Starting phenix.real_space_refine on Fri Jul 19 22:00:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf4_34712/07_2024/8hf4_34712.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf4_34712/07_2024/8hf4_34712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf4_34712/07_2024/8hf4_34712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf4_34712/07_2024/8hf4_34712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf4_34712/07_2024/8hf4_34712.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf4_34712/07_2024/8hf4_34712.cif" } resolution = 2.8 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 30 5.16 5 C 5732 2.51 5 N 1462 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 469": "OE1" <-> "OE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 657": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8916 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "B" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.45, per 1000 atoms: 0.61 Number of scatterers: 8916 At special positions: 0 Unit cell: (82.368, 81.51, 140.712, 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 30 16.00 P 6 15.00 O 1686 8.00 N 1462 7.00 C 5732 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: 3.82 Conformation dependent library (CDL) restraints added in 1.7 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 4 sheets defined 70.4% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 157 through 164 removed outlier: 3.511A pdb=" N VAL A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 195 removed outlier: 3.574A pdb=" N ILE A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 250 removed outlier: 3.720A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 4.038A pdb=" N PHE A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 258 " --> pdb=" O MET A 254 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 260' Processing helix chain 'A' and resid 261 through 276 removed outlier: 3.663A pdb=" N ILE A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 280 through 288 removed outlier: 3.742A pdb=" N LEU A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.640A pdb=" N MET A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 325 removed outlier: 3.979A pdb=" N ILE A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 353 removed outlier: 3.671A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 362 through 416 removed outlier: 4.021A pdb=" N ARG A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 459 removed outlier: 3.544A pdb=" N TYR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 3.733A pdb=" N ILE A 442 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 removed outlier: 3.603A pdb=" N LEU A 463 " --> pdb=" O GLU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.658A pdb=" N VAL A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 removed outlier: 3.501A pdb=" N LEU A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 588 through 598 Processing helix chain 'A' and resid 623 through 638 removed outlier: 3.834A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 666 removed outlier: 3.927A pdb=" N ALA A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 683 removed outlier: 4.390A pdb=" N ALA A 681 " --> pdb=" O ARG A 677 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 683' Processing helix chain 'A' and resid 700 through 706 Processing helix chain 'A' and resid 709 through 717 Processing helix chain 'B' and resid 157 through 163 removed outlier: 3.979A pdb=" N LYS B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 195 removed outlier: 3.533A pdb=" N ASN B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 185 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 192 " --> pdb=" O TYR B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 203 through 251 removed outlier: 3.702A pdb=" N ILE B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 211 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 removed outlier: 4.041A pdb=" N PHE B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 258 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 260' Processing helix chain 'B' and resid 261 through 276 removed outlier: 3.633A pdb=" N ILE B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 304 removed outlier: 3.815A pdb=" N ILE B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 Processing helix chain 'B' and resid 313 through 325 removed outlier: 4.019A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE B 325 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 353 removed outlier: 3.894A pdb=" N PHE B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU B 330 " --> pdb=" O MET B 326 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 362 through 417 removed outlier: 4.002A pdb=" N ARG B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 459 removed outlier: 3.978A pdb=" N VAL B 432 " --> pdb=" O ASN B 428 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR B 433 " --> pdb=" O THR B 429 " (cutoff:3.500A) Proline residue: B 437 - end of helix removed outlier: 4.056A pdb=" N THR B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 522 through 531 Processing helix chain 'B' and resid 549 through 551 No H-bonds generated for 