Starting phenix.real_space_refine on Wed Feb 14 11:59:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shl_25128/02_2024/7shl_25128.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shl_25128/02_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_25128/02_2024/7shl_25128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shl_25128/02_2024/7shl_25128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shl_25128/02_2024/7shl_25128.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shl_25128/02_2024/7shl_25128.pdb" } 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 Residue "A ASP 122": "OD1" <-> "OD2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2": "OD1" <-> "OD2" Residue "B ASP 17": "OD1" <-> "OD2" Residue "C TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 258": "OE1" <-> "OE2" Residue "L PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.02, per 1000 atoms: 0.55 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 - 3.50 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: 3.70 Conformation dependent library (CDL) restraints added in 1.9 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: 0.97 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: 2.65 Time building geometry restraints manager: 3.98 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: 97.99 - 105.20: 172 105.20 - 112.40: 4794 112.40 - 119.61: 3175 119.61 - 126.81: 4463 126.81 - 134.01: 100 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 2.520 nonbonded pdb=" O LEU A 226 " pdb=" OG SER A 230 " model vdw 2.144 2.440 nonbonded pdb=" OG1 THR C 57 " pdb=" OE1 GLU C 59 " model vdw 2.170 2.440 nonbonded pdb=" O GLY A 183 " pdb=" OG SER A 187 " model vdw 2.175 2.440 nonbonded pdb=" OG SER B 95 " pdb=" OD2 ASP C 25 " model vdw 2.211 2.440 ... (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 ========== 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: 1.590 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: 7.110 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 29.450 Find NCS groups from input model: 0.240 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.330 ------------------------------------------------------------------------------- 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 : 1.268 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: 0.2129 time to fit residues: 46.9524 Evaluate side-chains 120 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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: 4.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 44 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 ** 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: 0.7906 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9397 Z= 0.266 Angle : 0.623 6.315 12704 Z= 0.326 Chirality : 0.042 0.224 1435 Planarity : 0.004 0.044 1615 Dihedral : 4.510 20.659 1224 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.15 % Allowed : 10.64 % Favored : 88.21 % 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: 0.14 (0.26), residues: 1128 helix: 0.91 (0.22), residues: 556 sheet: -1.02 (0.55), residues: 94 loop : -0.55 (0.30), residues: 478 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 0.023 0.002 PHE A 543 TYR 0.020 0.002 TYR C 79 ARG 0.004 0.000 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 150 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7892 (tp30) cc_final: 0.7645 (tp30) REVERT: A 566 MET cc_start: -0.1124 (OUTLIER) cc_final: -0.1427 (mmp) REVERT: A 582 MET cc_start: 0.8905 (mtm) cc_final: 0.8624 (mtt) REVERT: B 41 ASP cc_start: 0.7915 (m-30) cc_final: 0.7524 (m-30) REVERT: B 45 TYR cc_start: 0.6672 (m-80) cc_final: 0.6449 (m-80) REVERT: L 300 PHE cc_start: 0.7397 (p90) cc_final: 0.7067 (p90) REVERT: L 366 PHE cc_start: 0.8408 (p90) cc_final: 0.7981 (p90) outliers start: 12 outliers final: 5 residues processed: 140 average time/residue: 0.2174 time to fit residues: 42.3800 Evaluate side-chains 123 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 0.0980 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.2980 chunk 99 optimal weight: 0.0570 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9397 Z= 0.157 Angle : 0.571 7.728 12704 Z= 0.293 Chirality : 0.041 0.192 1435 Planarity : 0.004 0.052 1615 Dihedral : 4.311 19.628 1224 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.96 % Allowed : 13.61 % Favored : 85.43 % 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: 1.23 (0.23), residues: 549 sheet: -0.99 (0.58), residues: 85 loop : -0.49 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 555 HIS 