Starting phenix.real_space_refine on Wed Mar 20 05:56:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3e_13790/03_2024/7q3e_13790_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3e_13790/03_2024/7q3e_13790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3e_13790/03_2024/7q3e_13790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3e_13790/03_2024/7q3e_13790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3e_13790/03_2024/7q3e_13790_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3e_13790/03_2024/7q3e_13790_trim_updated.pdb" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 72 5.16 5 C 8511 2.51 5 N 2248 2.21 5 O 2420 1.98 5 H 13368 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26622 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 8899 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 529} Chain breaks: 4 Chain: "B" Number of atoms: 7967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 7967 Classifications: {'peptide': 503} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 480} Chain breaks: 6 Chain: "C" Number of atoms: 6161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6161 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 358} Chain breaks: 1 Chain: "D" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3595 Unusual residues: {'GTP': 1} Classifications: {'peptide': 226, 'undetermined': 1} Link IDs: {'PTRANS': 12, 'TRANS': 213, None: 1} Not linked: pdbres="ALA D 245 " pdbres="GTP D 301 " Chain breaks: 1 Time building chain proxies: 11.80, per 1000 atoms: 0.44 Number of scatterers: 26622 At special positions: 0 Unit cell: (89.44, 142.76, 135.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 3 15.00 O 2420 8.00 N 2248 7.00 C 8511 6.00 H 13368 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.86 Conformation dependent library (CDL) restraints added in 2.6 seconds 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3146 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 15 sheets defined 35.2% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 123 through 126 removed outlier: 4.273A pdb=" N GLY A 126 " --> pdb=" O SER A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 457 through 466 Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 486 through 501 Processing helix chain 'A' and resid 507 through 521 removed outlier: 4.403A pdb=" N PHE A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 532 through 551 removed outlier: 5.195A pdb=" N GLU A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Proline residue: A 538 - end of helix Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.781A pdb=" N VAL A 564 " --> pdb=" O PHE A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 577 removed outlier: 4.959A pdb=" N HIS A 576 " --> pdb=" O MET A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 588 through 597 removed outlier: 3.545A pdb=" N ALA A 591 " --> pdb=" O ALA A 588 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 594 " --> pdb=" O ALA A 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 58 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 339 through 362 removed outlier: 3.865A pdb=" N LYS B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLY B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B 359 " --> pdb=" O CYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 419 Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 432 through 447 removed outlier: 4.081A pdb=" N HIS B 437 " --> pdb=" O PRO B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 473 removed outlier: 4.202A pdb=" N VAL B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASN B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 499 removed outlier: 3.683A pdb=" N ASP B 496 " --> pdb=" O THR B 492 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 507 through 510 No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 536 through 548 Processing helix chain 'B' and resid 551 through 555 Processing helix chain 'B' and resid 626 through 651 removed outlier: 3.912A pdb=" N LEU B 639 " --> pdb=" O THR B 635 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLY B 641 " --> pdb=" O HIS B 637 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL B 642 " --> pdb=" O GLN B 638 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER B 644 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ARG B 645 " --> pdb=" O GLY B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 665 removed outlier: 3.509A pdb=" N LEU B 665 " --> pdb=" O ASP B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 788 Processing helix chain 'B' and resid 817 through 821 Processing helix chain 'B' and resid 826 through 859 removed outlier: 3.815A pdb=" N GLN B 830 " --> pdb=" O SER B 826 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 