Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 09:07:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avg_15682/08_2023/8avg_15682_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avg_15682/08_2023/8avg_15682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avg_15682/08_2023/8avg_15682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avg_15682/08_2023/8avg_15682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avg_15682/08_2023/8avg_15682_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avg_15682/08_2023/8avg_15682_updated.pdb" } resolution = 4.01 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= 0.001 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 Fe 4 7.16 5 S 89 5.16 5 C 8712 2.51 5 N 2400 2.21 5 O 2541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 585": "OE1" <-> "OE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B GLU 569": "OE1" <-> "OE2" Residue "B PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 817": "OE1" <-> "OE2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C GLU 474": "OE1" <-> "OE2" Residue "C GLU 506": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 13746 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4720 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 25, 'TRANS': 577} Chain breaks: 9 Chain: "B" Number of atoms: 5494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5494 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 28, 'TRANS': 665} Chain breaks: 6 Chain: "C" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3532 Unusual residues: {'SF4': 1} Classifications: {'peptide': 436, 'undetermined': 1} Link IDs: {'PTRANS': 20, 'TRANS': 414, None: 2} Not linked: pdbres="LEU C 546 " pdbres="SF4 C 601 " Not linked: pdbres="SF4 C 601 " pdbres="SAM C 602 " Chain breaks: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10320 SG CYS C 99 46.109 48.121 84.283 1.00 35.37 S ATOM 10421 SG CYS C 112 51.785 48.553 81.278 1.00 47.71 S ATOM 10395 SG CYS C 109 46.698 46.131 78.253 1.00 46.71 S Time building chain proxies: 6.93, per 1000 atoms: 0.50 Number of scatterers: 13746 At special positions: 0 Unit cell: (79.98, 113.52, 156.52, 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) Fe 4 26.01 S 89 16.00 O 2541 8.00 N 2400 7.00 C 8712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.93 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 601 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 109 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 99 " pdb="FE2 SF4 C 601 " - pdb=" SG CYS C 112 " Number of angles added : 9 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3234 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 32 sheets defined 9.8% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 470 through 480 removed outlier: 4.381A pdb=" N GLU B 474 " --> pdb=" O ARG B 470 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'C' and resid 100 through 103 removed outlier: 3.956A pdb=" N SER C 103 " --> pdb=" O PRO C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 103' Processing helix chain 'C' and resid 132 through 140 Processing helix chain 'C' and resid 144 through 158 Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 179 through 191 Processing helix chain 'C' and resid 201 through 210 removed outlier: 4.594A pdb=" N ARG C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 226 No H-bonds generated for 'chain 'C' and resid 224 through 226' Processing helix chain 'C' and resid 229 through 238 Processing helix chain 'C' and resid 252 through 258 Processing helix chain 'C' and resid 264 through 277 removed outlier: 3.595A pdb=" N ASP C 276 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 306 Processing helix chain 'C' and resid 327 through 333 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 383 through 394 Processing helix chain 'C' and resid 497 through 511 Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.820A pdb=" N THR A 376 " --> pdb=" O ASN A 3 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.571A pdb=" N PHE A 12 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR A 368 " --> pdb=" O PHE A 12 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 41 through 43 removed outlier: 3.929A pdb=" N CYS A 23 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 71 through 76 removed outlier: 6.522A pdb=" N ALA A 86 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A 74 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS A 84 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR A 87 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP A 91 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 94 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N CYS A 104 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 115 through 117 removed outlier: 3.835A pdb=" N SER A 116 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 125 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 144 " --> pdb=" O MET A 135 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N THR A 137 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL A 142 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 197 through 200 Processing sheet with id= G, first strand: chain 'A' and resid 264 through 266 Processing sheet