'chain 'B' and resid 549 through 551' Processing helix chain 'B' and resid 552 through 559 Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 588 through 598 Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 623 through 638 removed outlier: 3.702A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 666 removed outlier: 3.829A pdb=" N ALA B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.787A pdb=" N GLU B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG B 683 " --> pdb=" O THR B 679 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 684 " --> pdb=" O ILE B 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 678 through 684' Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.589A pdb=" N LEU B 704 " --> pdb=" O LYS B 700 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 717 Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 503 removed outlier: 4.062A pdb=" N LEU A 500 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL A 489 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 542 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 487 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 540 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 489 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLN A 538 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 562 removed outlier: 6.577A pdb=" N ASN A 561 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASP A 646 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 513 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 512 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N VAL A 688 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA A 514 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU A 690 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 516 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 699 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU A 697 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 504 through 505 removed outlier: 3.792A pdb=" N LEU B 505 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N PHE B 486 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N SER B 542 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLN B 488 " --> pdb=" O GLU B 540 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU B 540 " --> pdb=" O GLN B 488 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 538 " --> pdb=" O HIS B 490 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 560 through 563 removed outlier: 6.795A pdb=" N ASN B 561 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE B 643 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE B 674 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 645 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 513 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL B 688 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA B 514 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU B 690 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B 516 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU B 697 " --> pdb=" O VAL B 689 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1575 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: 2.87 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 2896 1.37 - 1.54: 6074 1.54 - 1.72: 22 1.72 - 1.89: 56 1.89 - 2.07: 2 Bond restraints: 9050 Sorted by residual: bond pdb=" C4 AGS A 801 " pdb=" C5 AGS A 801 " ideal model delta sigma weight residual 1.386 1.458 -0.072 1.00e-02 1.00e+04 5.25e+01 bond pdb=" C4 AGS B 801 " pdb=" C5 AGS B 801 " ideal model delta sigma weight residual 1.386 1.458 -0.072 1.00e-02 1.00e+04 5.21e+01 bond pdb=" PG AGS A 801 " pdb=" S1G AGS A 801 " ideal model delta sigma weight residual 1.949 2.070 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" PG AGS B 801 " pdb=" S1G AGS B 801 " ideal model delta sigma weight residual 1.949 2.069 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C5 AGS B 801 " pdb=" C6 AGS B 801 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.61e+01 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.62: 166 106.62 - 113.88: 5379 113.88 - 121.14: 4728 121.14 - 128.40: 1973 128.40 - 135.67: 32 Bond angle restraints: 12278 Sorted by residual: angle pdb=" C5 AGS A 801 " pdb=" C4 AGS A 801 " pdb=" N3 AGS A 801 " ideal model delta sigma weight residual 126.80 118.84 7.96 7.41e-01 1.82e+00 1.16e+02 angle pdb=" C5 AGS B 801 " pdb=" C4 AGS B 801 " pdb=" N3 AGS B 801 " ideal model delta sigma weight residual 126.80 118.87 7.93 7.41e-01 1.82e+00 1.15e+02 angle pdb=" C4 AGS B 801 " pdb=" C5 AGS B 801 " pdb=" N7 AGS B 801 " ideal model delta sigma weight residual 110.73 106.97 3.76 4.52e-01 4.89e+00 6.92e+01 angle pdb=" C5 AGS B 801 " pdb=" N7 AGS B 801 " pdb=" C8 AGS B 801 " ideal model delta sigma weight residual 103.67 107.21 -3.54 4.26e-01 5.51e+00 6.92e+01 angle pdb=" C4 AGS A 801 " pdb=" C5 AGS A 801 " pdb=" N7 AGS A 801 " ideal model delta sigma weight residual 110.73 106.97 3.76 4.52e-01 4.89e+00 6.91e+01 ... (remaining 12273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 5110 23.82 - 47.64: 347 47.64 - 71.46: 20 71.46 - 95.27: 11 95.27 - 119.09: 2 Dihedral angle restraints: 5490 sinusoidal: 2196 