Starting phenix.real_space_refine (version: dev) on Fri May 13 06:02:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qwl_4660/05_2022/6qwl_4660.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qwl_4660/05_2022/6qwl_4660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qwl_4660/05_2022/6qwl_4660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qwl_4660/05_2022/6qwl_4660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qwl_4660/05_2022/6qwl_4660.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qwl_4660/05_2022/6qwl_4660.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "E GLU 260": "OE1" <-> "OE2" Residue "E TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 549": "NH1" <-> "NH2" Residue "E ARG 574": "NH1" <-> "NH2" Residue "E GLU 585": "OE1" <-> "OE2" Residue "E TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 657": "OE1" <-> "OE2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "K ASP 169": "OD1" <-> "OD2" Residue "K GLU 178": "OE1" <-> "OE2" Residue "K GLU 256": "OE1" <-> "OE2" Residue "K GLU 311": "OE1" <-> "OE2" Residue "K ASP 438": "OD1" <-> "OD2" Residue "K PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 460": "OE1" <-> "OE2" Residue "K ASP 521": "OD1" <-> "OD2" Residue "Q ASP 65": "OD1" <-> "OD2" Residue "Q GLU 73": "OE1" <-> "OE2" Residue "Q PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 179": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 10408 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 4084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4084 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain: "K" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4206 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 514} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1565 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "T" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'RNA': 12} Modifications used: {'rna3p_pyr': 5, 'rna3p_pur': 3, 'rna2p_pyr': 4} Link IDs: {'rna3p': 7, 'rna2p': 4} Chain: "W" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna3p_pyr': 4, 'rna2p_pur': 2, 'rna3p_pur': 8} Link IDs: {'rna3p': 11, 'rna2p': 2} Time building chain proxies: 6.57, per 1000 atoms: 0.63 Number of scatterers: 10408 At special positions: 0 Unit cell: (99.36, 104.76, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 26 15.00 O 2023 8.00 N 1787 7.00 C 6498 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: 4.49 Conformation dependent library (CDL) restraints added in 1.4 seconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 13 sheets defined 50.2% alpha, 7.8% beta 6 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 222 through 232 Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 258 through 262 removed outlier: 3.846A pdb=" N ASP E 261 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 270 removed outlier: 3.584A pdb=" N ILE E 269 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 313 removed outlier: 4.179A pdb=" N GLU E 311 " --> pdb=" O LYS E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 317 Processing helix chain 'E' and resid 332 through 345 removed outlier: 3.900A pdb=" N LEU E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS E 338 " --> pdb=" O ASN E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 removed outlier: 3.627A pdb=" N LYS E 363 " --> pdb=" O THR E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 380 removed outlier: 3.809A pdb=" N VAL E 379 " --> pdb=" O MET E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 410 Processing helix chain 'E' and resid 429 through 447 removed outlier: 3.511A pdb=" N ASN E 447 " --> pdb=" O VAL E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 472 Processing helix chain 'E' and resid 529 through 533 removed outlier: 3.513A pdb=" N TRP E 533 " --> pdb=" O SER E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 572 removed outlier: 3.509A pdb=" N GLU E 572 " --> pdb=" O LYS E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 596 removed outlier: 3.636A pdb=" N GLN E 579 " --> pdb=" O ARG E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 605 removed outlier: 3.702A pdb=" N LYS E 605 " --> pdb=" O LYS E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 646 removed outlier: 3.581A pdb=" N TYR E 644 " --> pdb=" O CYS E 640 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE E 646 " --> pdb=" O MET E 642 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 670 removed outlier: 3.734A pdb=" N GLU E 652 " --> pdb=" O ASN E 648 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARG E 660 " --> pdb=" O ALA E 656 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU E 661 " --> pdb=" O GLU E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 688 Processing helix chain 'E' and resid 693 through 714 removed outlier: 3.513A pdb=" N ILE E 697 " --> pdb=" O ASN E 693 