Starting phenix.real_space_refine on Fri Feb 16 00:07:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avg_15682/02_2024/8avg_15682_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avg_15682/02_2024/8avg_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_15682/02_2024/8avg_15682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avg_15682/02_2024/8avg_15682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avg_15682/02_2024/8avg_15682_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avg_15682/02_2024/8avg_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.36, per 1000 atoms: 0.54 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: 5.31 Conformation dependent library (CDL) restraints added in 2.5 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: 3.47 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: 4.39 Time building geometry restraints manager: 5.75 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: 7443 17.96 - 35.93: 726 35.93 - 53.89: 115 53.89 - 71.85: 31 71.85 - 89.82: 20 Dihedral angle restraints: 8335 sinusoidal: 3341 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 8332 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: 3.890 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: 15.310 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 41.970 Find NCS groups from input model: 0.430 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: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.940 ------------------------------------------------------------------------------- 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 : 15.122 89.816 5101 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 % Allowed : 0.66 % Favored : 99.28 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 236 HIS 0.012 0.001 HIS C 150 PHE 0.018 0.001 PHE A 228 TYR 0.013 0.001 TYR C 111 ARG 0.004 0.000 ARG A 697 *********************** 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 : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 347 GLU cc_start: 0.8015 (tp30) cc_final: 0.7715 (tp30) REVERT: C 434 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6460 (mt-10) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.2430 time to fit residues: 49.2056 Evaluate side-chains 87 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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: 0.7256 moved from start: 0.0551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14067 Z= 0.152 Angle : 0.537 8.039 19098 Z= 0.282 Chirality : 0.045 0.157 2138 Planarity : 0.004 0.047 2427 Dihedral : 6.773 68.330 1894 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.27 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % 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: -0.62 (0.23), residues: 546 loop : -2.56 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 236 HIS 0.009 0.001 HIS C 150 PHE 0.012 0.001 PHE B 684 TYR 0.013 0.001 TYR A 449 ARG 0.004 0.000 ARG A 49 *********************** 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 130 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 135 MET cc_start: 0.7039 (pmm) cc_final: 0.6764 (pmm) REVERT: C 434 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6460 (mt-10) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2340 time to fit residues: 47.4594 Evaluate side-chains 85 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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: 1.9990 chunk 106 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 156 optimal weight: 0.0060 chunk 169 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 155 optimal weight: 0.2980 chunk 53 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- 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 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7288 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14067 Z= 0.206 Angle : 0.561 7.960 19098 Z= 0.294 Chirality : 0.046 0.150 2138 Planarity : 0.004 0.042 2427 Dihedral : 6.591 67.990 1894 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.75 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: -2.45 (0.19), residues: 1692 helix: -0.57 (0.39), residues: 181 sheet: -0.63 (0.22), residues: 559 loop : -2.58 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 236 HIS 0.011 0.001 HIS C 150 PHE 0.013 0.001 PHE A 207 TYR 0.013 0.001 TYR C 181 ARG 0.003 0.000 ARG A 49 *********************** 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 142 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.733 Fit side-chains revert: symmetry clash REVERT: C 135 MET cc_start: 0.6960 (pmm) cc_final: 0.6623 (pmm) REVERT: C 347 GLU cc_start: 0.8024 (tp30) cc_final: 0.7708 (tp30) REVERT: C 434 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6547 (mt-10) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2519 time to fit residues: 54.1551 Evaluate side-chains 87 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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: 3.