with id= H, first strand: chain 'A' and resid 288 through 294 removed outlier: 6.503A pdb=" N TRP A 304 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 292 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA A 302 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 301 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N THR A 324 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU A 332 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 390 through 395 Processing sheet with id= J, first strand: chain 'A' and resid 481 through 484 Processing sheet with id= K, first strand: chain 'A' and resid 507 through 510 Processing sheet with id= L, first strand: chain 'A' and resid 610 through 616 removed outlier: 4.055A pdb=" N ALA A 639 " --> pdb=" O PHE A 631 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 633 " --> pdb=" O GLU A 637 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLU A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 645 through 648 Processing sheet with id= N, first strand: chain 'A' and resid 708 through 711 Processing sheet with id= O, first strand: chain 'B' and resid 32 through 36 Processing sheet with id= P, first strand: chain 'B' and resid 87 through 91 Processing sheet with id= Q, first strand: chain 'B' and resid 113 through 117 removed outlier: 3.550A pdb=" N ILE B 116 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 128 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN B 153 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N SER B 143 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TYR B 151 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 167 through 169 removed outlier: 3.711A pdb=" N LEU B 178 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE B 191 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LYS B 199 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 233 through 238 Processing sheet with id= T, first strand: chain 'B' and resid 294 through 296 Processing sheet with id= U, first strand: chain 'B' and resid 364 through 368 removed outlier: 3.863A pdb=" N ASP B 345 " --> pdb=" O HIS B 358 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 390 through 395 removed outlier: 7.023A pdb=" N THR B 405 " --> pdb=" O GLN B 391 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 393 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE B 403 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TRP B 395 " --> pdb=" O PHE B 401 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N PHE B 401 " --> pdb=" O TRP B 395 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 406 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA B 415 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLU B 432 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TRP B 417 " --> pdb=" O TRP B 430 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TRP B 430 " --> pdb=" O TRP B 417 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 464 through 467 Processing sheet with id= X, first strand: chain 'B' and resid 596 through 598 removed outlier: 3.555A pdb=" N LEU B 598 " --> pdb=" O GLN B 608 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B 608 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 619 through 622 Processing sheet with id= Z, first strand: chain 'B' and resid 716 through 718 removed outlier: 4.270A pdb=" N LYS B 692 " --> pdb=" O SER B 688 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER B 688 " --> pdb=" O LYS B 692 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 749 through 755 Processing sheet with id= AB, first strand: chain 'B' and resid 783 through 785 removed outlier: 3.944A pdb=" N PHE B 812 " --> pdb=" O TYR B 824 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 821 " --> pdb=" O PHE B 12 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG B 825 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL B 8 " --> pdb=" O ARG B 825 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 285 through 289 removed outlier: 6.778A pdb=" N ALA B 309 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL B 288 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 307 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 570 through 575 removed outlier: 7.042A pdb=" N ALA B 585 " --> pdb=" O VAL B 571 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL B 573 " --> pdb=" O ALA B 583 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA B 583 " --> pdb=" O VAL B 573 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 88 through 91 removed outlier: 3.586A pdb=" N ALA C 88 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU C 166 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS C 214 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N PHE C 167 " --> pdb=" O LYS C 214 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL C 216 " --> pdb=" O PHE C 167 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ARG C 242 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS C 280 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE C 245 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL C 282 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL C 247 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N HIS C 284 