harmonic: 3294 Sorted by residual: dihedral pdb=" C PHE B 673 " pdb=" N PHE B 673 " pdb=" CA PHE B 673 " pdb=" CB PHE B 673 " ideal model delta harmonic sigma weight residual -122.60 -111.61 -10.99 0 2.50e+00 1.60e-01 1.93e+01 dihedral pdb=" O1A AGS A 801 " pdb=" O3A AGS A 801 " pdb=" PA AGS A 801 " pdb=" PB AGS A 801 " ideal model delta sinusoidal sigma weight residual -67.73 51.36 -119.09 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" O1A AGS B 801 " pdb=" O3A AGS B 801 " pdb=" PA AGS B 801 " pdb=" PB AGS B 801 " ideal model delta sinusoidal sigma weight residual -67.73 51.35 -119.08 1 3.00e+01 1.11e-03 1.59e+01 ... (remaining 5487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1387 0.076 - 0.151: 89 0.151 - 0.227: 19 0.227 - 0.302: 3 0.302 - 0.378: 4 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CA SER B 519 " pdb=" N SER B 519 " pdb=" C SER B 519 " pdb=" CB SER B 519 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA LYS B 528 " pdb=" N LYS B 528 " pdb=" C LYS B 528 " pdb=" CB LYS B 528 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB ILE A 600 " pdb=" CA ILE A 600 " pdb=" CG1 ILE A 600 " pdb=" CG2 ILE A 600 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 1499 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 187 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C TYR B 187 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR B 187 " 0.021 2.00e-02 2.50e+03 pdb=" N TYR B 188 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 563 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO B 564 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 564 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 564 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 436 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO B 437 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 437 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 437 " -0.030 5.00e-02 4.00e+02 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1015 2.75 - 3.28: 9189 3.28 - 3.82: 14353 3.82 - 4.36: 15601 4.36 - 4.90: 27944 Nonbonded interactions: 68102 Sorted by model distance: nonbonded pdb=" OD1 ASP B 653 " pdb=" OG1 THR B 656 " model vdw 2.207 2.440 nonbonded pdb=" OG1 THR A 524 " pdb=" O2G AGS A 801 " model vdw 2.247 2.440 nonbonded pdb=" OG1 THR B 175 " pdb=" OE1 GLN B 226 " model vdw 2.263 2.440 nonbonded pdb=" O SER B 519 " pdb=" O1B AGS B 801 " model vdw 2.277 3.040 nonbonded pdb=" O ILE B 207 " pdb=" N SER B 209 " model vdw 2.293 2.520 ... (remaining 68097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 27.800 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 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 : 0.006 0.121 9050 Z= 0.399 Angle : 0.755 9.449 12278 Z= 0.509 Chirality : 0.048 0.378 1502 Planarity : 0.004 0.054 1522 Dihedral : 14.956 119.092 3366 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.72 % Favored : 94.92 % Rotamer: Outliers : 1.11 % Allowed : 1.41 % Favored : 97.47 % Cbeta Deviations : 0.09 % 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: 2.04 (0.26), residues: 1122 helix: 2.75 (0.20), residues: 686 sheet: 1.12 (0.69), residues: 72 loop : -1.50 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 408 HIS 0.002 0.001 HIS B 248 PHE 0.030 0.001 PHE B 673 TYR 0.013 0.001 TYR B 562 ARG 0.003 0.000 ARG A 677 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 1.014 Fit side-chains REVERT: A 683 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8097 (mtp85) REVERT: B 529 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8609 (mtt) outliers start: 11 outliers final: 1 residues processed: 99 average time/residue: 0.8831 time to fit residues: 95.8271 Evaluate side-chains 55 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 683 ARG Chi-restraints excluded: chain B residue 529 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B 566 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9050 Z= 0.195 Angle : 0.557 10.322 12278 Z= 0.291 Chirality : 0.040 0.359 1502 Planarity : 0.003 0.042 1522 Dihedral : 8.056 136.605 1261 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.12 % Allowed : 9.90 % Favored : 87.98 % 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: 2.15 (0.26), residues: 1122 helix: 2.81 (0.20), residues: 704 sheet: 0.57 (0.64), residues: 80 loop : -1.54 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 408 HIS 0.003 0.001 HIS A 490 PHE 0.012 0.001 PHE A 673 TYR 0.018 0.001 TYR A 559 ARG 0.004 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 1.057 Fit side-chains REVERT: A 193 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8603 (mp) REVERT: A 326 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7591 (ptp) REVERT: A 409 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8035 (tpp) REVERT: A 604 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8573 (pt) REVERT: A 676 HIS cc_start: 0.8789 (m170) cc_final: 0.8497 (m-70) REVERT: B 201 MET cc_start: 0.6801 (mmm) cc_final: 0.6291 (mmm) REVERT: B 458 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8496 (mp) outliers start: 21 outliers final: 7 residues processed: 73 average time/residue: 0.8490 time to fit residues: 68.8485 Evaluate