" C3' A 12967 " pdb=" C2' A 12967 " pdb=" C1' A 12967 " ideal model delta sinusoidal sigma weight residual 36.34 -37.00 73.34 1 3.10e+00 1.04e-01 7.13e+02 dihedral pdb=" C4' A 1 268 " pdb=" C3' A 1 268 " pdb=" C2' A 1 268 " pdb=" C1' A 1 268 " ideal model delta sinusoidal sigma weight residual 36.34 -36.47 72.82 1 3.10e+00 1.04e-01 7.04e+02 dihedral pdb=" C4' G 1 269 " pdb=" C3' G 1 269 " pdb=" C2' G 1 269 " pdb=" C1' G 1 269 " ideal model delta sinusoidal sigma weight residual 36.35 -36.39 72.73 1 3.10e+00 1.04e-01 7.02e+02 ... (remaining 12667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2868 0.060 - 0.119: 323 0.119 - 0.179: 25 0.179 - 0.239: 142 0.239 - 0.299: 63 Chirality restraints: 3421 Sorted by residual: chirality pdb=" C2' C 1 870 " pdb=" C3' C 1 870 " pdb=" O2' C 1 870 " pdb=" C1' C 1 870 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C2' C 1 42 " pdb=" C3' C 1 42 " pdb=" O2' C 1 42 " pdb=" C1' C 1 42 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C2' G 1 894 " pdb=" C3' G 1 894 " pdb=" O2' G 1 894 " pdb=" C1' G 1 894 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (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 3.120 nonbonded pdb=" OG SER q 312 " pdb=" O VAL q 314 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR l 19 " pdb=" OE1 GLN l 166 " model vdw 2.225 3.040 nonbonded pdb=" ND2 ASN 7 28 " pdb=" OD1 ASN m 159 " model vdw 2.248 3.120 nonbonded pdb=" OE2 GLU J 260 " pdb=" NH2 ARG J 263 " model vdw 2.251 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 6.560 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 20.370 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- 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= 0.129 Angle : 0.645 7.458 29210 Z= 0.310 Chirality : 0.069 0.299 3421 Planarity : 0.004 0.088 3160 Dihedral : 16.666 170.402 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 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG 7 92 TYR 0.018 0.001 TYR I 224 PHE 0.014 0.001 PHE 8 645 TRP 0.010 0.001 TRP G 52 HIS 0.005 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (21182) covalent geometry : angle 0.64508 / 0.31 (29210) hydrogen bonds : bond 0.15360 / 7.80 ( 881) hydrogen bonds : angle 5.42417 / 2.10 ( 2447) *********************** 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 to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.691 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: 0.1558 time to fit residues: 60.6579 Evaluate side-chains 218 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 0.2980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 8 621 ASN A 26 GLN I 265 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.124695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.095626 restraints weight = 35401.629| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.04 r_work: 0.3272 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21182 Z= 0.156 Angle : 0.773 15.872 29210 Z= 0.338 Chirality : 0.061 1.010 3421 Planarity : 0.005 0.068 3160 Dihedral : 14.146 160.325 4101 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.73 % Allowed : 6.74 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.19), residues: 2077 helix: 1.70 (0.16), residues: 1157 sheet: -1.08 (0.50), residues: 102 loop : -1.10 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG w 750 TYR 0.017 0.001 TYR q 322 PHE 0.015 0.001 PHE 8 645 TRP 0.010 0.001 TRP N 120 HIS 0.004 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (21182) covalent geometry : angle 0.77347 / 0.34 (29210) hydrogen bonds : bond 0.04549 / 2.34 ( 881) hydrogen bonds : angle 3.94696 / 1.52 ( 2447) *********************** 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 230 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 299 HIS cc_start: 0.8747 (m90) cc_final: 0.8530 (m90) REVERT: J 220 HIS cc_start: 0.8569 (p90) cc_final: 0.8145 (p90) REVERT: J 262 LYS cc_start: 0.8646 (mttp) cc_final: 0.8330 (mttm) REVERT: J 263 ARG cc_start: 0.8248 (ttt-90) cc_final: 0.8010 (ttt-90) REVERT: g 99 LYS cc_start: 0.8620 (mmtm) cc_final: 0.8308 (tptp) REVERT: m 159 ASN cc_start: 0.9129 (t0) cc_final: 0.8867 (t0) REVERT: w 551 LEU cc_start: 0.7719 (mm) cc_final: 0.7343 (tp) outliers start: 14 outliers final: 11 residues processed: 223 average time/residue: 0.1641 time to fit residues: 55.4901 Evaluate side-chains 218 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 G residue 67 ILE Chi-restraints excluded: chain I residue 426 ILE 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 Chi-restraints excluded: chain w residue 754 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 147 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 186 