0.003 0.001 HIS A 625 PHE 0.022 0.001 PHE A 543 TYR 0.020 0.001 TYR A 477 ARG 0.002 0.000 ARG C 82 *********************** 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 144 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 1.166 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: -0.1158 (OUTLIER) cc_final: -0.1502 (mmp) REVERT: A 582 MET cc_start: 0.8848 (mtm) cc_final: 0.8591 (mtt) REVERT: B 41 ASP cc_start: 0.7841 (m-30) cc_final: 0.7441 (m-30) REVERT: B 45 TYR cc_start: 0.6592 (m-80) cc_final: 0.6362 (m-80) REVERT: L 300 PHE cc_start: 0.7304 (p90) cc_final: 0.6942 (p90) REVERT: L 366 PHE cc_start: 0.8442 (p90) cc_final: 0.8021 (p90) outliers start: 10 outliers final: 5 residues processed: 139 average time/residue: 0.2208 time to fit residues: 42.8466 Evaluate side-chains 128 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 A residue 620 VAL Chi-restraints excluded: chain A residue 642 MET 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: 0.5980 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 0.0070 chunk 96 optimal weight: 0.0170 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 HIS ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9397 Z= 0.154 Angle : 0.574 9.599 12704 Z= 0.287 Chirality : 0.041 0.198 1435 Planarity : 0.004 0.055 1615 Dihedral : 4.196 19.564 1224 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.82 % Allowed : 14.09 % Favored : 84.08 % 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: 0.51 (0.26), residues: 1128 helix: 1.35 (0.23), residues: 549 sheet: -0.82 (0.56), residues: 89 loop : -0.53 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 35 HIS 0.005 0.001 HIS A 474 PHE 0.020 0.001 PHE A 543 TYR 0.017 0.001 TYR A 477 ARG 0.002 0.000 ARG C 63 *********************** 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 156 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6872 (ttm) REVERT: A 162 MET cc_start: 0.8624 (mpp) cc_final: 0.8325 (mpp) REVERT: A 566 MET cc_start: -0.1356 (OUTLIER) cc_final: -0.1819 (mmp) REVERT: A 582 MET cc_start: 0.8859 (mtm) cc_final: 0.8576 (mtt) REVERT: B 41 ASP cc_start: 0.7910 (m-30) cc_final: 0.7673 (m-30) REVERT: L 176 LYS cc_start: 0.8089 (mppt) cc_final: 0.7569 (tptp) REVERT: L 300 PHE cc_start: 0.7341 (p90) cc_final: 0.6956 (p90) REVERT: L 366 PHE cc_start: 0.8481 (p90) cc_final: 0.8096 (p90) outliers start: 19 outliers final: 6 residues processed: 147 average time/residue: 0.2111 time to fit residues: 43.8875 Evaluate side-chains 132 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain B residue 63 THR 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: 0.6980 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9397 Z= 0.177 Angle : 0.602 11.871 12704 Z= 0.295 Chirality : 0.041 0.256 1435 Planarity : 0.004 0.058 1615 Dihedral : 4.190 20.251 1224 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.53 % Allowed : 15.82 % Favored : 82.65 % 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: 0.57 (0.26), residues: 1128 helix: 1.39 (0.23), residues: 551 sheet: -0.84 (0.56), residues: 89 loop : -0.50 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.003 0.001 HIS L 156 PHE 0.019 0.001 PHE A 543 TYR 0.019 0.001 TYR A 477 ARG 0.001 0.000 ARG C 82 *********************** 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 149 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6971 (ttm) REVERT: A 162 MET cc_start: 0.8695 (mpp) cc_final: 0.8432 (mpp) REVERT: A 236 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8297 (mpp) REVERT: A 297 MET cc_start: 0.8707 (tpp) cc_final: 0.8432 (tpp) REVERT: A 582 MET cc_start: 0.8862 (mtm) cc_final: 0.8599 (mtt) REVERT: B 57 LEU cc_start: 0.8344 (tt) cc_final: 0.7661 (mm) REVERT: L 176 LYS cc_start: 0.8176 (mppt) cc_final: 0.7622 (tptp) REVERT: L 300 PHE cc_start: 0.7380 (p90) cc_final: 0.7009 (p90) REVERT: L 366 PHE cc_start: 0.8479 (p90) cc_final: 0.8103 (p90) outliers start: 16 outliers final: 9 residues processed: 142 average time/residue: 0.2087 time to fit residues: 42.3205 Evaluate side-chains 136 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 308 THR 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: 10.0000 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9397 Z= 0.272 Angle : 0.639 9.425 12704 Z= 0.322 Chirality : 0.043 0.264 1435 Planarity : 0.004 0.056 1615 Dihedral : 4.377 22.446 1224 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.30 % Allowed : 16.20 % Favored : 81.50 % 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: 0.34 (0.26), residues: 1128 helix: 1.17 (0.22), residues: 552 