Starting phenix.real_space_refine on Wed Sep 25 01:53:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shl_25128/09_2024/7shl_25128.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shl_25128/09_2024/7shl_25128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shl_25128/09_2024/7shl_25128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shl_25128/09_2024/7shl_25128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shl_25128/09_2024/7shl_25128.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shl_25128/09_2024/7shl_25128.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 69 5.16 5 C 5890 2.51 5 N 1527 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9207 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5291 Classifications: {'peptide': 645} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 627} Chain: "B" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 770 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 8, 'TRANS': 88} Chain: "C" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 773 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "L" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2228 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 264} Chain: "R" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 144 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8610 SG CYS L 356 45.750 26.931 137.545 1.00322.01 S ATOM 8624 SG CYS L 358 47.077 24.154 139.782 1.00323.88 S ATOM 8937 SG CYS L 400 49.431 25.769 137.231 1.00324.29 S ATOM 8964 SG CYS L 404 46.670 23.617 136.020 1.00365.62 S Time building chain proxies: 9.44, per 1000 atoms: 1.03 Number of scatterers: 9207 At special positions: 0 Unit cell: (113.025, 100.65, 180.675, 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) Zn 1 29.99 S 69 16.00 O 1720 8.00 N 1527 7.00 C 5890 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 - 3.00 Amino acid : True - 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: 2.77 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 500 " pdb="ZN ZN L 500 " - pdb=" SG CYS L 404 " pdb="ZN ZN L 500 " - pdb=" SG CYS L 400 " pdb="ZN ZN L 500 " - pdb=" SG CYS L 356 " pdb="ZN ZN L 500 " - pdb=" SG CYS L 358 " Number of angles added : 6 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 8 sheets defined 53.0% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 9 through 26 removed outlier: 3.863A pdb=" N THR A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 53 through 78 Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 155 through 172 Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.970A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 207 through 230 Processing helix chain 'A' and resid 231 through 254 Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 266 removed outlier: 3.899A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.603A pdb=" N GLU A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N HIS A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 304 removed outlier: 3.733A pdb=" N ALA A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 328 removed outlier: 4.515A pdb=" N HIS A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 357 Processing helix chain 'A' and resid 361 through 377 Processing helix chain 'A' and resid 386 through 400 Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.578A pdb=" N VAL A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 446 removed outlier: 4.269A pdb=" N PHE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.839A pdb=" N GLU A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 470 through 497 removed outlier: 3.618A pdb=" N TYR A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 478 " --> pdb=" O HIS A 474 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 548 removed outlier: 3.729A pdb=" N GLU A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 596 through 604 Processing helix chain 'A' and resid 606 through 620 removed outlier: 3.502A pdb=" N LEU A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.904A pdb=" N LEU B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 66 through 83 removed outlier: 4.154A pdb=" N LYS C 72 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'L' and resid 170 through 174 removed outlier: 3.786A pdb=" N LEU L 174 " --> pdb=" O MET L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 225 removed outlier: 3.925A pdb=" N THR L 220 " --> pdb=" O LEU L 217 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR L 221 " --> pdb=" O CYS L 218 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU L 222 " --> pdb=" O SER L 219 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG L 223 " --> pdb=" O