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 105 optimal weight: 0.0060 chunk 157 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- 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 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 HIS ** 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: 0.7337 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 14067 Z= 0.268 Angle : 0.596 8.333 19098 Z= 0.313 Chirality : 0.047 0.173 2138 Planarity : 0.004 0.052 2427 Dihedral : 6.679 67.219 1894 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.35 % Favored : 88.59 % Rotamer: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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: -2.57 (0.19), residues: 1692 helix: -0.80 (0.38), residues: 180 sheet: -0.61 (0.23), residues: 539 loop : -2.67 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 509 HIS 0.012 0.001 HIS C 150 PHE 0.016 0.002 PHE B 387 TYR 0.014 0.002 TYR C 181 ARG 0.003 0.000 ARG C 139 *********************** 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 125 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 135 MET cc_start: 0.7051 (pmm) cc_final: 0.6798 (pmm) REVERT: C 347 GLU cc_start: 0.8056 (tp30) cc_final: 0.7713 (tp30) REVERT: C 382 ASN cc_start: 0.7393 (p0) cc_final: 0.7122 (p0) REVERT: C 434 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6765 (mt-10) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2490 time to fit residues: 48.6876 Evaluate side-chains 81 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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: 0.5980 chunk 94 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 0.0570 chunk 149 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 14067 Z= 0.154 Angle : 0.538 7.427 19098 Z= 0.283 Chirality : 0.046 0.156 2138 Planarity : 0.004 0.045 2427 Dihedral : 6.214 60.707 1894 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.51 % Favored : 91.43 % Rotamer: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.24 % 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: -2.45 (0.20), residues: 1692 helix: -0.62 (0.39), residues: 181 sheet: -0.68 (0.22), residues: 564 loop : -2.53 (0.18), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 215 HIS 0.011 0.001 HIS C 150 PHE 0.014 0.001 PHE B 414 TYR 0.011 0.001 TYR C 181 ARG 0.003 0.000 ARG C 260 *********************** 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 133 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 LEU cc_start: 0.8047 (tp) cc_final: 0.7735 (pp) REVERT: B 315 MET cc_start: 0.8188 (tmm) cc_final: 0.6534 (tmm) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.2507 time to fit residues: 50.2729 Evaluate side-chains 90 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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: 6.9990 chunk 149 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 166 optimal weight: 4.9990 chunk 138 optimal weight: 0.2980 chunk 77 optimal weight: 8.9990 chunk 13 optimal weight: 0.2980 chunk 87 optimal weight: 7.9990 chunk 160 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** 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 150 HIS C 380 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1296 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= 0.155 Angle : 0.533 6.441 19098 Z= 0.280 Chirality : 0.045 0.149 2138 Planarity : 0.004 0.047 2427 Dihedral : 6.097 59.281 1894 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.22 % Favored : 90.72 % Rotamer: Outliers : 0.13 % Allowed : 2.83 % Favored : 97.04 % 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: -2.38 (0.20), residues: 1692 helix: -0.58 (0.39), residues: 179 sheet: -0.60 (0.22), residues: 564 loop : -2.50 (0.18), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 209 HIS 0.011 0.001 HIS C 150 PHE 0.013 0.001 PHE B 414 TYR 0.011 0.001 TYR C 181 ARG 0.003 0.000 ARG B 68 *********************** 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 136 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 LEU cc_start: 0.7978 (tp) cc_final: 0.7675 (pp) REVERT: B 184 ASP cc_start: 0.6363 (p0) cc_final: 0.5883 (p0) REVERT: B 315 MET cc_start: 0.8212 (tmm) cc_final: 0.6589 (tmm) REVERT: C 382 ASN cc_start: 0.7468 (p0) cc_final: 0.7205 (p0) outliers start: 2 outliers final: 1 residues processed: 136 average time/residue: 0.2393 time to fit residues: 50.0770 Evaluate side-chains 92 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.683 ------------------------------------------------------------------------------- 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: 2.9990 chunk 94 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 165 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- 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** C 262 HIS C 476 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 14067 Z= 0.250 Angle : 0.601 8.554 19098 Z= 0.314 Chirality : 0.047 0.170 2138 Planarity : 0.004 0.047 2427 Dihedral : 6.503 65.439 1894 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.82 % Favored : 89.13 % Rotamer: Outliers : 0.07 % Allowed : 2.10 % Favored : 97.83 % 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: -2.52 (0.19), residues: 1692 helix: -0.84 (0.37), residues: 181 sheet: -0.58 (0.23), residues: 539 loop : -2.61 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 209 HIS 0.012 0.001 HIS C 150 PHE 0.013 0.002 PHE A 207 TYR 0.014 0.001 TYR C 181 ARG 0.004 0.000 ARG C 260 *********************** 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 126 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.2319 time to fit residues: 46.6715 Evaluate side-chains 82 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.754 ------------------------------------------------------------------------------- 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: 7.9990 