Starting phenix.real_space_refine on Tue Feb 13 14:58:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v87_31792/02_2024/7v87_31792.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v87_31792/02_2024/7v87_31792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v87_31792/02_2024/7v87_31792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v87_31792/02_2024/7v87_31792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v87_31792/02_2024/7v87_31792.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v87_31792/02_2024/7v87_31792.pdb" } resolution = 3.3 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= 0.032 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 37 5.16 5 C 4222 2.51 5 N 1085 2.21 5 O 1273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "F PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6617 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1593 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.30, per 1000 atoms: 0.65 Number of scatterers: 6617 At special positions: 0 Unit cell: (77, 100.1, 126.5, 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 37 16.00 O 1273 8.00 N 1085 7.00 C 4222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG B 1 " - " ASN A 343 " " NAG C 1 " - " ASN F 90 " " NAG D 1 " - " ASN F 546 " " NAG F2001 " - " ASN F 53 " " NAG F2002 " - " ASN F 103 " " NAG F2003 " - " ASN F 322 " " NAG F2004 " - " ASN F 432 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.5 seconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 52.2% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.513A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.820A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.604A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.740A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 80 removed outlier: 3.644A pdb=" N VAL F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER F 70 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 101 removed outlier: 3.811A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'F' and resid 157 through 171 Processing helix chain 'F' and resid 175 through 194 removed outlier: 4.409A pdb=" N LEU F 179 " --> pdb=" O GLN F 175 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.635A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 231 removed outlier: 3.701A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 251 Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.687A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.878A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.673A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 412 removed outlier: 3.563A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.750A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 473 through 485 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 532 removed outlier: 3.502A pdb=" N THR F 517 " --> pdb=" O ILE F 513 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.680A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.598A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.885A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.024A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'F' and resid 347 through 350 281 hydrogen bonds defined for protein. 786 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: 2.04 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2104 1.35 - 1.47: 1807 1.47 - 1.59: 2830 1.59 - 1.72: 0 1.72 - 1.84: 58 Bond restraints: 6799 Sorted by residual: bond pdb=" C1 NAG F2004 " pdb=" O5 NAG F2004 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.97e+00 bond pdb=" C1 NAG F2002 " pdb=" O5 NAG F2002 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 ... (remaining 6794 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.45: 210 106.45 - 113.33: 3590 113.33 - 120.21: 2482 120.21 - 127.09: 2860 127.09 - 133.97: 97 Bond angle restraints: 9239 Sorted by residual: angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 125.97 -11.57 2.30e+00 1.89e-01 2.53e+01 angle pdb=" N GLU F 479 " pdb=" CA GLU F 479 " pdb=" CB GLU F 479 " ideal model delta sigma weight residual 110.28 116.35 -6.07 1.55e+00 4.16e-01 1.54e+01 angle pdb=" C TRP F 478 " pdb=" N GLU F 479 " pdb=" CA GLU F 479 " ideal model delta sigma weight residual 120.31 114.58 5.73 1.52e+00 4.33e-01 1.42e+01 angle pdb=" N ASN F 90 " pdb=" CA ASN F 90 " pdb=" CB ASN F 90 " ideal model delta sigma weight residual 114.17 110.09 4.08 1.14e+00 7.69e-01 1.28e+01 angle pdb=" C THR F 334 " pdb=" N ASP F 335 " pdb=" CA ASP F 335 " ideal model delta sigma weight residual 121.80 129.82 -8.02 2.44e+00 1.68e-01 1.08e+01 ... (remaining 9234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 3812 21.79 - 43.59: 288 43.59 - 65.38: 44 65.38 - 87.17: 18 87.17 - 108.97: 10 Dihedral angle restraints: 4172 sinusoidal: 1834 harmonic: 2338 Sorted by residual: dihedral pdb=" CA PRO F 146 " pdb=" C PRO F 146 " pdb=" N GLY F 147 " pdb=" CA GLY F 147 " ideal model delta harmonic sigma weight residual -180.00 -154.74 -25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA CYS A 379 " pdb=" C CYS A 379 " pdb=" N TYR A 380 " pdb=" CA TYR A 380 " ideal model delta harmonic sigma weight residual 180.00 -156.24 -23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA PHE A 377 " pdb=" C PHE A 377 " pdb=" N LYS A 378 " pdb=" CA LYS A 378 " ideal model delta harmonic sigma weight residual 180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 4169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 813 0.055 - 0.109: 166 0.109 - 0.164: 15 0.164 - 0.218: 4 0.218 - 0.273: 4 Chirality restraints: 1002 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C1 NAG F2002 " pdb=" ND2 ASN F 103 " pdb=" C2 NAG F2002 " pdb=" O5 NAG F2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 999 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A 521 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 582 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO F 583 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO F 583 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 583 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 89 