844 " --> pdb=" O LEU B 840 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE B 845 " --> pdb=" O SER B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 937 Processing helix chain 'C' and resid 40 through 54 removed outlier: 4.001A pdb=" N HIS C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 110 Processing helix chain 'C' and resid 112 through 115 No H-bonds generated for 'chain 'C' and resid 112 through 115' Processing helix chain 'C' and resid 121 through 139 removed outlier: 4.308A pdb=" N ARG C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N CYS C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 149 No H-bonds generated for 'chain 'C' and resid 146 through 149' Processing helix chain 'C' and resid 162 through 174 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.882A pdb=" N LEU C 204 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Proline residue: C 206 - end of helix Processing helix chain 'C' and resid 256 through 258 No H-bonds generated for 'chain 'C' and resid 256 through 258' Processing helix chain 'C' and resid 261 through 282 Proline residue: C 270 - end of helix removed outlier: 4.915A pdb=" N GLU C 273 " --> pdb=" O GLN C 269 " (cutoff:3.500A) Proline residue: C 274 - end of helix removed outlier: 3.651A pdb=" N LEU C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) Proline residue: C 280 - end of helix Processing helix chain 'C' and resid 323 through 339 Processing helix chain 'C' and resid 397 through 412 removed outlier: 4.684A pdb=" N ARG C 401 " --> pdb=" O HIS C 398 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 403 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 19 through 27 removed outlier: 3.717A pdb=" N CYS D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 76 Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.818A pdb=" N LYS D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 Proline residue: D 130 - end of helix Processing helix chain 'D' and resid 148 through 152 Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 187 through 197 Processing helix chain 'D' and resid 222 through 244 removed outlier: 4.702A pdb=" N HIS D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 381 through 384 Processing sheet with id= B, first strand: chain 'A' and resid 8 through 10 Processing sheet with id= C, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.701A pdb=" N LEU A 99 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER A 88 " --> pdb=" O GLN A 97 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLN A 97 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N SER A 111 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 142 through 145 Processing sheet with id= E, first strand: chain 'A' and resid 197 through 200 removed outlier: 3.555A pdb=" N SER A 247 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLY A 237 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL A 245 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A 239 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 255 through 260 removed outlier: 6.796A pdb=" N VAL A 271 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL A 258 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE A 269 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE A 260 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLN A 267 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLU A 289 " --> pdb=" O CYS A 297 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N CYS A 297 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 291 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 340 through 344 removed outlier: 4.109A pdb=" N SER A 329 " --> pdb=" O CYS A 325 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 351 through 354 removed outlier: 3.915A pdb=" N LEU A 351 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 368 through 373 removed outlier: 6.476A pdb=" N THR B 317 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE B 331 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 528 through 532 removed outlier: 6.880A pdb=" N LEU B 523 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER B 532 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER B 521 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU B 608 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER B 521 " --> pdb=" O CYS B 606 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS B 606 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B 523 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B 604 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR B 593 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU B 69 " --> pdb=" O GLY B 561 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU B 563 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR B 67 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE B 565 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 65 " --> pdb=" O ILE B 565 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 811 through 814 removed outlier: 6.946A pdb=" N CYS B 920 " --> pdb=" O PHE B 800 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR B 802 " --> pdb=" O TYR B 918 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TYR B 918 " --> pdb=" O TYR B 802 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ALA B 804 " --> pdb=" O GLU B 916 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU B 916 " --> pdb=" O ALA B 804 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 62 through 64 removed outlier: 5.987A pdb=" N ALA C 16 " --> pdb=" O PRO C 22 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 27 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 152 through 154 removed outlier: 4.184A pdb=" N PHE C 311 " --> pdb=" O CYS C 154 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 390 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU C 299 " --> pdb=" O LEU C 388 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU C 388 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU C 301 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C 386 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 217 through 223 removed outlier: 6.344A pdb=" N VAL C 183 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL C 187 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 202 through 204 removed outlier: 3.592A pdb=" N ASP D 52 " --> pdb=" O VAL D 107 " (cutoff:3.500A) 562 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.99 Time building geometry restraints manager: 23.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 13326 1.13 - 1.30: 2166 1.30 - 1.48: 5499 1.48 - 1.65: 5823 1.65 - 1.82: 102 Bond restraints: 26916 Sorted by residual: bond pdb=" NE1 TRP D 15 " pdb=" HE1 TRP D 15 " ideal model delta sigma weight residual 0.860 1.027 -0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" CD1 PHE A 400 " pdb=" HD1 PHE A 400 " ideal model delta sigma weight residual 0.930 1.096 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" CD2 PHE A 100 " pdb=" HD2 PHE A 100 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.85e+01 bond pdb=" NE ARG A 348 " pdb=" HE ARG A 348 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.81e+01 bond pdb=" CD1 PHE D 145 " pdb=" HD1 PHE D 145 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.78e+01 ... (remaining 26911 not shown) Histogram of bond angle deviations from ideal: 95.48 - 103.15: 245 103.15 - 110.81: 28593 110.81 - 118.48: 7297 118.48 - 126.15: 12341 126.15 - 133.81: 302 Bond angle restraints: 48778 Sorted by residual: angle pdb=" C PHE B 570 " pdb=" N PRO B 571 " pdb=" CA PRO B 571 " ideal model delta sigma weight residual 120.21 128.43 -8.22 9.60e-01 1.09e+00 7.33e+01 angle pdb=" C GLY A 188 " pdb=" N PRO A 189 " pdb=" CA PRO A 189 " ideal model delta sigma weight residual 120.03 128.29 -8.26 9.90e-01 1.02e+00 6.95e+01 angle pdb=" C GLN A 264 " pdb=" N PRO A 265 " pdb=" CA PRO A 265 " ideal model delta sigma weight residual 119.56 127.66 -8.10 1.01e+00 9.80e-01 6.43e+01 angle pdb=" C GLY B 655 " pdb=" N PRO B 656 " pdb=" CA PRO B 656 " ideal model delta sigma weight residual 120.03 127.48 -7.45 9.90e-01 1.02e+00 5.66e+01 angle pdb=" C VAL D 185 " pdb=" N PRO D 186 " pdb=" CA PRO D 186 " ideal model delta sigma weight residual 119.85 127.36 -7.51 1.01e+00 9.80e-01 5.53e+01 ... (remaining 48773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.94: 12222 32.94 - 65.88: 381 65.88 - 98.82: 17 98.82 - 131.76: 1 131.76 - 164.70: 4 Dihedral angle restraints: 12625 sinusoidal: 6923 harmonic: 5702 Sorted by residual: dihedral pdb=" O3B GTP D 301 " pdb=" O3A GTP D 301 " pdb=" PB GTP D 301 " pdb=" PA GTP D 301 " ideal model delta sinusoidal sigma weight residual -68.92 95.78 -164.70 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C5' GTP D 301 " pdb=" O5' GTP D 301 " pdb=" PA GTP D 301 " pdb=" O3A GTP D 301 " ideal model delta sinusoidal sigma weight residual 69.27 -80.66 149.93 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" C8 GTP D 301 " pdb=" C1' GTP D 301 " pdb=" N9 GTP D 301 " pdb=" O4' GTP D 301 " ideal model delta sinusoidal sigma weight residual 104.59 -33.30 137.89 1 2.00e+01 2.50e-03 4.18e+01 ... (remaining 12622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1493 0.072 - 0.145: 499 0.145 - 0.217: 96 0.217 - 0.289: 15 0.289 - 0.361: 6 Chirality restraints: 2109 Sorted by residual: chirality pdb=" CA PHE A 401 " pdb=" N PHE A 401 " pdb=" C PHE A 401 " pdb=" CB PHE A 401 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA LEU A 138 " pdb=" N LEU A 138 " pdb=" C LEU A 138 " pdb=" CB LEU A 138 