Starting phenix.real_space_refine on Fri Apr 5 13:34:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/04_2024/8thr_41269_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/04_2024/8thr_41269.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/04_2024/8thr_41269_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/04_2024/8thr_41269_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/04_2024/8thr_41269_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/04_2024/8thr_41269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/04_2024/8thr_41269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/04_2024/8thr_41269_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thr_41269/04_2024/8thr_41269_updated.pdb" } resolution = 3.12 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= 0.001 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 1954 2.51 5 N 454 2.21 5 O 501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2937 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2914 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'EBZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.07, per 1000 atoms: 0.70 Number of scatterers: 2937 At special positions: 0 Unit cell: (56.936, 71.817, 75.699, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 501 8.00 N 454 7.00 C 1954 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: 1.14 Conformation dependent library (CDL) restraints added in 553.8 milliseconds 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 702 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 0 sheets defined 81.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 18 through 39 removed outlier: 4.139A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 123 through 156 removed outlier: 3.856A pdb=" N ASN A 128 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 129 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER A 137 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 138 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 142 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 144 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 4.187A pdb=" N LEU A 151 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 153 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 156 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.811A pdb=" N MET A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 210 removed outlier: 3.585A pdb=" N ALA A 202 " --> pdb=" O CYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 245 removed outlier: 3.750A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 250 through 269 removed outlier: 3.812A pdb=" N LEU A 255 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 292 through 314 removed outlier: 4.020A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 332 through 355 Proline residue: A 336 - end of helix removed outlier: 3.751A pdb=" N SER A 340 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR A 341 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 346 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 347 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE A 348 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 349 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU A 351 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ALA A 352 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS A 353 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET A 355 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 377 removed outlier: 3.708A pdb=" N LEU A 362 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU A 363 " --> pdb=" O CYS A 360 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A 365 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE A 367 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Proline residue: A 376 - end of helix Processing helix chain 'A' and resid 381 through 413 removed outlier: 4.365A pdb=" N ALA A 386 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Proline residue: A 387 - end of helix removed outlier: 3.641A pdb=" N GLY A 390 " --> pdb=" O PRO A 387 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 392 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 393 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 395 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP A 399 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER A 400 " --> pdb=" O MET A 397 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N MET A 403 " --> pdb=" O SER A 400 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 3.546A pdb=" N LEU A 409 " --> pdb=" O MET A 406 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG A 413 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 4.293A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.703A pdb=" N LYS A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 446' Processing helix chain 'A' and resid 449 through 461 removed outlier: 3.503A pdb=" N ASP A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.642A pdb=" N CYS A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 174 hydrogen bonds defined for protein. 