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY C 314 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N MET C 285 " --> pdb=" O GLY C 314 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS C 316 " --> pdb=" O MET C 285 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG C 361 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU C 317 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N TYR C 363 " --> pdb=" O LEU C 317 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 421 through 425 removed outlier: 4.380A pdb=" N GLY C 449 " --> pdb=" O TYR C 439 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP C 441 " --> pdb=" O LEU C 447 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU C 447 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 474 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG C 454 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N VAL C 472 " --> pdb=" O ARG C 454 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYS C 517 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N VAL C 472 " --> pdb=" O LYS C 517 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA C 519 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLU C 474 " --> pdb=" O ALA C 519 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ILE C 521 " --> pdb=" O GLU C 474 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N HIS C 476 " --> pdb=" O ILE C 521 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 894 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: 4.65 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 5982 1.43 - 1.64: 7956 1.64 - 1.85: 117 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 14067 Sorted by residual: bond pdb=" N LYS A 20 " pdb=" CA LYS A 20 " ideal model delta sigma weight residual 1.452 1.490 -0.038 1.11e-02 8.12e+03 1.17e+01 bond pdb=" N ILE A 15 " pdb=" CA ILE A 15 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.04e+00 bond pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.48e+00 bond pdb=" N ARG A 48 " pdb=" CA ARG A 48 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.35e-02 5.49e+03 7.82e+00 bond pdb=" N GLN B 126 " pdb=" CA GLN B 126 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.25e-02 6.40e+03 7.76e+00 ... (remaining 14062 not shown) Histogram of bond angle deviations from ideal: 73.69 - 85.77: 12 85.77 - 97.86: 1 97.86 - 109.94: 2265 109.94 - 122.02: 13570 122.02 - 134.11: 3250 Bond angle restraints: 19098 Sorted by residual: angle pdb=" C PRO A 18 " pdb=" CA PRO A 18 " pdb=" CB PRO A 18 " ideal model delta sigma weight residual 111.64 106.01 5.63 1.27e+00 6.20e-01 1.96e+01 angle pdb=" N PRO A 18 " pdb=" CA PRO A 18 " pdb=" C PRO A 18 " ideal model delta sigma weight residual 111.26 117.97 -6.71 1.63e+00 3.76e-01 1.69e+01 angle pdb=" N HIS B 281 " pdb=" CA HIS B 281 " pdb=" CB HIS B 281 " ideal model delta sigma weight residual 114.17 109.59 4.58 1.14e+00 7.69e-01 1.62e+01 angle pdb=" CA ARG A 49 " pdb=" C ARG A 49 " pdb=" O ARG A 49 " ideal model delta sigma weight residual 122.44 117.24 5.20 1.32e+00 5.74e-01 1.55e+01 angle pdb=" N GLY B 105 " pdb=" CA GLY B 105 " pdb=" C GLY B 105 " ideal model delta sigma weight residual 111.93 116.22 -4.29 1.15e+00 7.56e-01 1.39e+01 ... (remaining 19093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7438 17.96 - 35.93: 719 35.93 - 53.89: 107 53.89 - 71.85: 21 71.85 - 89.82: 18 Dihedral angle restraints: 8303 sinusoidal: 3309 harmonic: 4994 Sorted by residual: dihedral pdb=" CA VAL A 510 " pdb=" C VAL A 510 " pdb=" N GLU A 511 " pdb=" CA GLU A 511 " ideal model delta harmonic sigma weight residual 180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA CYS B 185 " pdb=" C CYS B 185 " pdb=" N ARG B 186 " pdb=" CA ARG B 186 " ideal model delta harmonic sigma weight residual -180.00 -154.77 -25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ASP A 513 " pdb=" C ASP A 513 " pdb=" N THR A 514 " pdb=" CA THR A 514 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 8300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1597 0.048 - 0.096: 414 0.096 - 0.144: 121 0.144 - 0.192: 4 0.192 - 0.240: 2 Chirality restraints: 2138 Sorted by residual: chirality pdb=" CA SAM C 602 " pdb=" N SAM C 602 " pdb=" C SAM C 602 " pdb=" CB SAM C 602 " both_signs ideal model delta sigma weight residual False 2.45 2.69 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE A 15 " pdb=" N ILE A 15 " pdb=" C ILE A 15 " pdb=" CB ILE A 15 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA VAL A 699 " pdb=" N VAL A 699 " pdb=" C VAL A 699 " pdb=" CB VAL A 699 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 2135 not shown) Planarity restraints: 2427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 236 " -0.013 2.00e-02 2.50e+03 1.25e-02 3.92e+00 pdb=" CG TRP B 236 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 236 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 236 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 236 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 236 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 236 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 236 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 236 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 