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA TRP A 90 " pdb=" N TRP A 90 " pdb=" C TRP A 90 " pdb=" CB TRP A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 2106 not shown) Planarity restraints: 3894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 90 " 0.177 2.00e-02 2.50e+03 5.74e-02 1.32e+02 pdb=" CG TRP A 90 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP A 90 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP A 90 " -0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP A 90 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TRP A 90 " -0.035 2.00e-02 2.50e+03 pdb=" CE3 TRP A 90 " -0.046 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 90 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 90 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP A 90 " 0.025 2.00e-02 2.50e+03 pdb=" HD1 TRP A 90 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP A 90 " -0.011 2.00e-02 2.50e+03 pdb=" HE3 TRP A 90 " -0.057 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 90 " 0.056 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 90 " -0.013 2.00e-02 2.50e+03 pdb=" HH2 TRP A 90 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 845 " -0.122 2.00e-02 2.50e+03 4.78e-02 6.85e+01 pdb=" CG PHE B 845 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 845 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE B 845 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 PHE B 845 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE B 845 " 0.022 2.00e-02 2.50e+03 pdb=" CZ PHE B 845 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 PHE B 845 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 PHE B 845 " 0.021 2.00e-02 2.50e+03 pdb=" HE1 PHE B 845 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE B 845 " -0.010 2.00e-02 2.50e+03 pdb=" HZ PHE B 845 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 27 " 0.103 2.00e-02 2.50e+03 4.29e-02 5.51e+01 pdb=" CG TYR A 27 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 27 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 27 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 27 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR A 27 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR A 27 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 27 " 0.082 2.00e-02 2.50e+03 pdb=" HD1 TYR A 27 " -0.021 2.00e-02 2.50e+03 pdb=" HD2 TYR A 27 " -0.011 2.00e-02 2.50e+03 pdb=" HE1 TYR A 27 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 27 " -0.009 2.00e-02 2.50e+03 ... (remaining 3891 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2583 2.20 - 2.80: 53607 2.80 - 3.40: 75656 3.40 - 4.00: 102996 4.00 - 4.60: 154460 Nonbonded interactions: 389302 Sorted by model distance: nonbonded pdb="HG23 THR C 237 " pdb=" HG CYS C 247 " model vdw 1.600 2.440 nonbonded pdb=" O TYR D 24 " pdb=" HG CYS D 27 " model vdw 1.652 2.620 nonbonded pdb=" O PRO C 274 " pdb=" HG CYS C 278 " model vdw 1.670 2.620 nonbonded pdb=" O ASP B 423 " pdb=" HG CYS B 427 " model vdw 1.673 2.620 nonbonded pdb=" O THR C 239 " pdb=" H LEU D 39 " model vdw 1.693 1.850 ... (remaining 389297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.49 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.380 Extract box with map and model: 7.210 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 85.190 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 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 : 0.013 0.100 13548 Z= 0.851 Angle : 1.334 11.796 18387 Z= 0.898 Chirality : 0.074 0.361 2109 Planarity : 0.013 0.071 2326 Dihedral : 12.612 164.700 4998 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 1640 helix: -1.72 (0.16), residues: 521 sheet: 1.75 (0.25), residues: 382 loop : 1.57 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.121 0.014 TRP A 90 HIS 0.011 0.002 HIS C 341 PHE 0.079 0.009 PHE B 845 TYR 0.094 0.014 TYR A 27 ARG 0.009 0.001 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 ILE cc_start: 0.8950 (mm) cc_final: 0.8732 (mt) REVERT: D 16 HIS cc_start: 0.8453 (p-80) cc_final: 0.8240 (p90) REVERT: D 157 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7991 (mm110) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.5977 time to fit residues: 254.9368 Evaluate side-chains 176 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS B 848 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13548 Z= 0.201 Angle : 0.637 6.285 18387 Z= 0.346 Chirality : 0.042 0.204 2109 Planarity : 0.005 0.046 2326 Dihedral : 9.367 166.546 1810 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.28 % Favored : 98.54 % Rotamer: Outliers : 1.37 % Allowed : 7.85 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1640 helix: 0.44 (0.21), residues: 525 sheet: 1.11 (0.24), residues: 387 loop : 1.16 