side-chains 62 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 713 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 101 optimal weight: 0.0570 chunk 110 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B 538 GLN B 566 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9050 Z= 0.151 Angle : 0.505 9.870 12278 Z= 0.260 Chirality : 0.038 0.274 1502 Planarity : 0.003 0.039 1522 Dihedral : 8.234 139.711 1252 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.32 % Allowed : 12.73 % Favored : 84.95 % 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: 2.25 (0.26), residues: 1122 helix: 2.92 (0.20), residues: 702 sheet: 0.67 (0.64), residues: 80 loop : -1.56 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 408 HIS 0.003 0.001 HIS B 248 PHE 0.008 0.001 PHE A 673 TYR 0.012 0.001 TYR B 187 ARG 0.002 0.000 ARG B 629 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 1.048 Fit side-chains REVERT: A 604 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8599 (pt) REVERT: A 676 HIS cc_start: 0.8734 (m170) cc_final: 0.8487 (m-70) REVERT: B 201 MET cc_start: 0.7436 (mmm) cc_final: 0.6823 (mmm) outliers start: 23 outliers final: 10 residues processed: 77 average time/residue: 0.8274 time to fit residues: 70.7203 Evaluate side-chains 63 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 676 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 90 optimal weight: 8.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B 200 GLN B 538 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9050 Z= 0.390 Angle : 0.643 7.084 12278 Z= 0.340 Chirality : 0.043 0.218 1502 Planarity : 0.003 0.041 1522 Dihedral : 8.446 150.010 1252 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.43 % Allowed : 15.35 % Favored : 81.21 % 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: 1.77 (0.26), residues: 1122 helix: 2.48 (0.19), residues: 702 sheet: 0.26 (0.63), residues: 80 loop : -1.54 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 408 HIS 0.005 0.001 HIS A 248 PHE 0.008 0.001 PHE B 250 TYR 0.019 0.001 TYR B 187 ARG 0.003 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 49 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: B 201 MET cc_start: 0.8137 (mmm) cc_final: 0.7406 (mmm) outliers start: 34 outliers final: 14 residues processed: 75 average time/residue: 0.7879 time to fit residues: 65.7148 Evaluate side-chains 60 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 453 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 0.0000 chunk 55 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.0570 overall best weight: 0.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 GLN B 538 GLN B 566 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9050 Z= 0.147 Angle : 0.505 8.470 12278 Z= 0.262 Chirality : 0.038 0.198 1502 Planarity : 0.003 0.037 1522 Dihedral : 8.393 153.368 1252 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.12 % Allowed : 17.88 % Favored : 80.00 % 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: 2.14 (0.26), residues: 1122 helix: 2.84 (0.19), residues: 702 sheet: 0.34 (0.62), residues: 80 loop : -1.53 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 408 HIS 0.003 0.001 HIS B 248 PHE 0.009 0.001 PHE A 673 TYR 0.012 0.001 TYR A 559 ARG 0.002 0.000 ARG A 677 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 53 time to evaluate : 1.020 Fit side-chains REVERT: B 201 MET cc_start: 0.8036 (mmm) cc_final: 0.7563 (mtp) outliers start: 21 outliers final: 10 residues processed: 68 average time/residue: 0.8570 time to fit residues: 64.7074 Evaluate side-chains 59 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 529 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 368 GLN B 538 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9050 Z= 0.276 Angle : 0.554 7.223 12278 Z= 0.289 Chirality : 0.039 0.184 1502 Planarity : 0.003 0.037 1522 Dihedral : 8.420 157.229 1252 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.93 % Allowed : 18.48 % Favored : 78.59 % 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: 2.00 (0.26), residues: 1122 helix: 2.73 (0.19), residues: 702 sheet: 0.99 (0.71), residues: 60 loop : -1.65 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 408 HIS 0.004 0.001 HIS A 248 PHE 0.006 0.001 PHE A 673 TYR 0.015 0.001 TYR B 187 ARG 0.002 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 50 time to evaluate : 1.048 Fit side-chains REVERT: A 409 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8003 (ttm) REVERT: B 201 MET cc_start: 0.8287 (mmm) cc_final: 0.7916 (mtp) outliers start: 29 outliers final: 16 residues processed: 72 average time/residue: 0.8273 time to fit residues: 66.2649 Evaluate side-chains 62 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 45 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 676 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN B 566 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9050 Z= 0.163 Angle : 0.509 8.729 12278 Z= 0.264 Chirality : 0.038 0.183 1502 Planarity : 0.003 0.038 1522 Dihedral : 8.412 159.365 1252 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.12 % Allowed : 19.39 % Favored : 78.48 % 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: 