sheet: -0.98 (0.56), residues: 90 loop : -0.56 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 14 HIS 0.005 0.001 HIS A 474 PHE 0.020 0.002 PHE A 543 TYR 0.020 0.002 TYR C 79 ARG 0.003 0.000 ARG A 379 *********************** 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 153 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6944 (ttm) REVERT: A 236 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8308 (mpp) REVERT: A 582 MET cc_start: 0.8836 (mtm) cc_final: 0.8550 (mtt) REVERT: L 176 LYS cc_start: 0.8221 (mppt) cc_final: 0.7642 (tptp) REVERT: L 300 PHE cc_start: 0.7586 (p90) cc_final: 0.7263 (p90) REVERT: L 366 PHE cc_start: 0.8486 (p90) cc_final: 0.8092 (p90) outliers start: 24 outliers final: 15 residues processed: 141 average time/residue: 0.2020 time to fit residues: 40.6159 Evaluate side-chains 141 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 101 MET 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 492 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 308 THR 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: 0.8980 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9397 Z= 0.273 Angle : 0.657 12.150 12704 Z= 0.333 Chirality : 0.044 0.263 1435 Planarity : 0.004 0.055 1615 Dihedral : 4.513 22.723 1224 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.49 % Allowed : 17.16 % Favored : 80.35 % 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: 0.15 (0.26), residues: 1128 helix: 1.01 (0.22), residues: 552 sheet: -1.09 (0.57), residues: 86 loop : -0.67 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 14 HIS 0.004 0.001 HIS A 557 PHE 0.018 0.002 PHE A 543 TYR 0.029 0.002 TYR B 45 ARG 0.002 0.000 ARG A 379 *********************** 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 160 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.6918 (ttm) REVERT: A 236 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8296 (mpp) REVERT: A 278 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8278 (mm) REVERT: A 582 MET cc_start: 0.8857 (mtm) cc_final: 0.8624 (mtt) REVERT: B 45 TYR cc_start: 0.7031 (m-80) cc_final: 0.6785 (m-80) REVERT: B 57 LEU cc_start: 0.8420 (tt) cc_final: 0.7632 (mm) REVERT: L 176 LYS cc_start: 0.8218 (mppt) cc_final: 0.7636 (tptp) REVERT: L 253 LYS cc_start: 0.8503 (mmtm) cc_final: 0.8191 (mmpt) REVERT: L 300 PHE cc_start: 0.7592 (p90) cc_final: 0.7248 (p90) REVERT: L 366 PHE cc_start: 0.8480 (p90) cc_final: 0.8079 (p90) outliers start: 26 outliers final: 18 residues processed: 147 average time/residue: 0.2062 time to fit residues: 42.8994 Evaluate side-chains 146 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 101 MET 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 329 ASN Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 308 THR Chi-restraints excluded: chain L residue 345 THR 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: 0.7980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 0.0970 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 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 313 GLN ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2242 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= 0.180 Angle : 0.639 11.932 12704 Z= 0.316 Chirality : 0.043 0.269 1435 Planarity : 0.004 0.061 1615 Dihedral : 4.325 21.938 1224 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.82 % Allowed : 18.31 % Favored : 79.87 % 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: 0.38 (0.26), residues: 1128 helix: 1.29 (0.23), residues: 553 sheet: -1.00 (0.59), residues: 81 loop : -0.66 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 91 HIS 0.003 0.001 HIS L 156 PHE 0.017 0.001 PHE A 543 TYR 0.021 0.001 TYR B 45 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 156 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.6820 (ttm) REVERT: A 236 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8095 (mpp) REVERT: A 297 MET cc_start: 0.8779 (tpp) cc_final: 0.8569 (mmp) REVERT: A 582 MET cc_start: 0.8844 (mtm) cc_final: 0.8611 (mtt) REVERT: B 57 LEU cc_start: 0.8252 (tt) cc_final: 0.7532 (mm) REVERT: L 176 LYS cc_start: 0.8204 (mppt) cc_final: 0.7615 (tptp) REVERT: L 300 PHE cc_start: 0.7543 (p90) cc_final: 0.7194 (p90) REVERT: L 366 PHE cc_start: 0.8473 (p90) cc_final: 0.8060 (p90) outliers start: 19 outliers final: 12 residues processed: 146 average time/residue: 0.2097 time to fit residues: 43.1074 Evaluate side-chains 141 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET 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 492 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 308 THR 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: 6.