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 22 GLN A 31 GLN A 84 ASN q 402 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.122015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.092813 restraints weight = 35689.759| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.96 r_work: 0.3221 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21182 Z= 0.188 Angle : 0.704 10.852 29210 Z= 0.319 Chirality : 0.055 0.586 3421 Planarity : 0.005 0.069 3160 Dihedral : 14.070 159.428 4101 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.25 % Allowed : 9.41 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 2077 helix: 1.67 (0.16), residues: 1142 sheet: -1.47 (0.50), residues: 102 loop : -1.08 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG q 274 TYR 0.013 0.002 TYR 8 516 PHE 0.016 0.002 PHE l 143 TRP 0.010 0.001 TRP N 120 HIS 0.005 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (21182) covalent geometry : angle 0.70441 / 0.32 (29210) hydrogen bonds : bond 0.04540 / 2.35 ( 881) hydrogen bonds : angle 3.84855 / 1.49 ( 2447) *********************** 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 241 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 299 HIS cc_start: 0.8812 (m90) cc_final: 0.8588 (m90) REVERT: 8 397 LEU cc_start: 0.7814 (tt) cc_final: 0.7351 (mm) REVERT: I 224 TYR cc_start: 0.8313 (t80) cc_final: 0.8084 (t80) REVERT: J 220 HIS cc_start: 0.8576 (p90) cc_final: 0.8163 (p90) REVERT: J 260 GLU cc_start: 0.8441 (tp30) cc_final: 0.8130 (tp30) REVERT: J 262 LYS cc_start: 0.8603 (mttp) cc_final: 0.8314 (mttm) REVERT: J 263 ARG cc_start: 0.8248 (ttt-90) cc_final: 0.7915 (ttt-90) REVERT: J 289 LYS cc_start: 0.7287 (tttt) cc_final: 0.7086 (tppt) REVERT: r 170 ARG cc_start: 0.7318 (tpt90) cc_final: 0.6969 (tpt90) outliers start: 24 outliers final: 17 residues processed: 229 average time/residue: 0.1584 time to fit residues: 54.8872 Evaluate side-chains 227 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 A residue 26 GLN 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 184 VAL 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 g residue 101 VAL Chi-restraints excluded: chain l residue 28 VAL 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 691 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 214 optimal weight: 0.0870 chunk 149 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN A 159 ASN N 123 GLN q 326 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.123142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.094209 restraints weight = 35519.172| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.00 r_work: 0.3246 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21182 Z= 0.140 Angle : 0.651 9.815 29210 Z= 0.295 Chirality : 0.051 0.407 3421 Planarity : 0.004 0.072 3160 Dihedral : 13.932 159.819 4101 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.36 % Allowed : 11.03 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 2077 helix: 1.76 (0.16), residues: 1143 sheet: -1.39 (0.51), residues: 102 loop : -1.05 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG q 406 TYR 0.019 0.001 TYR q 322 PHE 0.015 0.001 PHE 8 645 TRP 0.008 0.001 TRP N 120 HIS 0.004 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (21182) covalent geometry : angle 0.65057 / 0.29 (29210) hydrogen bonds : bond 0.04033 / 2.09 ( 881) hydrogen bonds : angle 3.68463 / 1.42 ( 2447) *********************** 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 240 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 299 HIS cc_start: 0.8810 (m90) cc_final: 0.8495 (m90) REVERT: 8 389 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7047 (mm-30) REVERT: I 224 TYR cc_start: 0.8326 (t80) cc_final: 0.8066 (t80) REVERT: I 400 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8111 (mm-30) REVERT: J 220 HIS cc_start: 0.8516 (p90) cc_final: 0.7973 (p90) REVERT: J 262 LYS cc_start: 0.8600 (mttp) cc_final: 0.8334 (mttm) REVERT: J 263 ARG cc_start: 0.8254 (ttt-90) cc_final: 0.7967 (ttt-90) REVERT: g 99 LYS cc_start: 0.8750 (mmtm) cc_final: 0.8455 (tptp) REVERT: m 159 ASN cc_start: 0.9159 (t0) cc_final: 0.8823 (t0) REVERT: q 281 ARG cc_start: 0.8178 (mmt180) cc_final: 0.7462 (mtt180) REVERT: w 551 LEU cc_start: 0.7685 (mm) cc_final: 0.7274 (tp) outliers start: 26 outliers final: 18 residues processed: 230 average time/residue: 0.1627 time to fit residues: 56.9555 Evaluate side-chains 221 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 389 GLU Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain 8 residue 522 ILE Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain I residue 254 GLN Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 451 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN I 319 ASN I 530 ASN N 123 GLN w 694 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.120466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.091539 restraints weight = 35738.573| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.94 r_work: 0.3204 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2007 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= 0.210 Angle : 0.711 10.214 29210 Z= 0.324 Chirality : 0.054 0.438 3421 Planarity : 0.005 0.080 3160 Dihedral : 13.957 163.250 4101 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.88 % Allowed : 12.