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 90 HIS 0.012 0.001 HIS A 576 PHE 0.023 0.002 PHE B 845 TYR 0.023 0.002 TYR B 902 ARG 0.003 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 516 TYR cc_start: 0.7320 (m-80) cc_final: 0.6803 (m-80) REVERT: C 219 ASP cc_start: 0.7820 (t0) cc_final: 0.7604 (t0) REVERT: D 157 GLN cc_start: 0.8438 (mm-40) cc_final: 0.7849 (mm110) outliers start: 20 outliers final: 16 residues processed: 206 average time/residue: 0.5780 time to fit residues: 174.6284 Evaluate side-chains 177 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 135 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN B 428 GLN B 562 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 13548 Z= 0.396 Angle : 0.680 8.586 18387 Z= 0.364 Chirality : 0.041 0.153 2109 Planarity : 0.005 0.048 2326 Dihedral : 8.881 160.155 1810 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.32 % Favored : 97.56 % Rotamer: Outliers : 2.05 % Allowed : 8.33 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1640 helix: 0.72 (0.21), residues: 526 sheet: 0.33 (0.25), residues: 388 loop : 0.68 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 115 HIS 0.007 0.001 HIS A 499 PHE 0.015 0.002 PHE A 373 TYR 0.016 0.002 TYR B 902 ARG 0.005 0.001 ARG B 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 157 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8127 (mm110) REVERT: D 231 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8503 (mp) outliers start: 30 outliers final: 21 residues processed: 178 average time/residue: 0.5793 time to fit residues: 151.3615 Evaluate side-chains 163 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 231 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 0.0470 chunk 160 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13548 Z= 0.290 Angle : 0.595 6.612 18387 Z= 0.311 Chirality : 0.040 0.156 2109 Planarity : 0.005 0.050 2326 Dihedral : 7.890 130.711 1810 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.18 % Allowed : 8.87 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1640 helix: 0.79 (0.22), residues: 535 sheet: 0.14 (0.25), residues: 381 loop : 0.50 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 115 HIS 0.005 0.001 HIS A 499 PHE 0.011 0.001 PHE B 883 TYR 0.013 0.001 TYR B 902 ARG 0.012 0.000 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 2.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 25 residues processed: 173 average time/residue: 0.5545 time to fit residues: 144.4835 Evaluate side-chains 163 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 135 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS A 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13548 Z= 0.279 Angle : 0.580 6.655 18387 Z= 0.302 Chirality : 0.040 0.145 2109 Planarity : 0.004 0.048 2326 Dihedral : 7.522 131.052 1810 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.12 % Allowed : 10.31 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1640 helix: 0.87 (0.22), residues: 529 sheet: -0.02 (0.25), residues: 380 loop : 0.34 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 115 HIS 0.017 0.001 HIS A 296 PHE 0.012 0.001 PHE A 560 TYR 0.013 0.001 TYR B 902 ARG 0.007 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 26 residues processed: 165 average time/residue: 0.5297 time to fit residues: 130.1781 Evaluate side-chains 160 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 135 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 HIS B 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13548 Z= 0.181 Angle : 0.543 7.059 18387 Z= 0.279 Chirality : 0.040 0.154 2109 Planarity : 0.004 0.048 2326 Dihedral : 7.268 132.749 1810 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.77 % Allowed : 11.26 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1640 helix: 1.16 (0.23), residues: 529 sheet: -0.02 (0.25), residues: 380 loop : 0.37 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 115 HIS 0.033 0.001 HIS A 296 PHE 0.014 0.001 PHE A 560 TYR 0.018 0.001 TYR B 902 ARG 0.006 0.000 ARG C 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 248 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6915 (mt) REVERT: D 230 VAL cc_start: 0.8537 (m) cc_final: 0.8248 (p) outliers start: 26 outliers final: 24 residues processed: 164 average time/residue: 0.5439 time to fit residues: 133.7995 Evaluate side-chains 156 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 135 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13548 Z= 0.234 Angle : 0.554 6.428 18387 Z= 0.285 Chirality : 0.040 0.149 2109 Planarity : 0.004 0.047 2326 Dihedral : 7.061 134.106 1810 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.84 % Allowed : 11.33 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1640 helix: 1.25 (0.23), residues: 523 sheet: -0.08 (0.25), residues: 