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN E 698 " --> pdb=" O PRO E 694 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 11 removed outlier: 3.839A pdb=" N LEU K 8 " --> pdb=" O PRO K 5 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 17 Processing helix chain 'K' and resid 37 through 48 Processing helix chain 'K' and resid 49 through 51 No H-bonds generated for 'chain 'K' and resid 49 through 51' Processing helix chain 'K' and resid 85 through 98 Processing helix chain 'K' and resid 101 through 116 removed outlier: 3.743A pdb=" N MET K 115 " --> pdb=" O MET K 111 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 123 removed outlier: 3.973A pdb=" N LEU K 122 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR K 123 " --> pdb=" O ASP K 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 119 through 123' Processing helix chain 'K' and resid 141 through 151 Processing helix chain 'K' and resid 152 through 154 No H-bonds generated for 'chain 'K' and resid 152 through 154' Processing helix chain 'K' and resid 162 through 172 removed outlier: 3.851A pdb=" N PHE K 166 " --> pdb=" O GLY K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 176 Processing helix chain 'K' and resid 214 through 223 removed outlier: 3.922A pdb=" N ALA K 221 " --> pdb=" O TYR K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 264 removed outlier: 4.462A pdb=" N GLY K 250 " --> pdb=" O ILE K 246 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N PHE K 251 " --> pdb=" O GLN K 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 326 removed outlier: 3.751A pdb=" N PHE K 318 " --> pdb=" O ASN K 314 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 329 No H-bonds generated for 'chain 'K' and resid 327 through 329' Processing helix chain 'K' and resid 330 through 338 removed outlier: 3.535A pdb=" N ARG K 334 " --> pdb=" O PRO K 330 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER K 338 " --> pdb=" O ARG K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 344 Processing helix chain 'K' and resid 377 through 381 removed outlier: 4.068A pdb=" N TYR K 381 " --> pdb=" O LEU K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 382 through 393 removed outlier: 3.636A pdb=" N ARG K 386 " --> pdb=" O ASN K 382 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS K 391 " --> pdb=" O ALA K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 394 through 396 No H-bonds generated for 'chain 'K' and resid 394 through 396' Processing helix chain 'K' and resid 413 through 426 Processing helix chain 'K' and resid 454 through 471 Processing helix chain 'K' and resid 518 through 537 removed outlier: 4.165A pdb=" N ASN K 536 " --> pdb=" O ASN K 532 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY K 537 " --> pdb=" O MET K 533 " (cutoff:3.500A) Processing helix chain 'K' and resid 539 through 558 removed outlier: 3.680A pdb=" N GLN K 548 " --> pdb=" O GLN K 544 " (cutoff:3.500A) Processing helix chain 'K' and resid 571 through 582 removed outlier: 3.825A pdb=" N ILE K 575 " --> pdb=" O ARG K 571 " (cutoff:3.500A) Processing helix chain 'K' and resid 589 through 593 Processing helix chain 'K' and resid 607 through 612 Processing helix chain 'K' and resid 616 through 624 Processing helix chain 'Q' and resid 64 through 69 removed outlier: 3.941A pdb=" N ARG Q 69 " --> pdb=" O MET Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 105 removed outlier: 4.079A pdb=" N ASN Q 102 " --> pdb=" O VAL Q 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY Q 105 " --> pdb=" O TRP Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 117 removed outlier: 4.133A pdb=" N TYR Q 117 " --> pdb=" O PHE Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 118 through 129 Processing helix chain 'Q' and resid 157 through 170 Processing helix chain 'Q' and resid 178 through 193 removed outlier: 5.077A pdb=" N GLU Q 186 " --> pdb=" O TRP Q 182 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU Q 187 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 198 removed outlier: 4.225A pdb=" N GLY Q 197 " --> pdb=" O LYS Q 194 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR Q 198 " --> pdb=" O LEU Q 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 194 through 198' Processing helix chain 'Q' and resid 201 through 214 removed outlier: 3.594A pdb=" N VAL Q 214 " --> pdb=" O GLU Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 227 through 233 Processing helix chain 'Q' and resid 233 through 238 Processing sheet with id=AA1, first strand: chain 'E' and resid 373 through 374 removed outlier: 6.659A pdb=" N GLN E 373 " --> pdb=" O LYS K 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 480 through 486 removed outlier: 4.799A pdb=" N ILE E 481 " --> pdb=" O TYR E 497 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN E 483 " --> pdb=" O MET E 495 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET E 495 " --> pdb=" O ASN E 483 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 499 " --> pdb=" O PHE E 519 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 521 through 522 removed outlier: 3.923A pdb=" N TYR E 554 " --> pdb=" O SER E 522 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR E 537 " --> pdb=" O CYS E 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 521 through 522 removed outlier: 3.923A pdb=" N TYR E 554 " --> pdb=" O SER E 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 623 through 627 removed outlier: 3.859A pdb=" N GLY E 618 " --> pdb=" O VAL E 625 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY E 627 " --> pdb=" O SER E 616 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER E 616 " --> pdb=" O GLY E 627 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN K 2 " --> pdb=" O THR E 619 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'K' and resid 128 through 129 Processing sheet with id=AA8, first strand: chain 'K' and resid 178 through 181 Processing sheet with id=AA9, first strand: chain 'K' and resid 435 through 437 removed outlier: 3.721A pdb=" N MET K 300 " --> pdb=" O VAL K 450 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 348 through 350 Processing sheet with id=AB2, first strand: chain 'Q' and resid 73 through 74 Processing sheet with id=AB3, first strand: chain 'Q' and resid 131 through 135 removed outlier: 5.691A pdb=" N ILE Q 245 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 143 through 148 removed outlier: 3.845A pdb=" N ARG Q 218 " --> pdb=" O VAL Q 147 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2799 1.33 - 1.46: 2522 1.46 - 1.58: 5173 1.58 - 1.70: 50 1.70 - 1.83: 124 Bond restraints: 10668 Sorted by residual: bond pdb=" CB TRP E 340 " pdb=" CG TRP E 340 " ideal model delta sigma weight residual 1.498 1.428 0.070 3.10e-02 1.04e+03 5.09e+00 bond pdb=" CA ILE E 479 " pdb=" C ILE E 479 " ideal model delta sigma weight residual 1.525 1.506 0.019 8.80e-03 1.29e+04 4.60e+00 bond pdb=" CG MET E 407 " pdb=" SD MET E 407 " ideal model delta sigma weight residual 1.803 1.751 0.052 2.50e-02 1.60e+03 4.33e+00 bond pdb=" CB ASN E 560 " pdb=" CG ASN E 560 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.09e+00 bond pdb=" C ILE E 479 " pdb=" N PRO E 480 " ideal model delta sigma weight residual 1.333 1.312 0.021 1.17e-02 7.31e+03 3.27e+00 ... (remaining 10663 not shown) Histogram of bond angle deviations from ideal: 96.95 - 104.44: 300 104.44 - 111.92: 4875 111.92 - 119.41: 4086 119.41 - 126.90: 5068 126.90 - 134.38: 194 Bond angle restraints: 14523 Sorted by residual: angle pdb=" N ILE E 347 " pdb=" CA ILE E 347 " pdb=" C ILE E 347 " ideal model delta sigma weight residual 112.12 107.85 4.27 8.40e-01 1.42e+00 2.58e+01 angle pdb=" N LYS K 393 " pdb=" CA LYS K 393 " pdb=" C LYS K 393 " ideal model delta sigma weight residual 109.81 119.35 -9.54 2.21e+00 2.05e-01 1.86e+01 angle pdb=" C3' G T 2 " pdb=" O3' G T 2 " pdb=" P C T 3 " ideal model delta sigma weight residual 120.20 126.48 -6.28 1.50e+00 4.44e-01 1.75e+01 angle pdb=" N GLY E 367 " pdb=" CA GLY E 367 " pdb=" C GLY E 367 " ideal model delta sigma weight residual 113.18 122.07 -8.89 2.37e+00 1.78e-01 1.41e+01 angle pdb=" C ASN K 153 " pdb=" N ASP K 154 " pdb=" CA ASP K 154 " ideal model delta sigma weight residual 122.08 127.43 -5.35 1.47e+00 4.63e-01 1.32e+01 ... (remaining 14518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 6250 35.58 - 71.16: 148 71.16 - 106.74: 9 106.74 - 142.32: 1 142.32 - 177.90: 1 Dihedral angle restraints: 6409 sinusoidal: 2823 harmonic: 3586 Sorted by residual: dihedral pdb=" O4' U T 6 " pdb=" C1' U T 6 " pdb=" N1 U T 6 " pdb=" C2 U T 6 " ideal model delta sinusoidal sigma weight residual -128.00 49.90 -177.90 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA GLU K 399 " pdb=" C GLU K 399 " pdb=" N GLY K 400 " pdb=" CA GLY K 400 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA THR E 366 " pdb=" C THR E 366 " pdb=" N GLY E 367 " pdb=" CA GLY E 367 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 6406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1098 0.056 - 0.112: 404 0.112 - 0.168: 94 0.168 - 0.224: 27 0.224 - 0.280: 2 Chirality restraints: 1625 Sorted by residual: chirality pdb=" CB VAL K 116 " pdb=" CA VAL K 116 " pdb=" CG1 VAL K 116 " pdb=" CG2 VAL K 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB THR K 401 " pdb=" CA THR K 401 " pdb=" OG1 THR K 401 " pdb=" CG2 THR K 401 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CG LEU Q 79 " pdb=" CB LEU Q 79 " pdb=" CD1 LEU Q 79 " pdb=" CD2 LEU Q 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1622 not shown) Planarity restraints: 1767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE Q 70 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO Q 71 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO Q 71 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO Q 71 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 605 " -0.048 5.00e-02 4.00e+02 7.19e-02 8.28e+00 pdb=" N PRO K 606 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO K 606 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO K 606 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 405 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO K 406 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO K 406 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO K 406 " 0.040 5.00e-02 4.00e+02 ... (remaining 1764 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1704 2.75 - 3.29: 10241 3.29 - 3.83: 18346 3.83 - 4.36: 19733 4.36 - 4.90: 32328 Nonbonded interactions: 82352 Sorted by model distance: nonbonded pdb=" O ASP K 553 " pdb=" OG1 THR K 557 " model vdw 2.214 2.440 nonbonded pdb=" O LEU K 114 " pdb=" OG1 THR K 117 " model vdw 2.244 2.440 nonbonded pdb=" O SER E 215 " pdb=" OG SER E 215 " model vdw 2.251 2.440 nonbonded pdb=" O ALA E 362 " pdb=" OG1 THR E 366 " model vdw 2.257 2.440 nonbonded pdb=" OG SER E 328 " pdb=" OE1 GLU E 329 " model vdw 2.269 2.440 ... (remaining 82347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 74 5.16 5 C 6498 2.51 5 N 1787 2.21 5 O 2023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.860 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: 4.590 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 33.030 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.008 0.077 10668 Z= 0.493 Angle : 1.013 9.537 14523 Z= 0.547 Chirality : 0.062 0.280 1625 Planarity : 0.008 0.075 1767 Dihedral : 16.055 177.903 4097 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.85 % Favored : 89.07 % Rotamer Outliers : 0.93 % 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: -4.69 (0.18), residues: 1226 helix: -2.72 (0.16), residues: 530 sheet: -3.72 (0.51), residues: 73 loop : -3.44 (0.20), residues: 623 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 179 average time/residue: 0.2393 time to fit residues: 59.3414 Evaluate side-chains 110 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0992 time to fit residues: 2.0501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 ASN ** E 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN E 643 HIS ** E 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 261 ASN ** K 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 544 GLN Q 184 HIS Q 235 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 10668 Z= 0.179 Angle : 0.642 8.076 14523 Z= 0.335 Chirality : 0.043 0.189 1625 Planarity : 0.005 0.059 1767 Dihedral : 11.847 176.405 1644 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % 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: -3.36 (0.21), residues: 1226 helix: -1.18 (0.20), residues: 549 sheet: -3.59 (0.48), residues: 82 loop : -3.11 (0.22), residues: 595 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2298 time to fit residues: 50.6599 Evaluate side-chains 119 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 242 ASN E 349 ASN ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 ASN ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 ASN E 650 GLN E 693 ASN ** E 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 561 HIS K 663 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 10668 Z= 0.386 Angle : 0.758 8.130 14523 Z= 0.399 Chirality : 0.048 0.184 1625 Planarity : 0.006 0.067 1767 Dihedral : 11.901 177.298 1644 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer Outliers : 0.19 % 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: -3.13 (0.22), residues: 1226 helix: -0.83 (0.21), residues: 549 sheet: -3.51 (0.47), residues: 94 loop : -3.14 (0.23), residues: 583 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 144 average time/residue: 0.2307 time to fit residues: 47.7901 Evaluate side-chains 119 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1008 time to fit residues: 1.9159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 ASN E 666 GLN ** E 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 247 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 10668 Z= 0.245 Angle : 0.652 9.425 14523 Z= 0.338 Chirality : 0.044 0.161 1625 Planarity : 0.005 0.055 1767 Dihedral : 11.606 176.731 1644 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer Outliers : 0.19 % 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: -2.60 (0.23), residues: 1226 helix: -0.29 (0.22), residues: 548 sheet: -3.66 (0.50), residues: 84 loop : -2.90 (0.23), residues: 594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 153 average time/residue: 0.2357 time to fit residues: 50.6106 Evaluate side-chains 117 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.294 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 83 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10668 