357 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: 0.80 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 498 1.32 - 1.45: 745 1.45 - 1.57: 1716 1.57 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 3007 Sorted by residual: bond pdb=" C05 EBZ A 601 " pdb=" C06 EBZ A 601 " ideal model delta sigma weight residual 1.622 1.497 0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" CA VAL A 220 " pdb=" CB VAL A 220 " ideal model delta sigma weight residual 1.539 1.491 0.049 1.20e-02 6.94e+03 1.65e+01 bond pdb=" C15 EBZ A 601 " pdb=" O01 EBZ A 601 " ideal model delta sigma weight residual 1.437 1.370 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" N PRO A 437 " pdb=" CD PRO A 437 " ideal model delta sigma weight residual 1.473 1.427 0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" N PRO A 313 " pdb=" CD PRO A 313 " ideal model delta sigma weight residual 1.473 1.428 0.045 1.40e-02 5.10e+03 1.02e+01 ... (remaining 3002 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.52: 104 105.52 - 112.98: 1403 112.98 - 120.44: 1563 120.44 - 127.90: 996 127.90 - 135.36: 24 Bond angle restraints: 4090 Sorted by residual: angle pdb=" N MET A 319 " pdb=" CA MET A 319 " pdb=" C MET A 319 " ideal model delta sigma weight residual 111.40 118.41 -7.01 1.22e+00 6.72e-01 3.30e+01 angle pdb=" N VAL A 427 " pdb=" CA VAL A 427 " pdb=" CB VAL A 427 " ideal model delta sigma weight residual 110.54 118.23 -7.69 1.36e+00 5.41e-01 3.20e+01 angle pdb=" N SER A 420 " pdb=" CA SER A 420 " pdb=" C SER A 420 " ideal model delta sigma weight residual 112.04 120.07 -8.03 1.44e+00 4.82e-01 3.11e+01 angle pdb=" CA ILE A 455 " pdb=" C ILE A 455 " pdb=" N ILE A 456 " ideal model delta sigma weight residual 117.28 123.73 -6.45 1.16e+00 7.43e-01 3.09e+01 angle pdb=" CA ASN A 154 " pdb=" CB ASN A 154 " pdb=" CG ASN A 154 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 4085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.92: 1660 20.92 - 41.83: 86 41.83 - 62.74: 16 62.74 - 83.66: 2 83.66 - 104.57: 3 Dihedral angle restraints: 1767 sinusoidal: 666 harmonic: 1101 Sorted by residual: dihedral pdb=" CA CYS A 360 " pdb=" C CYS A 360 " pdb=" N ALA A 361 " pdb=" CA ALA A 361 " ideal model delta harmonic sigma weight residual 180.00 153.16 26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ILE A 156 " pdb=" C ILE A 156 " pdb=" N GLY A 157 " pdb=" CA GLY A 157 " ideal model delta harmonic sigma weight residual 180.00 -155.51 -24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASN A 128 " pdb=" C ASN A 128 " pdb=" N VAL A 129 " pdb=" CA VAL A 129 " ideal model delta harmonic sigma weight residual -180.00 -156.54 -23.46 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 1764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 288 0.089 - 0.179: 154 0.179 - 0.268: 33 0.268 - 0.358: 9 0.358 - 0.447: 3 Chirality restraints: 487 Sorted by residual: chirality pdb=" CA SER A 420 " pdb=" N SER A 420 " pdb=" C SER A 420 " pdb=" CB SER A 420 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" C13 EBZ A 601 " pdb=" C10 EBZ A 601 " pdb=" C11 EBZ A 601 " pdb=" C18 EBZ A 601 " both_signs ideal model delta sigma weight residual False 2.85 2.47 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA LEU A 152 " pdb=" N LEU A 152 " pdb=" C LEU A 152 " pdb=" CB LEU A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 484 not shown) Planarity restraints: 501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 176 " 0.112 2.00e-02 2.50e+03 7.03e-02 8.64e+01 pdb=" CG PHE A 176 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A 176 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 PHE A 176 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 PHE A 176 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 176 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 176 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 EBZ A 601 " -0.062 2.00e-02 2.50e+03 5.00e-02 