THR L 220 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR L 225 " --> pdb=" O LEU L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 246 Processing helix chain 'L' and resid 264 through 269 removed outlier: 4.312A pdb=" N GLY L 267 " --> pdb=" O PHE L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 292 Processing helix chain 'L' and resid 321 through 334 Processing helix chain 'L' and resid 343 through 352 Processing helix chain 'L' and resid 375 through 378 No H-bonds generated for 'chain 'L' and resid 375 through 378' Processing helix chain 'L' and resid 401 through 415 removed outlier: 3.737A pdb=" N GLN L 407 " --> pdb=" O THR L 403 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE L 408 " --> pdb=" O CYS L 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 506 through 508 removed outlier: 6.369A pdb=" N VAL R 24 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LYS A 565 " --> pdb=" O VAL R 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 511 through 513 Processing sheet with id=AA3, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 44 removed outlier: 3.769A pdb=" N ALA B 78 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR B 13 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N LYS C 32 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N PHE B 15 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 135 through 138 removed outlier: 3.627A pdb=" N LEU L 203 " --> pdb=" O SER L 228 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP L 230 " --> pdb=" O LEU L 203 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU L 229 " --> pdb=" O SER L 251 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS L 253 " --> pdb=" O LEU L 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 274 through 276 removed outlier: 7.098A pdb=" N LEU L 275 " --> pdb=" O ASP L 298 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU L 295 " --> pdb=" O THR L 381 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N VAL L 383 " --> pdb=" O GLU L 295 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU L 297 " --> pdb=" O VAL L 383 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 313 through 314 removed outlier: 3.661A pdb=" N ASP L 313 " --> pdb=" O GLN L 368 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN L 368 " --> pdb=" O ASP L 313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 354 through 355 453 hydrogen bonds defined for protein. 1299 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: 2.74 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2958 1.34 - 1.46: 2025 1.46 - 1.58: 4306 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 9397 Sorted by residual: bond pdb=" CA ASN L 281 " pdb=" CB ASN L 281 " ideal model delta sigma weight residual 1.523 1.542 -0.019 1.27e-02 6.20e+03 2.12e+00 bond pdb=" CB GLN L 348 " pdb=" CG GLN L 348 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CA LYS A 117 " pdb=" C LYS A 117 " ideal model delta sigma weight residual 1.523 1.505 0.018 1.56e-02 4.11e+03 1.31e+00 bond pdb=" N ILE L 314 " pdb=" CA ILE L 314 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.17e+00 bond pdb=" CB LYS B 11 " pdb=" CG LYS B 11 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.00e+00 ... (remaining 9392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 12293 1.55 - 3.11: 326 3.11 - 4.66: 61 4.66 - 6.21: 18 6.21 - 7.76: 6 Bond angle restraints: 12704 Sorted by residual: angle pdb=" N ILE L 314 " pdb=" CA ILE L 314 " pdb=" C ILE L 314 " ideal model delta sigma weight residual 106.21 109.98 -3.77 1.07e+00 8.73e-01 1.24e+01 angle pdb=" CB LYS B 11 " pdb=" CG LYS B 11 " pdb=" CD LYS B 11 " ideal model delta sigma weight residual 111.30 118.35 -7.05 2.30e+00 1.89e-01 9.39e+00 angle pdb=" CB ARG C 82 " pdb=" CG ARG C 82 " pdb=" CD ARG C 82 " ideal model delta sigma weight residual 111.30 118.32 -7.02 2.30e+00 1.89e-01 9.31e+00 angle pdb=" N LYS A 615 " pdb=" CA LYS A 615 " pdb=" CB LYS A 615 " ideal model delta sigma weight residual 110.12 114.24 -4.12 1.47e+00 4.63e-01 7.84e+00 angle pdb=" CB LYS A 615 " pdb=" CG LYS A 615 " pdb=" CD LYS A 615 " ideal model delta sigma weight residual 111.30 117.67 -6.37 2.30e+00 1.89e-01 7.68e+00 ... (remaining 12699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 5123 17.38 - 34.77: 526 34.77 - 52.15: 79 52.15 - 69.54: 8 69.54 - 86.92: 11 Dihedral angle restraints: 5747 sinusoidal: 2366 harmonic: 3381 Sorted by residual: dihedral pdb=" CA TYR A 253 " pdb=" C TYR A 253 " pdb=" N LEU A 254 " pdb=" CA LEU A 254 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ARG B 37 " pdb=" C ARG B 37 " pdb=" N PRO B 38 " pdb=" CA PRO B 38 " ideal