Z= 0.166 Angle : 0.611 8.460 14523 Z= 0.313 Chirality : 0.042 0.190 1625 Planarity : 0.005 0.054 1767 Dihedral : 11.312 176.825 1644 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % 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: -2.13 (0.24), residues: 1226 helix: 0.21 (0.23), residues: 539 sheet: -3.69 (0.52), residues: 73 loop : -2.72 (0.23), residues: 614 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2261 time to fit residues: 50.6228 Evaluate side-chains 117 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.313 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 100 optimal weight: 0.3980 chunk 55 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 579 GLN ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 163 ASN ** Q 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 10668 Z= 0.361 Angle : 0.739 9.142 14523 Z= 0.385 Chirality : 0.047 0.189 1625 Planarity : 0.006 0.070 1767 Dihedral : 11.572 177.182 1644 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % 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: -2.44 (0.23), residues: 1226 helix: -0.11 (0.22), residues: 545 sheet: -3.52 (0.48), residues: 94 loop : -2.84 (0.23), residues: 587 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.259 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2390 time to fit residues: 48.9496 Evaluate side-chains 112 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 0.0870 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10668 Z= 0.186 Angle : 0.630 8.960 14523 Z= 0.323 Chirality : 0.043 0.178 1625 Planarity : 0.005 0.066 1767 Dihedral : 11.337 176.697 1644 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % 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: -1.98 (0.24), residues: 1226 helix: 0.28 (0.23), residues: 542 sheet: -3.63 (0.51), residues: 73 loop : -2.59 (0.24), residues: 611 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2213 time to fit residues: 50.2624 Evaluate side-chains 120 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10668 Z= 0.175 Angle : 0.612 8.599 14523 Z= 0.315 Chirality : 0.043 0.184 1625 Planarity : 0.005 0.070 1767 Dihedral : 11.161 176.916 1644 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % 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: -1.84 (0.24), residues: 1226 helix: 0.41 (0.23), residues: 541 sheet: -3.51 (0.48), residues: 84 loop : -2.50 (0.24), residues: 601 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2158 time to fit residues: 45.8842 Evaluate side-chains 115 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.257 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 73 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 ASN E 693 ASN ** E 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 10668 Z= 0.226 Angle : 0.652 12.818 14523 Z= 0.333 Chirality : 0.044 0.185 1625 Planarity : 0.005 0.070 1767 Dihedral : 11.215 176.827 1644 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.24), residues: 1226 helix: 0.34 (0.23), residues: 542 sheet: -3.56 (0.48), residues: 83 loop : -2.48 (0.24), residues: 601 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.2140 time to fit residues: 45.4683 Evaluate side-chains 115 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 10668 Z= 0.189 Angle : 0.626 12.677 14523 Z= 0.318 Chirality : 0.043 0.185 1625 Planarity : 0.006 0.135 1767 Dihedral : 11.142 176.565 1644 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % 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: -1.73 (0.24), residues: 1226 helix: 0.44 (0.23), residues: 547 sheet: -3.39 (0.50), residues: 83 loop : -2.42 (0.24), residues: 596 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.218 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2157 time to fit residues: 46.7249 Evaluate side-chains 115 residues out of total 1081 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.284 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 ASN E 693 ASN ** E 704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.120103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.099800 restraints weight = 27707.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.098835 restraints weight = 30163.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.099984 restraints weight = 27585.850| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 10668 Z= 0.182 Angle : 0.632 13.051 14523 Z= 0.319 Chirality : 0.042 0.185 1625 Planarity : 0.005 0.117 1767 Dihedral : 11.077 176.558 1644 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.24), residues: 1226 helix: 0.60 (0.23), residues: 539 sheet: -3.31 (0.51), residues: 83 loop : -2.37 (0.24), residues: 604 =============================================================================== Job complete usr+sys time: 1948.69 seconds wall clock time: 36 minutes 40.65 seconds (2200.65 seconds total)