236 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 369 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO C 370 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 370 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 370 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 20 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 21 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " -0.021 5.00e-02 4.00e+02 ... (remaining 2424 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 933 2.73 - 3.27: 13521 3.27 - 3.82: 21371 3.82 - 4.36: 25067 4.36 - 4.90: 44072 Nonbonded interactions: 104964 Sorted by model distance: nonbonded pdb=" OE1 GLN C 248 " pdb=" NH1 ARG C 260 " model vdw 2.189 2.520 nonbonded pdb=" OG SER A 118 " pdb=" OD1 ASP A 120 " model vdw 2.199 2.440 nonbonded pdb=" O ARG B 237 " pdb=" OG1 THR B 273 " model vdw 2.203 2.440 nonbonded pdb=" OG1 THR A 609 " pdb=" OD1 ASP A 627 " model vdw 2.204 2.440 nonbonded pdb=" OG1 THR A 128 " pdb=" OG1 THR A 132 " model vdw 2.207 2.440 ... (remaining 104959 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.860 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 38.510 Find NCS groups from input model: 0.400 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 0.038 14067 Z= 0.220 Angle : 0.698 7.442 19098 Z= 0.413 Chirality : 0.046 0.240 2138 Planarity : 0.004 0.045 2427 Dihedral : 14.666 89.816 5069 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.34 % Favored : 90.48 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.19), residues: 1692 helix: -0.24 (0.39), residues: 180 sheet: -0.67 (0.23), residues: 535 loop : -2.62 (0.18), residues: 977 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.2413 time to fit residues: 48.6616 Evaluate side-chains 85 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.535 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 156 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS B 330 GLN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.0541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 14067 Z= 0.153 Angle : 0.538 7.759 19098 Z= 0.283 Chirality : 0.045 0.152 2138 Planarity : 0.004 0.044 2427 Dihedral : 4.900 29.802 1862 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.27 % Favored : 91.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.19), residues: 1692 helix: -0.35 (0.39), residues: 180 sheet: -0.58 (0.23), residues: 543 loop : -2.58 (0.18), residues: 969 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2347 time to fit residues: 47.5302 Evaluate side-chains 83 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.502 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 156 optimal weight: 0.0770 chunk 169 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 155 optimal weight: 0.0170 chunk 53 optimal weight: 0.3980 chunk 125 optimal weight: 9.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 HIS B 330 GLN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 14067 Z= 0.136 Angle : 0.528 7.837 19098 Z= 0.275 Chirality : 0.045 0.155 2138 Planarity : 0.004 0.041 2427 Dihedral : 4.748 29.637 1862 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.27 % Favored : 91.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.20), residues: 1692 helix: -0.35 (0.40), residues: 181 sheet: -0.63 (0.22), residues: 569 loop : -2.49 (0.18), residues: 942 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2568 time to fit residues: 55.6281 Evaluate side-chains 87 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.682 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 0.0870 chunk 157 optimal weight: 0.0770 chunk 166 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 overall best weight: 0.8318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 HIS ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 14067 Z= 0.178 Angle : 0.547 8.446 19098 Z= 0.284 Chirality : 0.045 0.142 2138 Planarity : 0.004 0.049 2427 Dihedral : 4.848 30.197 1862 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.69 % Favored : 90.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.32 (0.20), residues: 1692 helix: -0.42 (0.39), residues: 181 sheet: -0.53 (0.22), residues: 559 loop : -2.51 (0.18), residues: 952 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.594 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2372 time to fit residues: 47.6073 Evaluate side-chains 84 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.488 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 0.0870 chunk 94 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 0.2980 chunk 149 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A 659 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 14067 Z= 0.153 Angle : 0.535 7.842 19098 Z= 0.278 Chirality : 0.045 0.158 2138 Planarity : 0.004 0.043 2427 Dihedral : 4.771 30.442 1862 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.63 % Favored : 91.31 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.30 (0.20), residues: 1692 helix: -0.42 (0.39), residues: 181 sheet: -0.58 (0.22), residues: 569 loop : -2.46 (0.18), residues: 942 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.2549 time to fit residues: 48.6835 Evaluate side-chains 87 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 