6.24e+01 pdb=" C06 EBZ A 601 " -0.039 2.00e-02 2.50e+03 pdb=" C07 EBZ A 601 " -0.019 2.00e-02 2.50e+03 pdb=" C09 EBZ A 601 " 0.017 2.00e-02 2.50e+03 pdb=" C14 EBZ A 601 " 0.098 2.00e-02 2.50e+03 pdb=" C15 EBZ A 601 " 0.028 2.00e-02 2.50e+03 pdb=" C16 EBZ A 601 " -0.010 2.00e-02 2.50e+03 pdb=" C17 EBZ A 601 " -0.015 2.00e-02 2.50e+03 pdb=" O01 EBZ A 601 " 0.065 2.00e-02 2.50e+03 pdb=" O02 EBZ A 601 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 422 " 0.091 2.00e-02 2.50e+03 4.75e-02 4.51e+01 pdb=" CG TYR A 422 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 422 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A 422 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR A 422 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 422 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 422 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 422 " 0.064 2.00e-02 2.50e+03 ... (remaining 498 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1560 3.01 - 3.48: 3450 3.48 - 3.95: 4910 3.95 - 4.43: 5609 4.43 - 4.90: 9120 Nonbonded interactions: 24649 Sorted by model distance: nonbonded pdb=" OD1 ASP A 411 " pdb=" OH TYR A 418 " model vdw 2.537 2.440 nonbonded pdb=" O SER A 420 " pdb=" N ALA A 423 " model vdw 2.561 2.520 nonbonded pdb=" N THR A 249 " pdb=" N ALA A 250 " model vdw 2.562 2.560 nonbonded pdb=" O ILE A 455 " pdb=" CA ILE A 456 " model vdw 2.574 2.776 nonbonded pdb=" OD1 ASP A 411 " pdb=" OG SER A 416 " model vdw 2.601 2.440 ... (remaining 24644 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 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: 0.000 Extract box with map and model: 11.020 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.560 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 : 0.013 0.125 3007 Z= 0.828 Angle : 1.924 12.369 4090 Z= 1.264 Chirality : 0.110 0.447 487 Planarity : 0.014 0.070 501 Dihedral : 14.131 104.570 1065 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.96 % Allowed : 7.03 % Favored : 92.01 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.37), residues: 385 helix: -1.94 (0.25), residues: 275 sheet: None (None), residues: 0 loop : -1.95 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.016 TRP A 451 HIS 0.003 0.002 HIS A 353 PHE 0.112 0.016 PHE A 176 TYR 0.091 0.015 TYR A 422 ARG 0.004 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 443 ILE cc_start: 0.7773 (mt) cc_final: 0.7455 (mt) outliers start: 3 outliers final: 0 residues processed: 83 average time/residue: 0.1038 time to fit residues: 11.2799 Evaluate side-chains 67 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.2980 chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN A 154 ASN A 192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3007 Z= 0.241 Angle : 0.785 7.297 4090 Z= 0.383 Chirality : 0.046 0.169 487 Planarity : 0.006 0.057 501 Dihedral : 10.570 88.587 418 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.19 % Allowed : 13.10 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.42), residues: 385 helix: -0.83 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -1.70 (0.66), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 451 HIS 0.001 0.000 HIS A 353 PHE 0.020 0.002 PHE A 238 TYR 0.012 0.002 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7259 (mtm) REVERT: A 443 ILE cc_start: 0.7781 (mt) cc_final: 0.7455 (mt) outliers start: 10 outliers final: 3 residues processed: 78 average time/residue: 0.1004 time to fit residues: 10.3154 Evaluate side-chains 71 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 339 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3007 Z= 0.303 Angle : 0.781 6.759 4090 Z= 0.377 Chirality : 0.047 0.165 487 Planarity : 0.006 0.065 501 Dihedral : 9.655 88.351 418 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.28 % Allowed : 18.21 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.43), residues: 385 helix: -0.73 (0.30), residues: 290 sheet: None (None), residues: 0 loop : -1.96 (0.68), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.014 0.002 PHE A 238 TYR 0.018 0.002 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7767 (mtm) REVERT: A 288 LEU cc_start: 0.8181 (mt) cc_final: 0.7978 (mp) REVERT: A 323 MET cc_start: 0.6251 (ppp) cc_final: 0.5806 (ppp) REVERT: A 324 CYS cc_start: 0.3247 (p) cc_final: 0.2996 (m) REVERT: A 443 ILE cc_start: 0.7854 (mt) cc_final: 0.7519 (mt) outliers start: 4 outliers final: 2 residues processed: 71 average time/residue: 0.1029 time to fit residues: 9.5903 Evaluate side-chains 