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.19), residues: 2077 helix: 1.57 (0.15), residues: 1143 sheet: -1.47 (0.51), residues: 102 loop : -1.11 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG q 406 TYR 0.014 0.002 TYR 8 516 PHE 0.018 0.002 PHE l 143 TRP 0.010 0.001 TRP N 120 HIS 0.005 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (21182) covalent geometry : angle 0.71089 / 0.32 (29210) hydrogen bonds : bond 0.04471 / 2.32 ( 881) hydrogen bonds : angle 3.82587 / 1.48 ( 2447) *********************** 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 243 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 299 HIS cc_start: 0.8854 (m170) cc_final: 0.8507 (m90) REVERT: 8 389 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7129 (mm-30) REVERT: A 159 ASN cc_start: 0.8169 (t0) cc_final: 0.7820 (t0) REVERT: I 511 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8925 (mp) REVERT: J 220 HIS cc_start: 0.8552 (p90) cc_final: 0.8009 (p90) REVERT: J 260 GLU cc_start: 0.8452 (tp30) cc_final: 0.8087 (tp30) REVERT: J 262 LYS cc_start: 0.8578 (mttp) cc_final: 0.8335 (mttm) REVERT: J 263 ARG cc_start: 0.8374 (ttt-90) cc_final: 0.8093 (ttt-90) REVERT: g 99 LYS cc_start: 0.8913 (mmtm) cc_final: 0.8529 (tptp) REVERT: q 410 LYS cc_start: 0.7462 (pttp) cc_final: 0.6945 (tptt) REVERT: w 551 LEU cc_start: 0.7658 (mm) cc_final: 0.7270 (tp) outliers start: 36 outliers final: 24 residues processed: 232 average time/residue: 0.1564 time to fit residues: 55.0004 Evaluate side-chains 224 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 389 GLU Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain I residue 184 VAL Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 451 VAL 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 N residue 125 SER Chi-restraints excluded: chain g residue 101 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 314 VAL Chi-restraints excluded: chain q residue 334 SER Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 688 THR 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 198 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 29 optimal weight: 0.0030 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 319 ASN N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.123084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.094195 restraints weight = 35414.224| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.94 r_work: 0.3243 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2056 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= 0.124 Angle : 0.634 9.398 29210 Z= 0.289 Chirality : 0.049 0.347 3421 Planarity : 0.004 0.078 3160 Dihedral : 13.899 167.074 4101 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.36 % Allowed : 12.60 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 2077 helix: 1.75 (0.16), residues: 1141 sheet: -1.49 (0.51), residues: 102 loop : -1.03 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG q 406 TYR 0.016 0.001 TYR q 322 PHE 0.015 0.001 PHE J 217 TRP 0.008 0.001 TRP N 120 HIS 0.004 0.000 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (21182) covalent geometry : angle 0.63434 / 0.29 (29210) hydrogen bonds : bond 0.03862 / 2.01 ( 881) hydrogen bonds : angle 3.64059 / 1.40 ( 2447) *********************** 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 233 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 299 HIS cc_start: 0.8825 (m170) cc_final: 0.8537 (m90) REVERT: 8 389 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7067 (mm-30) REVERT: A 159 ASN cc_start: 0.8086 (t0) cc_final: 0.7751 (t0) REVERT: I 400 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8086 (mm-30) REVERT: J 220 HIS cc_start: 0.8488 (p90) cc_final: 0.8000 (p90) REVERT: J 260 GLU cc_start: 0.8407 (tp30) cc_final: 0.8022 (tp30) REVERT: J 262 LYS cc_start: 0.8591 (mttp) cc_final: 0.8353 (mttm) REVERT: J 263 ARG cc_start: 0.8340 (ttt-90) cc_final: 0.8027 (ttt-90) REVERT: g 99 LYS cc_start: 0.8846 (mmtm) cc_final: 0.8480 (tptp) REVERT: m 159 ASN cc_start: 0.9141 (t0) cc_final: 0.8791 (t0) REVERT: q 403 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7608 (m-10) REVERT: w 469 MET cc_start: 0.7687 (ttt) cc_final: 0.7440 (mtp) REVERT: w 551 LEU cc_start: 0.7613 (mm) cc_final: 0.7320 (tp) outliers start: 26 outliers final: 21 residues processed: 223 average time/residue: 0.1594 time to fit residues: 54.1100 Evaluate side-chains 225 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 389 GLU Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain 8 residue 522 ILE Chi-restraints excluded: chain 8 residue 603 THR 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 280 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 451 VAL Chi-restraints excluded: chain I residue 489 MET Chi-restraints excluded: chain N residue 125 SER 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 w residue 567 VAL Chi-restraints excluded: chain w residue 691 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 118 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 57 optimal weight: 0.0570 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 530 ASN N 123 GLN i 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.120631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.091575 restraints weight = 35993.332| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.04 r_work: 0.3203 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21182 Z= 0.193 Angle : 0.691 10.189 29210 Z= 0.315 Chirality : 0.052 0.387 3421 Planarity : 0.005 0.091 3160 Dihedral : 13.907 170.552 4101 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.78 % Allowed : 12.60 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.19), residues: 2077 helix: 1.62 (0.15), residues: 1141 sheet: -1.56 (0.51), residues: 102 loop : -1.13 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG q 406 TYR 0.014 0.002 TYR 8 516 PHE 0.016 0.002 PHE l 143 TRP 0.009 0.001 TRP N 120 HIS 0.005 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (21182) covalent geometry : angle 0.69127 / 0.32 (29210) hydrogen bonds : bond 0.04313 / 2.24 ( 881) hydrogen bonds : angle 3.76576 / 1.46 ( 2447) *********************** 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 240 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 299 HIS cc_start: 0.8849 (m170) cc_final: 0.8552 (m90) REVERT: 8 389 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: I 400 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8099 (mm-30) REVERT: I 511 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8931 (mp) REVERT: J 220 HIS cc_start: 0.8532 (p90) cc_final: 0.8176 (p90) REVERT: J 262 LYS cc_start: 0.8618 (mttp) cc_final: 0.8374 (mttm) REVERT: g 99 LYS cc_start: 0.8869 (mmtm) cc_final: 0.8496 (tptp) REVERT: l 42 ASP cc_start: 0.7893 (p0) cc_final: 0.7671 (p0) REVERT: q 403 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7510 (m-10) REVERT: w 469 MET cc_start: 0.7825 (ttt) cc_final: 0.7520 (mtp) REVERT: w 551 LEU cc_start: 0.7678 (mm) cc_final: 0.7345 (tp) outliers start: 34 outliers final: 26 residues processed: 228 average time/residue: 0.1566 time to fit residues: 54.7352 Evaluate side-chains 230 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 353 MET Chi-restraints excluded: chain 8 residue 389 GLU Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain 8 residue 522 ILE Chi-restraints excluded: chain 8 residue 603 THR 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 451 VAL 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 N residue 125 SER 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 314 VAL Chi-restraints excluded: chain q residue 334 SER Chi-restraints excluded: chain q residue 403 TYR Chi-restraints excluded: chain w residue 567 VAL Chi-restraints excluded: chain w residue 691 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 205 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 120 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 213 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 HIS A 159 ASN I 530 ASN N 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.123909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094971 restraints weight = 35587.944| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.00 r_work: 0.3258 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2216 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= 0.114 Angle : 0.627 9.037 29210 Z= 0.287 Chirality : 0.048 0.313 3421 Planarity : 0.004 0.085 3160 Dihedral : 13.822 174.230 4101 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.62 % Allowed : 12.75 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 2077 helix: 1.86 (0.16), residues: 1139 sheet: -1.51 (0.52), residues: 102 loop : -1.02 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG w 653 TYR 0.020 0.001 TYR q 322 PHE 0.014 0.001 PHE J 217 TRP 0.007 0.001 TRP N 120 HIS 