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C GLN F 89 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN F 89 " 0.008 2.00e-02 2.50e+03 pdb=" N ASN F 90 " 0.008 2.00e-02 2.50e+03 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 196 2.71 - 3.26: 6592 3.26 - 3.81: 10294 3.81 - 4.35: 12193 4.35 - 4.90: 21047 Nonbonded interactions: 50322 Sorted by model distance: nonbonded pdb=" O LEU F 156 " pdb=" OH TYR F 252 " model vdw 2.167 2.440 nonbonded pdb=" NH1 ARG F 161 " pdb=" O HIS F 265 " model vdw 2.244 2.520 nonbonded pdb=" O SER F 77 " pdb=" NE2 GLN F 81 " model vdw 2.283 2.520 nonbonded pdb=" OG SER F 170 " pdb=" OE1 GLU F 171 " model vdw 2.302 2.440 nonbonded pdb=" NZ LYS A 529 " pdb=" O SER A 530 " model vdw 2.304 2.520 ... (remaining 50317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } 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: 12.040 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: 13.420 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.430 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 0.036 6799 Z= 0.214 Angle : 0.646 11.570 9239 Z= 0.342 Chirality : 0.046 0.273 1002 Planarity : 0.004 0.036 1181 Dihedral : 16.491 108.968 2651 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.30), residues: 793 helix: 1.12 (0.28), residues: 375 sheet: 0.05 (0.79), residues: 42 loop : -1.51 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 477 HIS 0.005 0.001 HIS F 374 PHE 0.013 0.001 PHE A 347 TYR 0.015 0.001 TYR A 380 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: F 249 MET cc_start: 0.7919 (tpt) cc_final: 0.7684 (mmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2121 time to fit residues: 16.2699 Evaluate side-chains 43 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 58 ASN F 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 6799 Z= 0.450 Angle : 0.691 8.291 9239 Z= 0.359 Chirality : 0.048 0.309 1002 Planarity : 0.004 0.044 1181 Dihedral : 10.318 65.329 1114 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.14 % Allowed : 8.57 % Favored : 90.29 % 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: -0.39 (0.30), residues: 793 helix: 0.91 (0.27), residues: 389 sheet: 0.02 (0.78), residues: 39 loop : -1.63 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 477 HIS 0.005 0.001 HIS F 378 PHE 0.017 0.002 PHE A 347 TYR 0.019 0.002 TYR F 50 ARG 0.003 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: 0.7694 (ttm) cc_final: 0.7347 (tpp) REVERT: F 479 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8283 (pm20) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.1868 time to fit residues: 12.2824 Evaluate side-chains 47 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 479 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 0.0030 chunk 71 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6799 Z= 0.156 Angle : 0.554 10.893 9239 Z= 0.281 Chirality : 0.042 0.250 1002 Planarity : 0.004 0.041 1181 Dihedral : 8.008 57.363 1114 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.00 % Allowed : 10.43 % Favored : 87.57 % 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: -0.12 (0.30), residues: 793 helix: 1.10 (0.28), residues: 382 sheet: 0.30 (0.80), residues: 39 loop : -1.42 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 PHE 0.012 0.001 PHE F 72 TYR 0.015 0.001 TYR F 50 ARG 0.001 0.000 ARG F 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7310 (tpp) outliers start: 14 outliers final: 8 residues processed: 51 average time/residue: 0.1796 time to fit residues: 13.2786 Evaluate side-chains 52 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 471 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 76 optimal weight: 0.0970 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 0.0170 chunk 43 optimal weight: 0.0970 chunk 1 optimal weight: 0.7980 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6799 Z= 0.127 Angle : 0.507 8.901 9239 Z= 0.260 Chirality : 0.041 0.262 1002 Planarity : 0.003 0.039 1181 Dihedral : 6.519 54.326 1114 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.00 % Allowed : 13.14 % Favored : 84.86 % 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: -0.04 (0.30), residues: 793 helix: 1.18 (0.28), residues: 383 sheet: 0.11 (0.79), residues: 42 loop : -1.37 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 PHE 0.013 0.001 PHE F 72 TYR 0.012 0.001 TYR F 50 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: F 323 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7119 (tpp) outliers start: 14 outliers final: 6 residues processed: 57 average time/residue: 0.1888 time to fit residues: 14.9753 Evaluate side-chains 50 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 468 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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: 0.8424 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6799 Z= 0.304 Angle : 0.594 8.565 9239 Z= 0.306 Chirality : 0.044 0.276 1002 Planarity : 0.004 0.046 1181 Dihedral : 6.594 57.638 1114 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.29 % Allowed : 14.57 % Favored : 83.14 % 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: -0.09 (0.30), residues: 793 helix: 1.19 (0.28), residues: 381 sheet: 0.46 (0.80), residues: 39 loop : -1.50 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 165 HIS 0.004 0.001 HIS F 493 PHE 0.011 0.001 PHE F 369 TYR 0.012 0.001 TYR A 453 ARG 0.003 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: F 323 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7448 (tpp) outliers start: 16 outliers final: 11 residues processed: 50 average time/residue: 0.1810 time to fit residues: 12.9731 Evaluate side-chains 53 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 73 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.8388 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6799 Z= 0.192 Angle : 0.535 8.241 9239 Z= 0.276 Chirality : 0.042 0.260 1002 Planarity : 0.004 0.043 1181 Dihedral : 6.365 56.451 1114 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.71 % Allowed : 15.43 % Favored : 81.86 % 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: -0.00 (0.30), residues: 793 helix: 1.25 (0.28), residues: 382 sheet: 0.63 (0.81), residues: 39 loop : -1.46 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 PHE 0.012 0.001 PHE F 72 TYR 0.011 0.001 TYR F 50 ARG 0.001 0.000 ARG F 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 42 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: F 323 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7409 (tpp) REVERT: F 455 MET cc_start: 0.8210 (tmm) cc_final: 0.8005 (tmm) outliers start: 19 outliers final: 11 residues processed: 56 average time/residue: 0.1696 time to fit residues: 14.0109 Evaluate side-chains 52 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 479 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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: 0.8361 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6799 Z= 0.152 Angle : 0.516 7.899 9239 Z= 0.264 Chirality : 0.041 0.260 1002 Planarity : 0.003 0.041 1181 Dihedral : 6.053 55.208 1114 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.00 % Allowed : 15.43 % Favored : 81.57 % 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: 0.15 (0.30), residues: 793 helix: 1.36 (0.28), residues: 381 sheet: 0.83 (0.82), residues: 39 loop : -1.36 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 168 HIS 0.004 0.001 HIS F 493 PHE 0.013 0.001 PHE F 72 TYR 0.011 0.001 TYR F 50 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 43 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7330 (tpp) outliers start: 21 outliers final: 17 residues processed: 58 average time/residue: 0.1557 time to fit residues: 13.0313 Evaluate side-chains 59 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 41 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 432 ASN Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 0.0770 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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: 0.8360 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6799 Z= 0.156 Angle : 0.521 7.844 9239 Z= 0.264 Chirality : 0.041 0.264 1002 Planarity : 0.003 0.039 1181 Dihedral : 5.937 55.305 1114 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.86 % Allowed : 16.29 % Favored : 80.86 % 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: 0.18 (0.30), residues: 793 helix: 1.38 (0.28), residues: 380 sheet: 0.93 (0.82), residues: 39 loop : -1.36 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 477 HIS 0.004 0.001 HIS F 493 PHE 0.012 0.001 PHE F 72 TYR 0.010 0.001 TYR F 50 ARG 0.001 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 42 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7295 (tpp) outliers start: 20 outliers final: 15 residues processed: 55 average time/residue: 0.1629 time to fit residues: 13.0210 Evaluate side-chains 57 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 41 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 432 ASN Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 67 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8364 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6799 Z= 0.166 Angle : 0.528 7.774 9239 Z= 0.268 Chirality : 0.042 0.265 1002 Planarity : 0.003 0.040 1181 Dihedral : 5.889 55.557 1114 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.14 % Allowed : 16.14 % Favored : 80.71 % 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: 0.21 (0.30), residues: 793 helix: 1.41 (0.28), residues: 380 sheet: 1.02 (0.82), residues: 39 loop : -1.36 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 477 HIS 0.003 0.001 HIS F 493 PHE 0.012 0.001 PHE F 72 TYR 0.011 0.001 TYR F 50 ARG 0.001 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 41 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7290 (tpp) outliers start: 22 outliers final: 17 residues processed: 55 average time/residue: 0.1592 time to fit residues: 12.8134 Evaluate side-chains 59 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 41 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 432 ASN Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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: 0.8395 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6799 Z= 0.213 Angle : 0.554 8.068 9239 Z= 0.282 Chirality : 0.043 0.267 1002 Planarity : 0.003 0.040 1181 Dihedral : 5.988 56.643 1114 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.71 % Allowed : 16.57 % Favored : 80.71 % 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: 0.20 (0.30), residues: 793 helix: 1.43 (0.28), residues: 380 sheet: 1.05 (0.82), residues: 39 loop : -1.40 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 477 HIS 0.004 0.001 HIS F 374 PHE 0.011 0.001 PHE F 72 TYR 0.011 0.001 TYR F 50 ARG 0.002 0.000 ARG A 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 43 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7373 (tpp) outliers start: 19 outliers final: 18 residues processed: 56 average time/residue: 0.1660 time to fit residues: 13.5963 Evaluate side-chains 61 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 42 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 432 ASN Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 479 GLU Chi-restraints excluded: chain F residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.063136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053767 restraints weight = 24027.609| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.40 r_work: 0.2902 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6799 Z= 0.170 Angle : 0.546 8.816 9239 Z= 0.275 Chirality : 0.042 0.262 1002 Planarity : 0.003 0.039 1181 Dihedral : 5.902 55.792 1114 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.57 % Allowed : 17.14 % Favored : 80.29 % 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: 0.21 (0.30), residues: 793 helix: 1.42 (0.28), residues: 381 sheet: 1.16 (0.83), residues: 39 loop : -1.39 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 477 HIS 0.003 0.001 HIS F 374 PHE 0.012 0.001 PHE F 72 TYR 0.010 0.001 TYR F 50 ARG 0.001 0.000 ARG F 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1644.58 seconds wall clock time: 30 minutes 59.89 seconds (1859.89 seconds total)