model delta harmonic sigma weight residual -180.00 -162.74 -17.26 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA MET A 576 " pdb=" C MET A 576 " pdb=" N VAL A 577 " pdb=" CA VAL A 577 " ideal model delta harmonic sigma weight residual -180.00 -163.17 -16.83 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 957 0.036 - 0.072: 360 0.072 - 0.108: 90 0.108 - 0.144: 24 0.144 - 0.180: 4 Chirality restraints: 1435 Sorted by residual: chirality pdb=" CB THR L 308 " pdb=" CA THR L 308 " pdb=" OG1 THR L 308 " pdb=" CG2 THR L 308 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CB THR C 57 " pdb=" CA THR C 57 " pdb=" OG1 THR C 57 " pdb=" CG2 THR C 57 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA ILE A 593 " pdb=" N ILE A 593 " pdb=" C ILE A 593 " pdb=" CB ILE A 593 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 1432 not shown) Planarity restraints: 1615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY L 393 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO L 394 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO L 394 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO L 394 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN L 348 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" CD GLN L 348 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLN L 348 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN L 348 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE L 342 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.27e+00 pdb=" N PRO L 343 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO L 343 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 343 " 0.021 5.00e-02 4.00e+02 ... (remaining 1612 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 170 2.65 - 3.21: 9239 3.21 - 3.77: 15113 3.77 - 4.34: 20217 4.34 - 4.90: 32093 Nonbonded interactions: 76832 Sorted by model distance: nonbonded pdb=" OG1 THR A 611 " pdb=" NZ LYS A 615 " model vdw 2.087 3.120 nonbonded pdb=" O LEU A 226 " pdb=" OG SER A 230 " model vdw 2.144 3.040 nonbonded pdb=" OG1 THR C 57 " pdb=" OE1 GLU C 59 " model vdw 2.170 3.040 nonbonded pdb=" O GLY A 183 " pdb=" OG SER A 187 " model vdw 2.175 3.040 nonbonded pdb=" OG SER B 95 " pdb=" OD2 ASP C 25 " model vdw 2.211 3.040 ... (remaining 76827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 13.770 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.010 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9397 Z= 0.202 Angle : 0.646 7.763 12704 Z= 0.344 Chirality : 0.041 0.180 1435 Planarity : 0.004 0.054 1615 Dihedral : 14.140 86.922 3547 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1128 helix: 0.89 (0.23), residues: 542 sheet: -0.79 (0.58), residues: 85 loop : -0.70 (0.30), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.005 0.001 HIS A 474 PHE 0.014 0.001 PHE A 64 TYR 0.022 0.002 TYR A 596 ARG 0.006 0.000 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8713 (mpp) cc_final: 0.8176 (mpp) REVERT: A 476 MET cc_start: 0.8306 (mtp) cc_final: 0.7916 (mtm) REVERT: A 553 LEU cc_start: 0.8800 (mt) cc_final: 0.8589 (mp) REVERT: A 582 MET cc_start: 0.8862 (mtm) cc_final: 0.8635 (mtt) REVERT: B 41 ASP cc_start: 0.7808 (m-30) cc_final: 0.7573 (m-30) REVERT: B 68 ARG cc_start: 0.7796 (tpt170) cc_final: 0.7526 (tpt170) REVERT: L 300 PHE cc_start: 0.7339 (p90) cc_final: 0.6951 (p90) REVERT: L 324 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7295 (tp30) REVERT: L 366 PHE cc_start: 0.8544 (p90) cc_final: 0.8061 (p90) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2104 time to fit residues: 47.0390 Evaluate side-chains 120 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 44 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.0020 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 HIS A 547 HIS A 641 ASN ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9397 Z= 0.282 Angle : 0.660 6.346 12704 Z= 0.344 Chirality : 0.043 0.220 1435 Planarity : 0.004 0.044 1615 Dihedral : 4.565 21.063 1224 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.25 % Allowed : 10.83 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1128 helix: 0.85 (0.22), residues: 556 sheet: -1.04 (0.57), residues: 89 loop : -0.50 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 14 HIS 0.004 0.001 HIS A 474 PHE 0.024 0.002 PHE A 543 TYR 0.021 0.002 TYR A 596 ARG 0.004 0.001 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7870 (tp30) cc_final: 0.7599 (tp30) REVERT: A 566 MET cc_start: -0.0968 (OUTLIER) cc_final: -0.1225 (mmp) REVERT: A 582 MET cc_start: 0.8905 (mtm) cc_final: 0.8590 (mtt) REVERT: A 621 LYS cc_start: 0.8006 (tptp) cc_final: 0.7515 (pttp) REVERT: B 41 ASP cc_start: 