0.003 0.000 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (21182) covalent geometry : angle 0.62658 / 0.29 (29210) hydrogen bonds : bond 0.03716 / 1.94 ( 881) hydrogen bonds : angle 3.57813 / 1.39 ( 2447) *********************** 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 245 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 299 HIS cc_start: 0.8759 (m170) cc_final: 0.8467 (m90) REVERT: 8 389 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7051 (mm-30) REVERT: I 400 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7978 (mm-30) REVERT: I 511 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8882 (mp) REVERT: J 220 HIS cc_start: 0.8468 (p90) cc_final: 0.7995 (p90) REVERT: J 260 GLU cc_start: 0.8339 (tp30) cc_final: 0.7980 (tp30) REVERT: J 262 LYS cc_start: 0.8572 (mttp) cc_final: 0.8357 (mttm) REVERT: J 263 ARG cc_start: 0.8477 (ttt-90) cc_final: 0.8268 (ttt-90) REVERT: g 99 LYS cc_start: 0.8795 (mmtm) cc_final: 0.8480 (tptp) REVERT: m 159 ASN cc_start: 0.9078 (t0) cc_final: 0.8744 (t0) REVERT: q 403 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7635 (m-10) REVERT: w 469 MET cc_start: 0.7641 (ttt) cc_final: 0.7417 (mtp) REVERT: w 551 LEU cc_start: 0.7661 (mm) cc_final: 0.7388 (tp) outliers start: 31 outliers final: 22 residues processed: 231 average time/residue: 0.1556 time to fit residues: 54.7218 Evaluate side-chains 231 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 7 residue 108 LEU Chi-restraints excluded: chain 8 residue 303 GLU Chi-restraints excluded: chain 8 residue 341 PHE Chi-restraints excluded: chain 8 residue 389 GLU Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain I residue 280 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 451 VAL 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 g residue 101 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 188 optimal weight: 0.6980 chunk 182 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 203 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 530 ASN w 694 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.123712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.094791 restraints weight = 35343.539| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.98 r_work: 0.3253 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2279 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= 0.124 Angle : 0.634 9.070 29210 Z= 0.292 Chirality : 0.048 0.316 3421 Planarity : 0.004 0.091 3160 Dihedral : 13.764 177.359 4101 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.62 % Allowed : 12.65 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 2077 helix: 1.86 (0.16), residues: 1140 sheet: -1.52 (0.52), residues: 102 loop : -1.01 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG q 406 TYR 0.014 0.001 TYR 8 516 PHE 0.014 0.001 PHE J 217 TRP 0.007 0.001 TRP N 120 HIS 0.004 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (21182) covalent geometry : angle 0.63448 / 0.29 (29210) hydrogen bonds : bond 0.03821 / 1.99 ( 881) hydrogen bonds : angle 3.60113 / 1.40 ( 2447) *********************** 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 236 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 299 HIS cc_start: 0.8801 (m170) cc_final: 0.8507 (m90) REVERT: 8 389 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7034 (mm-30) REVERT: I 400 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8040 (mm-30) REVERT: I 511 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8903 (mp) REVERT: J 220 HIS cc_start: 0.8480 (p90) cc_final: 0.8017 (p90) REVERT: J 262 LYS cc_start: 0.8559 (mttp) cc_final: 0.8348 (mttp) REVERT: J 263 ARG cc_start: 0.8445 (ttt-90) cc_final: 0.8220 (ttt-90) REVERT: g 99 LYS cc_start: 0.8741 (mmtm) cc_final: 0.8508 (tptm) REVERT: m 159 ASN cc_start: 0.9080 (t0) cc_final: 0.8743 (t0) REVERT: q 403 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7652 (m-10) REVERT: w 469 MET cc_start: 0.7648 (ttt) cc_final: 0.7429 (mtp) REVERT: w 551 LEU cc_start: 0.7679 (mm) cc_final: 0.7400 (tp) outliers start: 31 outliers final: 25 residues processed: 226 average time/residue: 0.1524 time to fit residues: 52.6759 Evaluate side-chains 228 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 7 residue 108 LEU Chi-restraints excluded: chain 8 residue 303 GLU Chi-restraints excluded: chain 8 residue 341 PHE Chi-restraints excluded: chain 8 residue 389 GLU Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain 8 residue 603 THR 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 280 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 451 VAL 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 g residue 101 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 694 