67 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 283 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.4980 chunk 23 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 0.0010 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 0 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3007 Z= 0.224 Angle : 0.734 7.105 4090 Z= 0.348 Chirality : 0.044 0.157 487 Planarity : 0.006 0.066 501 Dihedral : 9.066 87.917 418 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.51 % Allowed : 18.53 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.43), residues: 385 helix: -0.66 (0.31), residues: 272 sheet: None (None), residues: 0 loop : -1.71 (0.63), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.014 0.002 PHE A 238 TYR 0.015 0.002 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7466 (mtt) REVERT: A 288 LEU cc_start: 0.8175 (mt) cc_final: 0.7960 (mp) REVERT: A 323 MET cc_start: 0.6219 (ppp) cc_final: 0.5900 (ppp) REVERT: A 443 ILE cc_start: 0.7870 (mt) cc_final: 0.7540 (mt) outliers start: 11 outliers final: 6 residues processed: 70 average time/residue: 0.1027 time to fit residues: 9.4150 Evaluate side-chains 71 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 339 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 overall best weight: 0.2238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3007 Z= 0.201 Angle : 0.734 8.306 4090 Z= 0.341 Chirality : 0.043 0.154 487 Planarity : 0.006 0.066 501 Dihedral : 8.521 84.996 418 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.24 % Allowed : 20.13 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.43), residues: 385 helix: -0.48 (0.31), residues: 271 sheet: None (None), residues: 0 loop : -1.74 (0.61), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 328 HIS 0.001 0.000 HIS A 414 PHE 0.010 0.001 PHE A 238 TYR 0.015 0.002 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 44 ILE cc_start: 0.7766 (mm) cc_final: 0.6843 (mt) REVERT: A 323 MET cc_start: 0.6058 (ppp) cc_final: 0.5842 (ppp) REVERT: A 388 ASN cc_start: 0.7848 (t0) cc_final: 0.7641 (t0) REVERT: A 403 MET cc_start: 0.8387 (mmt) cc_final: 0.8178 (mmt) REVERT: A 443 ILE cc_start: 0.7854 (mt) cc_final: 0.7519 (mt) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 0.1038 time to fit residues: 9.4493 Evaluate side-chains 67 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 339 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 26 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3007 Z= 0.266 Angle : 0.771 11.782 4090 Z= 0.358 Chirality : 0.046 0.165 487 Planarity : 0.006 0.067 501 Dihedral : 8.256 84.800 418 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.56 % Allowed : 21.73 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.43), residues: 385 helix: -0.50 (0.31), residues: 272 sheet: None (None), residues: 0 loop : -1.73 (0.63), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 328 HIS 0.003 0.001 HIS A 414 PHE 0.010 0.002 PHE A 178 TYR 0.020 0.002 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.290 Fit side-chains REVERT: A 44 ILE cc_start: 0.7830 (mm) cc_final: 0.6925 (mt) REVERT: A 320 MET cc_start: 0.4906 (ppp) cc_final: 0.4629 (ttm) REVERT: A 323 MET cc_start: 0.6085 (ppp) cc_final: 0.5847 (ppp) REVERT: A 388 ASN cc_start: 0.7897 (t0) cc_final: 0.7661 (t0) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.1018 time to fit residues: 9.3202 Evaluate side-chains 71 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 339 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.0570 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 16 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3007 Z= 0.245 Angle : 0.748 10.565 4090 Z= 0.348 Chirality : 0.045 0.161 487 Planarity : 0.006 0.067 501 Dihedral : 7.889 83.965 418 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.19 % Allowed : 23.00 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.43), residues: 385 helix: -0.43 (0.32), residues: 268 sheet: None (None), residues: 0 loop : -1.81 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.009 0.001 PHE A 238 TYR 0.018 0.002 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.334 Fit side-chains REVERT: A 44 ILE cc_start: 0.7822 (mm) cc_final: 0.6910 (mt) REVERT: A 244 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6273 (tp30) REVERT: A 320 MET cc_start: 0.5021 (ppp) cc_final: 0.4724 (ttm) REVERT: A 323 MET cc_start: 0.6022 (ppp) cc_final: 0.5767 (ppp) REVERT: A 388 ASN cc_start: 0.7921 (t0) cc_final: 0.7686 (t0) outliers start: 10 outliers