0.7968 (m-30) cc_final: 0.7543 (m-30) REVERT: B 45 TYR cc_start: 0.6732 (m-80) cc_final: 0.6460 (m-80) REVERT: L 300 PHE cc_start: 0.7261 (p90) cc_final: 0.6927 (p90) REVERT: L 366 PHE cc_start: 0.8466 (p90) cc_final: 0.8032 (p90) outliers start: 13 outliers final: 6 residues processed: 144 average time/residue: 0.2217 time to fit residues: 44.0896 Evaluate side-chains 131 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain L residue 298 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 83 optimal weight: 0.3980 chunk 68 optimal weight: 0.0270 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 0.0870 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9397 Z= 0.160 Angle : 0.601 10.832 12704 Z= 0.305 Chirality : 0.042 0.181 1435 Planarity : 0.004 0.053 1615 Dihedral : 4.314 19.590 1224 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.25 % Allowed : 13.71 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1128 helix: 1.12 (0.23), residues: 554 sheet: -0.95 (0.60), residues: 85 loop : -0.47 (0.30), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 555 HIS 0.003 0.001 HIS L 156 PHE 0.021 0.001 PHE A 543 TYR 0.020 0.001 TYR A 477 ARG 0.006 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 MET cc_start: -0.1109 (OUTLIER) cc_final: -0.1453 (mmp) REVERT: A 582 MET cc_start: 0.8837 (mtm) cc_final: 0.8542 (mtt) REVERT: B 41 ASP cc_start: 0.7965 (m-30) cc_final: 0.7578 (m-30) REVERT: B 45 TYR cc_start: 0.6584 (m-80) cc_final: 0.6313 (m-80) REVERT: B 57 LEU cc_start: 0.8536 (tt) cc_final: 0.7855 (mm) REVERT: L 300 PHE cc_start: 0.7187 (p90) cc_final: 0.6826 (p90) REVERT: L 366 PHE cc_start: 0.8487 (p90) cc_final: 0.8043 (p90) outliers start: 13 outliers final: 5 residues processed: 156 average time/residue: 0.2159 time to fit residues: 46.8469 Evaluate side-chains 134 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain L residue 298 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 0.0970 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 0.0170 chunk 60 optimal weight: 3.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 HIS A 590 ASN A 641 ASN ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9397 Z= 0.159 Angle : 0.589 8.212 12704 Z= 0.295 Chirality : 0.041 0.169 1435 Planarity : 0.004 0.055 1615 Dihedral : 4.220 19.406 1224 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.53 % Allowed : 15.24 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.26), residues: 1128 helix: 1.12 (0.22), residues: 556 sheet: -0.98 (0.62), residues: 81 loop : -0.38 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 91 HIS 0.004 0.001 HIS A 474 PHE 0.020 0.001 PHE A 543 TYR 0.017 0.001 TYR A 477 ARG 0.005 0.000 ARG L 334 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8210 (mpp) REVERT: A 297 MET cc_start: 0.8656 (tpp) cc_final: 0.8368 (tpp) REVERT: A 582 MET cc_start: 0.8845 (mtm) cc_final: 0.8566 (mtt) REVERT: B 41 ASP cc_start: 0.7964 (m-30) cc_final: 0.7597 (m-30) REVERT: B 57 LEU cc_start: 0.8555 (tt) cc_final: 0.8026 (mm) REVERT: C 32 LYS cc_start: 0.8372 (mmtt) cc_final: 0.8019 (mmtm) REVERT: L 176 LYS cc_start: 0.8068 (mppt) cc_final: 0.7554 (tptp) REVERT: L 300 PHE cc_start: 0.7221 (p90) cc_final: 0.6928 (p90) REVERT: L 366 PHE cc_start: 0.8405 (p90) cc_final: 0.8054 (p90) outliers start: 16 outliers final: 5 residues processed: 156 average time/residue: 0.2395 time to fit residues: 50.9628 Evaluate side-chains 135 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain R residue 24 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9397 Z= 0.174 Angle : 0.597 8.562 12704 Z= 0.301 Chirality : 0.042 0.239 1435 Planarity : 0.004 0.057 1615 Dihedral : 4.224 19.417 1224 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.82 % Allowed : 15.44 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1128 helix: 1.17 (0.22), residues: 556 sheet: -0.88 (0.60), residues: 85 loop : -0.37 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.006 0.001 HIS A 474 PHE 0.018 0.001 PHE A 543 TYR 0.019 0.001 TYR A 477 ARG 0.007 0.000 ARG L 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 MET cc_start: 0.8699 (mpp) cc_final: 0.8493 (mpp) REVERT: A 236 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8357 (mpp) REVERT: A 297 MET cc_start: 0.8665 (tpp) cc_final: 0.8406 (tpp) REVERT: A 476 MET cc_start: 0.8261 (mtp) cc_final: 0.7698 (mtm) REVERT: A 582 MET cc_start: 0.8872 (mtm) cc_final: 0.8612 (mtt) REVERT: B 57 LEU cc_start: 0.8577 (tt) cc_final: 0.7982 (mm) REVERT: L 176 LYS cc_start: 0.8123 (mppt) cc_final: 0.7560 (tptp) REVERT: L 300 PHE cc_start: 0.7282 (p90) cc_final: 0.6910 (p90) REVERT: L 366 PHE cc_start: 0.8443 (p90) cc_final: 