32 optimal weight: 0.0670 chunk 97 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 166 optimal weight: 0.7980 chunk 138 optimal weight: 0.0470 chunk 77 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 14067 Z= 0.196 Angle : 0.550 7.289 19098 Z= 0.287 Chirality : 0.045 0.147 2138 Planarity : 0.004 0.046 2427 Dihedral : 4.896 30.809 1862 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.05 % Favored : 89.89 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.34 (0.19), residues: 1692 helix: -0.60 (0.38), residues: 181 sheet: -0.58 (0.22), residues: 569 loop : -2.48 (0.18), residues: 942 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.2387 time to fit residues: 47.7313 Evaluate side-chains 83 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.507 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.0980 chunk 94 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A 659 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 14067 Z= 0.189 Angle : 0.557 8.547 19098 Z= 0.289 Chirality : 0.046 0.154 2138 Planarity : 0.004 0.045 2427 Dihedral : 4.930 31.205 1862 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.10 % Favored : 90.84 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.33 (0.19), residues: 1692 helix: -0.52 (0.39), residues: 180 sheet: -0.53 (0.22), residues: 556 loop : -2.50 (0.18), residues: 956 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.2436 time to fit residues: 47.4917 Evaluate side-chains 91 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.676 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 105 optimal weight: 0.0970 chunk 112 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 130 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 634 ASN A 659 HIS ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 14067 Z= 0.165 Angle : 0.551 8.218 19098 Z= 0.285 Chirality : 0.045 0.146 2138 Planarity : 0.004 0.045 2427 Dihedral : 4.844 30.836 1862 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.28 % Favored : 90.66 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.29 (0.20), residues: 1692 helix: -0.49 (0.39), residues: 180 sheet: -0.50 (0.23), residues: 553 loop : -2.46 (0.18), residues: 959 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.2506 time to fit residues: 49.3077 Evaluate side-chains 89 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 1.654 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1254 time to fit residues: 2.5149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 163 optimal weight: 0.3980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A 659 HIS B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 GLN B 590 GLN ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 14067 Z= 0.169 Angle : 0.556 9.585 19098 Z= 0.287 Chirality : 0.046 0.161 2138 Planarity : 0.004 0.044 2427 Dihedral : 4.856 30.549 1862 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.10 % Favored : 90.84 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.26 (0.20), residues: 1692 helix: -0.48 (0.39), residues: 181 sheet: -0.52 (0.22), residues: 562 loop : -2.43 (0.18), residues: 949 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.2544 time to fit residues: 51.5203 Evaluate side-chains 92 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.579 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 157 optimal weight: 0.3980 chunk 136 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 GLN B 590 GLN ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 14067 Z= 0.168 Angle : 0.558 9.354 19098 Z= 0.288 Chirality : 0.046 0.168 2138 Planarity : 0.004 0.044 2427 Dihedral : 4.864 30.618 1862 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.28 % Favored : 90.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.25 (0.20), residues: 1692 helix: -0.51 (0.39), residues: 181 sheet: -0.48 (0.23), residues: 553 loop : -2.43 (0.18), residues: 958 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2431 time to fit residues: 46.6773 Evaluate side-chains 87 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 5.9990 chunk 125 optimal weight: 0.0570 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 140 optimal weight: 0.0060 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.5114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A 659 HIS B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.108227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089901 restraints weight = 38154.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.091679 restraints weight = 40169.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.092052 restraints weight = 28085.575| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 14067 Z= 0.142 Angle : 0.539 9.440 19098 Z= 0.278 Chirality : 0.045 0.165 2138 Planarity : 0.004 0.044 2427 Dihedral : 4.718 30.225 1862 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.68 % Favored : 92.26 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.17 (0.20), residues: 1692 helix: -0.34 (0.40), residues: 179 sheet: -0.42 (0.23), residues: 552 loop : -2.39 (0.18), residues: 961 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2413.34 seconds wall clock time: 45 minutes 16.68 seconds (2716.68 seconds total)