392 loop : 0.25 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 97 HIS 0.010 0.001 HIS A 296 PHE 0.014 0.001 PHE A 560 TYR 0.023 0.001 TYR B 902 ARG 0.003 0.000 ARG B 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 248 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6943 (mt) REVERT: D 230 VAL cc_start: 0.8487 (m) cc_final: 0.8205 (p) outliers start: 27 outliers final: 23 residues processed: 156 average time/residue: 0.5533 time to fit residues: 129.4355 Evaluate side-chains 154 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 135 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13548 Z= 0.263 Angle : 0.561 6.453 18387 Z= 0.290 Chirality : 0.040 0.147 2109 Planarity : 0.004 0.048 2326 Dihedral : 6.993 133.482 1810 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.91 % Allowed : 11.88 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.21), residues: 1640 helix: 1.23 (0.23), residues: 523 sheet: -0.16 (0.25), residues: 393 loop : 0.15 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 115 HIS 0.021 0.001 HIS A 296 PHE 0.011 0.001 PHE B 883 TYR 0.017 0.001 TYR B 902 ARG 0.004 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 831 LEU cc_start: 0.8169 (tp) cc_final: 0.7902 (tt) REVERT: C 248 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7030 (mt) REVERT: D 230 VAL cc_start: 0.8476 (m) cc_final: 0.8171 (p) outliers start: 28 outliers final: 24 residues processed: 163 average time/residue: 0.5646 time to fit residues: 137.1944 Evaluate side-chains 160 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 135 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 134 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 830 GLN B 834 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13548 Z= 0.204 Angle : 0.542 6.872 18387 Z= 0.278 Chirality : 0.040 0.160 2109 Planarity : 0.004 0.048 2326 Dihedral : 6.900 132.877 1810 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.77 % Allowed : 12.01 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1640 helix: 1.35 (0.23), residues: 522 sheet: -0.09 (0.25), residues: 387 loop : 0.14 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 253 HIS 0.006 0.001 HIS A 296 PHE 0.012 0.001 PHE A 560 TYR 0.015 0.001 TYR B 902 ARG 0.005 0.000 ARG A 594 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 831 LEU cc_start: 0.8089 (tp) cc_final: 0.7849 (tt) REVERT: C 248 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6967 (mt) REVERT: D 230 VAL cc_start: 0.8502 (m) cc_final: 0.8203 (p) outliers start: 26 outliers final: 23 residues processed: 157 average time/residue: 0.5733 time to fit residues: 135.8441 Evaluate side-chains 156 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 135 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13548 Z= 0.193 Angle : 0.543 6.786 18387 Z= 0.275 Chirality : 0.040 0.171 2109 Planarity : 0.004 0.047 2326 Dihedral : 6.798 132.216 1810 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.50 % Allowed : 12.35 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1640 helix: 1.34 (0.23), residues: 531 sheet: -0.09 (0.26), residues: 389 loop : 0.16 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 115 HIS 0.003 0.001 HIS B 533 PHE 0.011 0.001 PHE A 560 TYR 0.015 0.001 TYR B 902 ARG 0.005 0.000 ARG A 593 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 831 LEU cc_start: 0.8077 (tp) cc_final: 0.7845 (tt) REVERT: C 248 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6973 (mt) REVERT: D 230 VAL cc_start: 0.8457 (m) cc_final: 0.8164 (p) outliers start: 22 outliers final: 21 residues processed: 153 average time/residue: 0.5827 time to fit residues: 133.6087 Evaluate side-chains 153 residues out of total 1465 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 140 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 3.9990 chunk 40 optimal weight: 0.0970 chunk 121 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.086007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.067791 restraints weight = 140818.909| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 4.96 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13548 Z= 0.224 Angle : 0.545 6.652 18387 Z= 0.279 Chirality : 0.040 0.164 2109 Planarity : 0.004 0.047 2326 Dihedral : 6.799 131.981 1810 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.57 % Allowed : 12.42 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1640 helix: 1.36 (0.23), residues: 526 sheet: -0.16 (0.26), residues: 402 loop : 0.17 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 115 HIS 0.014 0.001 HIS A 296 PHE 0.010 0.001 PHE A 560 TYR 0.014 0.001 TYR B 902 ARG 0.004 0.000 ARG A 593 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5382.91 seconds wall clock time: 95 minutes 43.15 seconds (5743.15 seconds total)