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 0.0270 chunk 130 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 158 optimal weight: 0.0170 chunk 144 optimal weight: 2.9990 overall best weight: 0.5280 ------------------------------------------------------------------------------- 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 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 150 HIS C 262 HIS C 476 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14067 Z= 0.144 Angle : 0.548 7.956 19098 Z= 0.284 Chirality : 0.045 0.148 2138 Planarity : 0.004 0.045 2427 Dihedral : 5.960 59.012 1894 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.33 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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 (0.20), residues: 1692 helix: -0.56 (0.39), residues: 180 sheet: -0.57 (0.22), residues: 571 loop : -2.49 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 209 HIS 0.011 0.001 HIS C 150 PHE 0.013 0.001 PHE B 414 TYR 0.013 0.001 TYR B 344 ARG 0.002 0.000 ARG A 49 *********************** 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 134 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8356 (mmp) cc_final: 0.7904 (mmp) REVERT: C 135 MET cc_start: 0.7079 (pmm) cc_final: 0.6825 (pmm) REVERT: C 347 GLU cc_start: 0.7999 (tp30) cc_final: 0.7651 (tp30) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2578 time to fit residues: 52.3004 Evaluate side-chains 88 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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: 0.0000 chunk 158 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- 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 445 GLN ** 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 453 GLN B 590 GLN ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS C 262 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14067 Z= 0.172 Angle : 0.572 10.028 19098 Z= 0.295 Chirality : 0.046 0.165 2138 Planarity : 0.004 0.045 2427 Dihedral : 6.062 59.332 1894 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.22 % Favored : 90.72 % Rotamer: Outliers : 0.07 % Allowed : 0.72 % Favored : 99.21 % 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 (0.20), residues: 1692 helix: -0.68 (0.38), residues: 180 sheet: -0.60 (0.22), residues: 568 loop : -2.45 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 209 HIS 0.012 0.001 HIS C 150 PHE 0.014 0.001 PHE B 685 TYR 0.012 0.001 TYR C 181 ARG 0.003 0.000 ARG C 260 *********************** 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 132 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 MET cc_start: 0.8071 (mmt) cc_final: 0.7800 (mmt) REVERT: C 347 GLU cc_start: 0.7979 (tp30) cc_final: 0.7643 (tp30) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.2365 time to fit residues: 48.2449 Evaluate side-chains 88 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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: 6.9990 chunk 77 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 0.0030 chunk 108 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** C 262 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1542 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= 0.159 Angle : 0.565 9.472 19098 Z= 0.291 Chirality : 0.046 0.167 2138 Planarity : 0.004 0.045 2427 Dihedral : 6.011 57.902 1894 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.69 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -0.56 (0.39), residues: 179 sheet: -0.53 (0.22), residues: 562 loop : -2.44 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 209 HIS 0.005 0.001 HIS B 819 PHE 0.013 0.001 PHE B 684 TYR 0.011 0.001 TYR C 181 ARG 0.002 0.000 ARG C 260 ********************** 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 127 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8243 (mmp) cc_final: 0.7758 (mmp) REVERT: A 413 MET cc_start: 0.8090 (mmt) cc_final: 0.7794 (mmt) REVERT: C 306 GLU cc_start: 0.8312 (pt0) cc_final: 0.8108 (tm-30) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2431 time to fit residues: 47.7921 Evaluate side-chains 87 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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: 2.9990 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 0.0570 chunk 57 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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** C 150 HIS C 262 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.107183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.088856 restraints weight = 38427.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.090444 restraints weight = 40676.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.090774 restraints weight = 29901.318| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14067 Z= 0.166 Angle : 0.564 9.494 19098 Z= 0.291 Chirality : 0.046 0.187 2138 Planarity : 0.004 0.044 2427 Dihedral : 6.031 58.190 1894 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.75 % Favored : 91.19 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.31 (0.20), residues: 1692 helix: -0.60 (0.38), residues: 179 sheet: -0.60 (0.22), residues: 568 loop : -2.42 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 209 HIS 0.012 0.001 HIS C 150 PHE 0.013 0.001 PHE B 684 TYR 0.013 0.001 TYR C 181 ARG 0.003 0.000 ARG B 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.82 seconds wall clock time: 47 minutes 21.27 seconds (2841.27 seconds total)