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 163 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 130 optimal weight: 0.0770 chunk 220 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.3140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 530 ASN N 123 GLN l 155 ASN w 694 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.121868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092817 restraints weight = 35717.271| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.94 r_work: 0.3223 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21182 Z= 0.173 Angle : 0.677 11.027 29210 Z= 0.313 Chirality : 0.050 0.360 3421 Planarity : 0.005 0.088 3160 Dihedral : 13.811 179.754 4101 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.67 % Allowed : 12.91 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.19), residues: 2077 helix: 1.71 (0.16), residues: 1142 sheet: -1.39 (0.58), residues: 88 loop : -1.09 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG q 406 TYR 0.028 0.002 TYR q 322 PHE 0.016 0.001 PHE l 143 TRP 0.008 0.001 TRP 8 326 HIS 0.004 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (21182) covalent geometry : angle 0.67702 / 0.31 (29210) hydrogen bonds : bond 0.04203 / 2.19 ( 881) hydrogen bonds : angle 3.72422 / 1.45 ( 2447) ********************** 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 233 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 299 HIS cc_start: 0.8828 (m170) cc_final: 0.8533 (m90) REVERT: 8 389 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7117 (mm-30) REVERT: I 400 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8072 (mm-30) REVERT: I 511 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8923 (mp) REVERT: J 220 HIS cc_start: 0.8515 (p90) cc_final: 0.8021 (p90) REVERT: J 260 GLU cc_start: 0.8434 (tp30) cc_final: 0.7977 (tp30) REVERT: J 262 LYS cc_start: 0.8595 (mttp) cc_final: 0.8375 (mttm) REVERT: J 263 ARG cc_start: 0.8478 (ttt-90) cc_final: 0.8184 (ttt-90) REVERT: g 98 GLN cc_start: 0.7570 (tp40) cc_final: 0.7070 (tp-100) REVERT: g 99 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8429 (tptp) REVERT: m 159 ASN cc_start: 0.9133 (t0) cc_final: 0.8754 (t0) REVERT: q 403 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: w 469 MET cc_start: 0.7766 (ttt) cc_final: 0.7511 (mtp) REVERT: w 694 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8516 (t0) outliers start: 32 outliers final: 26 residues processed: 223 average time/residue: 0.1595 time to fit residues: 53.9428 Evaluate side-chains 231 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 7 residue 108 LEU Chi-restraints excluded: chain 8 residue 303 GLU Chi-restraints excluded: chain 8 residue 341 PHE Chi-restraints excluded: chain 8 residue 389 GLU Chi-restraints excluded: chain 8 residue 412 HIS Chi-restraints excluded: chain 8 residue 603 THR 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 280 ILE Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 451 VAL 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 N residue 125 SER Chi-restraints excluded: chain l residue 28 VAL Chi-restraints excluded: chain l residue 150 THR Chi-restraints excluded: chain l residue 155 ASN 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 694 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 15 optimal weight: 0.0870 chunk 51 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 178 optimal weight: 0.0870 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 123 GLN ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 191 GLN w 694 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.124644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.095783 restraints weight = 35446.074| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.98 r_work: 0.3269 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2370 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= 0.108 Angle : 0.630 10.175 29210 Z= 0.291 Chirality : 0.048 0.300 3421 Planarity : 0.004 0.092 3160 Dihedral : 13.757 178.607 4101 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.36 % Allowed : 13.33 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 2077 helix: 1.84 (0.16), residues: 1145 sheet: -1.30 (0.58), residues: 88 loop : -1.04 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG q 406 TYR 0.014 0.001 TYR 8 516 PHE 0.014 0.001 PHE J 217 TRP 0.007 0.001 TRP 8 326 HIS 0.003 0.000 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (21182) covalent geometry : angle 0.63015 / 0.29 (29210) hydrogen bonds : bond 0.03717 / 1.94 ( 881) hydrogen bonds : angle 3.58756 / 1.39 ( 2447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6710.76 seconds wall clock time: 115 minutes 23.80 seconds (6923.80 seconds total)