0.8205 (p90) outliers start: 19 outliers final: 11 residues processed: 145 average time/residue: 0.2213 time to fit residues: 44.5125 Evaluate side-chains 137 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain R residue 24 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 56 optimal weight: 0.0980 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9397 Z= 0.170 Angle : 0.608 9.228 12704 Z= 0.302 Chirality : 0.042 0.226 1435 Planarity : 0.004 0.060 1615 Dihedral : 4.192 18.554 1224 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.63 % Allowed : 16.49 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1128 helix: 1.15 (0.23), residues: 559 sheet: -0.89 (0.60), residues: 85 loop : -0.38 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 35 HIS 0.007 0.001 HIS A 474 PHE 0.019 0.001 PHE A 543 TYR 0.020 0.001 TYR A 477 ARG 0.004 0.000 ARG L 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 MET cc_start: 0.8765 (mpp) cc_final: 0.8461 (mpp) REVERT: A 236 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8316 (mpp) REVERT: A 297 MET cc_start: 0.8614 (tpp) cc_final: 0.8400 (tpp) REVERT: A 476 MET cc_start: 0.8226 (mtp) cc_final: 0.7621 (mtm) REVERT: A 582 MET cc_start: 0.8865 (mtm) cc_final: 0.8631 (mtt) REVERT: B 51 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8134 (tt) REVERT: B 57 LEU cc_start: 0.8618 (tt) cc_final: 0.8029 (mm) REVERT: L 176 LYS cc_start: 0.8121 (mppt) cc_final: 0.7563 (tptp) REVERT: L 300 PHE cc_start: 0.7290 (p90) cc_final: 0.6929 (p90) REVERT: L 366 PHE cc_start: 0.8419 (p90) cc_final: 0.8192 (p90) outliers start: 17 outliers final: 11 residues processed: 150 average time/residue: 0.2375 time to fit residues: 48.3847 Evaluate side-chains 144 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain R residue 24 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 90 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 42 optimal weight: 0.0030 chunk 63 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN A 474 HIS ** A 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN L 184 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 9397 Z= 0.384 Angle : 0.741 10.481 12704 Z= 0.383 Chirality : 0.046 0.227 1435 Planarity : 0.005 0.054 1615 Dihedral : 4.736 21.881 1224 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.78 % Allowed : 16.20 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1128 helix: 0.63 (0.22), residues: 560 sheet: -1.19 (0.58), residues: 86 loop : -0.59 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 14 HIS 0.007 0.002 HIS A 474 PHE 0.019 0.002 PHE L 289 TYR 0.032 0.003 TYR B 45 ARG 0.005 0.001 ARG L 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 MET cc_start: 0.8862 (mpp) cc_final: 0.8597 (mpp) REVERT: A 236 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8368 (mpp) REVERT: A 297 MET cc_start: 0.8706 (tpp) cc_final: 0.8449 (tpp) REVERT: A 582 MET cc_start: 0.8871 (mtm) cc_final: 0.8620 (mtt) REVERT: B 51 LEU cc_start: 0.8770 (tt) cc_final: 0.8526 (tt) REVERT: L 176 LYS cc_start: 0.8189 (mppt) cc_final: 0.7598 (tptp) REVERT: L 300 PHE cc_start: 0.7410 (p90) cc_final: 0.7046 (p90) REVERT: L 366 PHE cc_start: 0.8439 (p90) cc_final: 0.8096 (p90) REVERT: L 370 ILE cc_start: 0.7668 (mp) cc_final: 0.7300 (tp) outliers start: 29 outliers final: 19 residues processed: 152 average time/residue: 0.2055 time to fit residues: 43.7654 Evaluate side-chains 145 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 222 LEU Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain R residue 24 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 474 HIS ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN L 348 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9397 Z= 0.184 Angle : 0.672 11.458 12704 Z= 0.335 Chirality : 0.045 0.236 1435 Planarity : 0.004 0.060 1615 Dihedral : 4.475 22.997 1224 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.73 % Allowed : 16.97 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1128 helix: 0.91 (0.22), residues: 557 sheet: -1.14 (0.60), residues: 81 loop : -0.44 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 147 HIS 0.003 0.001 HIS L 156 PHE 0.019 0.001 PHE L 289 TYR 0.020 0.001 TYR A 477 ARG 0.004 0.000 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8320 (mpp) REVERT: A 278 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8120 (mm) REVERT: A 297 MET cc_start: 0.8637 (tpp) cc_final: 0.8365 (tpp) REVERT: A 582 MET cc_start: 0.8853 (mtm) cc_final: 0.8578 (mtt) REVERT: L 176 LYS cc_start: 0.8185 (mppt) cc_final: 0.7600 (tptp) REVERT: L 300 PHE cc_start: 0.7306 (p90) cc_final: 0.6950 (p90) REVERT: L 366 PHE cc_start: 0.8427 (p90) cc_final: 0.8151 (p90) REVERT: L 370 ILE cc_start: 0.7619 (mp) cc_final: 0.7229 (tp) outliers start: 18 outliers final: 11 residues processed: 145 average time/residue: 0.2042 time to fit residues: 41.6966 Evaluate side-chains 143 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain R residue 24 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 0.0870 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 105 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 HIS A 547 HIS A 600 GLN ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9397 Z= 0.180 Angle : 0.671 11.080 12704 Z= 0.333 Chirality : 0.044 0.254 1435 Planarity : 0.004 0.059 1615 Dihedral : 4.411 22.311 1224 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.34 % Allowed : 17.83 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.26), residues: 1128 helix: 1.04 (0.22), residues: 558 sheet: -1.09 (0.60), residues: 82 loop : -0.44 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.007 0.001 HIS A 474 PHE 0.018 0.001 PHE L 289 TYR 0.023 0.002 TYR A 477 ARG 0.004 0.000 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8283 (mpp) REVERT: A 278 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8080 (mm) REVERT: A 297 MET cc_start: 0.8650 (tpp) cc_final: 0.8393 (tpp) REVERT: A 476 MET cc_start: 0.8281 (mtp) cc_final: 0.7715 (mtm) REVERT: L 176 LYS cc_start: 0.8184 (mppt) cc_final: 0.7599 (tptp) REVERT: L 253 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8156 (mmtm) REVERT: L 300 PHE cc_start: 0.7219 (p90) cc_final: 0.6832 (p90) REVERT: L 366 PHE cc_start: 0.8412 (p90) cc_final: 0.8195 (p90) REVERT: L 370 ILE cc_start: 0.7595 (mp) cc_final: 0.7214 (tp) outliers start: 14 outliers final: 10 residues processed: 138 average time/residue: 0.2186 time to fit residues: 42.1543 Evaluate side-chains 141 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain R residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.4980 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 88 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 HIS A 600 GLN ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9397 Z= 0.186 Angle : 0.674 9.639 12704 Z= 0.336 Chirality : 0.044 0.250 1435 Planarity : 0.004 0.058 1615 Dihedral : 4.392 23.311 1224 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.44 % Allowed : 17.93 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1128 helix: 1.09 (0.23), residues: 553 sheet: -1.01 (0.61), residues: 81 loop : -0.50 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 14 HIS 0.003 0.001 HIS L 156 PHE 0.019 0.001 PHE A 543 TYR 0.022 0.001 TYR A 596 ARG 0.004 0.000 ARG C 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8283 (mpp) REVERT: A 278 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8074 (mm) REVERT: A 297 MET cc_start: 0.8657 (tpp) cc_final: 0.8427 (tpp) REVERT: A 476 MET cc_start: 0.8266 (mtp) cc_final: 0.7711 (mtm) REVERT: B 55 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8293 (ptmm) REVERT: L 176 LYS cc_start: 0.8164 (mppt) cc_final: 0.7591 (tptp) REVERT: L 300 PHE cc_start: 0.7191 (p90) cc_final: 0.6810 (p90) REVERT: L 366 PHE cc_start: 0.8369 (p90) cc_final: 0.8157 (p90) REVERT: L 370 ILE cc_start: 0.7595 (mp) cc_final: 0.7214 (tp) outliers start: 15 outliers final: 12 residues processed: 140 average time/residue: 0.2060 time to fit residues: 40.6577 Evaluate side-chains 145 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain R residue 24 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 chunk 88 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 63 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 HIS A 600 GLN ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.100704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.069994 restraints weight = 31777.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.071286 restraints weight = 16861.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.071928 restraints weight = 10582.135| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9397 Z= 0.181 Angle : 0.685 13.878 12704 Z= 0.342 Chirality : 0.044 0.240 1435 Planarity : 0.004 0.059 1615 Dihedral : 4.373 22.603 1224 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.53 % Allowed : 17.83 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1128 helix: 1.10 (0.23), residues: 553 sheet: -0.85 (0.57), residues: 92 loop : -0.47 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 14 HIS 0.003 0.001 HIS L 156 PHE 0.017 0.001 PHE A 543 TYR 0.021 0.001 TYR A 596 ARG 0.004 0.000 ARG C 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2300.70 seconds wall clock time: 45 minutes 36.31 seconds (2736.31 seconds total)