2.18 (0.26), residues: 1122 helix: 2.90 (0.19), residues: 702 sheet: 0.30 (0.62), residues: 80 loop : -1.57 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 408 HIS 0.003 0.001 HIS B 248 PHE 0.007 0.001 PHE A 673 TYR 0.010 0.001 TYR B 187 ARG 0.001 0.000 ARG A 677 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 51 time to evaluate : 1.133 Fit side-chains REVERT: A 409 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8029 (ttm) REVERT: B 201 MET cc_start: 0.8291 (mmm) cc_final: 0.7917 (mtp) outliers start: 21 outliers final: 12 residues processed: 67 average time/residue: 0.8515 time to fit residues: 64.2016 Evaluate side-chains 61 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 676 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN B 566 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9050 Z= 0.145 Angle : 0.500 7.849 12278 Z= 0.256 Chirality : 0.037 0.186 1502 Planarity : 0.003 0.037 1522 Dihedral : 8.339 161.445 1252 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.62 % Allowed : 20.51 % Favored : 77.88 % 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: 2.30 (0.26), residues: 1122 helix: 3.01 (0.20), residues: 702 sheet: 0.97 (0.70), residues: 60 loop : -1.60 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 408 HIS 0.003 0.001 HIS B 248 PHE 0.006 0.001 PHE B 468 TYR 0.012 0.001 TYR B 187 ARG 0.002 0.000 ARG B 606 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 1.227 Fit side-chains REVERT: B 201 MET cc_start: 0.8353 (mmm) cc_final: 0.7972 (mtp) outliers start: 16 outliers final: 14 residues processed: 67 average time/residue: 0.8509 time to fit residues: 63.8356 Evaluate side-chains 63 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 676 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0570 chunk 100 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 0.1980 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.3980 chunk 95 optimal weight: 0.0370 chunk 66 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9050 Z= 0.135 Angle : 0.508 8.861 12278 Z= 0.256 Chirality : 0.037 0.197 1502 Planarity : 0.003 0.037 1522 Dihedral : 8.320 163.051 1252 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.52 % Allowed : 20.61 % Favored : 77.88 % 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 (0.26), residues: 1122 helix: 3.12 (0.20), residues: 702 sheet: 0.30 (0.63), residues: 80 loop : -1.56 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 408 HIS 0.002 0.001 HIS A 490 PHE 0.010 0.001 PHE A 250 TYR 0.011 0.001 TYR A 427 ARG 0.004 0.000 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 1.084 Fit side-chains REVERT: B 201 MET cc_start: 0.8393 (mmm) cc_final: 0.8001 (mtp) REVERT: B 326 MET cc_start: 0.8031 (ttp) cc_final: 0.7769 (ttm) REVERT: B 407 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8099 (tm) REVERT: B 622 ILE cc_start: 0.7315 (mm) cc_final: 0.6711 (tp) outliers start: 15 outliers final: 9 residues processed: 73 average time/residue: 0.7986 time to fit residues: 65.0250 Evaluate side-chains 66 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 407 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 0.0670 chunk 88 optimal weight: 0.0770 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9050 Z= 0.134 Angle : 0.503 9.006 12278 Z= 0.251 Chirality : 0.038 0.236 1502 Planarity : 0.003 0.037 1522 Dihedral : 8.301 163.765 1252 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.11 % Allowed : 21.01 % Favored : 77.88 % 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 (0.26), residues: 1122 helix: 3.13 (0.20), residues: 702 sheet: 0.40 (0.63), residues: 80 loop : -1.50 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 408 HIS 0.002 0.001 HIS A 490 PHE 0.006 0.001 PHE B 468 TYR 0.010 0.001 TYR A 427 ARG 0.002 0.000 ARG B 677 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 1.100 Fit side-chains REVERT: B 201 MET cc_start: 0.8387 (mmm) cc_final: 0.8034 (mtp) REVERT: B 407 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8108 (tm) REVERT: B 622 ILE cc_start: 0.7312 (mm) cc_final: 0.6712 (tp) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.9120 time to fit residues: 61.6206 Evaluate side-chains 62 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 529 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.088341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.068097 restraints weight = 21577.433| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.24 r_work: 0.3063 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9050 Z= 0.138 Angle : 0.499 8.602 12278 Z= 0.250 Chirality : 0.037 0.239 1502 Planarity : 0.003 0.036 1522 Dihedral : 8.308 164.448 1252 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.11 % Allowed : 21.62 % Favored : 77.27 % 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 (0.27), residues: 1122 helix: 3.14 (0.20), residues: 704 sheet: 0.43 (0.64), residues: 80 loop : -1.58 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 408 HIS 0.002 0.001 HIS A 490 PHE 0.009 0.001 PHE B 250 TYR 0.009 0.001 TYR A 427 ARG 0.001 0.000 ARG A 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2222.37 seconds wall clock time: 40 minutes 17.82 seconds (2417.82 seconds total)