final: 6 residues processed: 67 average time/residue: 0.1025 time to fit residues: 9.0898 Evaluate side-chains 69 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 339 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0770 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.0970 chunk 33 optimal weight: 0.4980 chunk 35 optimal weight: 0.0000 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.0050 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.1354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3007 Z= 0.181 Angle : 0.705 9.807 4090 Z= 0.329 Chirality : 0.043 0.157 487 Planarity : 0.006 0.065 501 Dihedral : 7.024 81.547 418 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.56 % Allowed : 23.96 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.43), residues: 385 helix: -0.27 (0.32), residues: 268 sheet: None (None), residues: 0 loop : -1.89 (0.58), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 358 HIS 0.001 0.000 HIS A 414 PHE 0.010 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.003 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.309 Fit side-chains REVERT: A 44 ILE cc_start: 0.7721 (mm) cc_final: 0.6759 (mt) REVERT: A 319 MET cc_start: 0.3860 (mmm) cc_final: 0.3584 (mmp) outliers start: 8 outliers final: 5 residues processed: 76 average time/residue: 0.1199 time to fit residues: 11.6230 Evaluate side-chains 71 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 339 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3007 Z= 0.308 Angle : 0.804 11.911 4090 Z= 0.370 Chirality : 0.047 0.177 487 Planarity : 0.006 0.067 501 Dihedral : 7.033 77.641 418 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.24 % Allowed : 24.28 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.43), residues: 385 helix: -0.52 (0.31), residues: 277 sheet: None (None), residues: 0 loop : -2.00 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 PHE 0.011 0.002 PHE A 334 TYR 0.021 0.002 TYR A 422 ARG 0.004 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.332 Fit side-chains REVERT: A 44 ILE cc_start: 0.7860 (mm) cc_final: 0.6951 (mt) REVERT: A 319 MET cc_start: 0.4280 (mmm) cc_final: 0.3996 (mmp) outliers start: 7 outliers final: 6 residues processed: 70 average time/residue: 0.0984 time to fit residues: 9.0847 Evaluate side-chains 73 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 339 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.0170 chunk 32 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 12 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.0010 chunk 5 optimal weight: 0.9990 overall best weight: 0.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3007 Z= 0.170 Angle : 0.693 9.948 4090 Z= 0.324 Chirality : 0.042 0.162 487 Planarity : 0.006 0.064 501 Dihedral : 6.409 68.533 418 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.60 % Allowed : 24.60 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.43), residues: 385 helix: -0.25 (0.33), residues: 269 sheet: None (None), residues: 0 loop : -1.99 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 358 HIS 0.000 0.000 HIS A 414 PHE 0.011 0.001 PHE A 238 TYR 0.013 0.001 TYR A 422 ARG 0.002 0.000 ARG A 189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.298 Fit side-chains REVERT: A 44 ILE cc_start: 0.7711 (mm) cc_final: 0.6726 (mt) REVERT: A 234 VAL cc_start: 0.8509 (m) cc_final: 0.8223 (m) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.1135 time to fit residues: 10.0374 Evaluate side-chains 70 residues out of total 314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 339 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 21 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.144825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.134307 restraints weight = 4877.390| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.19 r_work: 0.3865 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3007 Z= 0.253 Angle : 0.734 10.341 4090 Z= 0.342 Chirality : 0.044 0.169 487 Planarity : 0.006 0.065 501 Dihedral : 6.472 70.122 418 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.24 % Allowed : 23.64 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.44), residues: 385 helix: -0.36 (0.32), residues: 275 sheet: None (None), residues: 0 loop : -2.04 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.031 0.002 PHE A 468 TYR 0.019 0.002 TYR A 422 ARG 0.002 0.000 ARG A 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1296.00 seconds wall clock time: 23 minutes 38.75 seconds (1418.75 seconds total)