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ** 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 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9397 Z= 0.305 Angle : 0.711 11.046 12704 Z= 0.361 Chirality : 0.045 0.328 1435 Planarity : 0.004 0.054 1615 Dihedral : 4.588 23.441 1224 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.40 % Allowed : 18.70 % Favored : 78.91 % 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: 0.08 (0.26), residues: 1128 helix: 0.95 (0.22), residues: 560 sheet: -1.08 (0.57), residues: 86 loop : -0.72 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 14 HIS 0.006 0.001 HIS A 474 PHE 0.017 0.002 PHE A 543 TYR 0.022 0.002 TYR C 79 ARG 0.003 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 159 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6943 (ttm) REVERT: A 236 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8319 (mpp) REVERT: A 582 MET cc_start: 0.8855 (mtm) cc_final: 0.8627 (mtt) REVERT: B 57 LEU cc_start: 0.8444 (tt) cc_final: 0.7711 (mm) REVERT: L 253 LYS cc_start: 0.8276 (mmpt) cc_final: 0.8003 (pttp) REVERT: L 300 PHE cc_start: 0.7612 (p90) cc_final: 0.7284 (p90) REVERT: L 366 PHE cc_start: 0.8466 (p90) cc_final: 0.8070 (p90) outliers start: 25 outliers final: 16 residues processed: 145 average time/residue: 0.2208 time to fit residues: 44.6123 Evaluate side-chains 145 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 329 ASN 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 566 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 308 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.0980 chunk 93 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** 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: 0.7896 moved from start: 0.2532 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= 0.190 Angle : 0.695 12.147 12704 Z= 0.342 Chirality : 0.045 0.299 1435 Planarity : 0.004 0.058 1615 Dihedral : 4.463 22.480 1224 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.44 % Allowed : 20.04 % Favored : 78.52 % 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: 0.28 (0.26), residues: 1128 helix: 1.14 (0.23), residues: 554 sheet: -1.08 (0.59), residues: 81 loop : -0.64 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.003 0.001 HIS L 156 PHE 0.016 0.001 PHE A 543 TYR 0.020 0.001 TYR A 477 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 : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.6806 (ttm) REVERT: A 236 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8077 (mpp) REVERT: A 480 MET cc_start: 0.7880 (tmm) cc_final: 0.7592 (tmm) REVERT: A 582 MET cc_start: 0.8844 (mtm) cc_final: 0.8618 (mtt) REVERT: B 57 LEU cc_start: 0.8263 (tt) cc_final: 0.7608 (mm) REVERT: L 253 LYS cc_start: 0.8259 (mmpt) cc_final: 0.7940 (pttp) REVERT: L 300 PHE cc_start: 0.7550 (p90) cc_final: 0.7210 (p90) REVERT: L 366 PHE cc_start: 0.8491 (p90) cc_final: 0.8090 (p90) outliers start: 15 outliers final: 13 residues processed: 138 average time/residue: 0.1902 time to fit residues: 37.9481 Evaluate side-chains 143 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET 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 492 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 308 THR Chi-restraints excluded: chain L residue 345 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.3980 chunk 13 optimal weight: 0.0980 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 HIS ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.099579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.068490 restraints weight = 32119.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.070016 restraints weight = 17397.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.070620 restraints weight = 11111.622| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9397 Z= 0.190 Angle : 0.708 11.201 12704 Z= 0.348 Chirality : 0.045 0.332 1435 Planarity : 0.004 0.057 1615 Dihedral : 4.501 22.287 1224 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.63 % Allowed : 20.52 % Favored : 77.85 % 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: 0.22 (0.26), residues: 1128 helix: 1.06 (0.23), residues: 554 sheet: -1.02 (0.60), residues: 81 loop : -0.63 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 14 HIS 0.003 0.001 HIS L 156 PHE 0.016 0.001 PHE A 543 TYR 0.020 0.001 TYR A 477 ARG 0.003 0.000 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2243.06 seconds wall clock time: 41 minutes 28.78 seconds (2488.78 seconds total)