Starting phenix.real_space_refine on Tue Feb 13 14:50:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v80_31785/02_2024/7v80_31785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v80_31785/02_2024/7v80_31785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v80_31785/02_2024/7v80_31785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v80_31785/02_2024/7v80_31785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v80_31785/02_2024/7v80_31785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v80_31785/02_2024/7v80_31785.pdb" } resolution = 3.9 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= 0.037 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 1082 2.21 5 O 1268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "F TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 206": "OD1" <-> "OD2" Residue "F TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 483": "OE1" <-> "OE2" Residue "F ASP 597": "OD1" <-> "OD2" 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: 6609 Number of models: 1 Model: "" Number of chains: 7 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: 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: "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: 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: "A" 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: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 4.18, per 1000 atoms: 0.63 Number of scatterers: 6609 At special positions: 0 Unit cell: (74.8, 99, 125.4, 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 1268 8.00 N 1082 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=2.03 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG B 1 " - " ASN F 90 " " NAG C 1 " - " ASN F 103 " " NAG D 1 " - " ASN F 546 " " NAG F2001 " - " ASN F 53 " " NAG F2002 " - " ASN F 322 " " NAG F2003 " - " ASN F 432 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.3 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 5 sheets defined 49.2% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.760A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.651A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.662A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.720A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 53 removed outlier: 3.714A pdb=" N ALA F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 73 removed outlier: 3.598A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.583A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.764A 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 152 removed outlier: 3.802A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 172 Processing helix chain 'F' and resid 176 through 193 removed outlier: 3.636A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 205 removed outlier: 3.528A pdb=" N TRP F 203 " --> pdb=" O TYR F 199 " (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 218 through 229 removed outlier: 3.848A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 252 removed outlier: 3.734A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.927A pdb=" N TYR F 279 " --> pdb=" O THR F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 300 removed outlier: 3.990A pdb=" N GLN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.556A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS F 313 " --> pdb=" O LYS F 309 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.730A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.920A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.715A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA F 413 " --> pdb=" O SER F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.519A pdb=" N GLN F 442 " --> pdb=" O PHE F 438 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 476 through 485 removed outlier: 4.969A pdb=" N GLU F 483 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 removed outlier: 4.117A pdb=" N SER F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 508' Processing helix chain 'F' and resid 513 through 532 removed outlier: 3.836A pdb=" N ARG F 518 " --> pdb=" O ARG F 514 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.883A pdb=" N GLN F 552 " --> pdb=" O THR F 548 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 4.184A 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 583 through 588 removed outlier: 3.990A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 596 removed outlier: 3.703A pdb=" N PHE F 592 " --> pdb=" O PHE F 588 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.712A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'F' and resid 132 through 133 removed outlier: 3.697A pdb=" N VAL F 132 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 262 through 263 removed outlier: 7.017A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 347 through 352 removed outlier: 5.967A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 687 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: 1.73 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2100 1.34 - 1.46: 1745 1.46 - 1.58: 2888 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 6792 Sorted by residual: bond pdb=" CA ASP F 350 " pdb=" CB ASP F 350 " ideal model delta sigma weight residual 1.531 1.666 -0.135 3.28e-02 9.30e+02 1.69e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.04e+00 bond pdb=" C1 NAG F2003 " pdb=" O5 NAG F2003 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.86e+00 bond pdb=" CB PRO F 284 " pdb=" CG PRO F 284 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.44e+00 ... (remaining 6787 not shown) Histogram of bond angle deviations from ideal: 99.85 - 106.69: 210 106.69 - 113.53: 3601 113.53 - 120.38: 2622 120.38 - 127.22: 2702 127.22 - 134.07: 96 Bond angle restraints: 9231 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 125.35 -10.95 2.30e+00 1.89e-01 2.27e+01 angle pdb=" N CYS A 432 " pdb=" CA CYS A 432 " pdb=" C CYS A 432 " ideal model delta sigma weight residual 107.88 113.57 -5.69 1.41e+00 5.03e-01 1.63e+01 angle pdb=" N GLU F 406 " pdb=" CA GLU F 406 " pdb=" CB GLU F 406 " ideal model delta sigma weight residual 110.41 116.02 -5.61 1.68e+00 3.54e-01 1.11e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 121.52 -7.12 2.30e+00 1.89e-01 9.58e+00 angle pdb=" C ASP F 431 " pdb=" N ASN F 432 " pdb=" CA ASN F 432 " ideal model delta sigma weight residual 121.19 125.95 -4.76 1.59e+00 3.96e-01 8.95e+00 ... (remaining 9226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3685 18.00 - 36.00: 378 36.00 - 53.99: 71 53.99 - 71.99: 8 71.99 - 89.99: 10 Dihedral angle restraints: 4152 sinusoidal: 1813 harmonic: 2339 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -3.11 -82.89 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -9.77 -76.23 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" CA CYS A 432 " pdb=" C CYS A 432 " pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 4149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 952 0.096 - 0.191: 44 0.191 - 0.287: 1 0.287 - 0.382: 0 0.382 - 0.478: 1 Chirality restraints: 998 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN F 546 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 995 not shown) Planarity restraints: 1189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 283 " -0.039 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO F 284 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO F 284 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 284 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 262 " 0.032 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO F 263 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO F 263 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 263 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 524 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C GLN F 524 " 0.031 2.00e-02 2.50e+03 pdb=" O GLN F 524 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE F 525 " -0.010 2.00e-02 2.50e+03 ... (remaining 1186 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 114 2.68 - 3.23: 6334 3.23 - 3.79: 9855 3.79 - 4.34: 12459 4.34 - 4.90: 20618 Nonbonded interactions: 49380 Sorted by model distance: nonbonded pdb=" OG SER F 109 " pdb=" OD1 ASP F 111 " model vdw 2.120 2.440 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.168 2.440 nonbonded pdb=" O ILE F 151 " pdb=" OG SER F 155 " model vdw 2.188 2.440 nonbonded pdb=" OD1 ASN A 487 " pdb=" OH TYR F 83 " model vdw 2.239 2.440 nonbonded pdb=" O SER A 530 " pdb=" OG SER A 530 " model vdw 2.241 2.440 ... (remaining 49375 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 'C' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.710 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.970 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 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 : 0.004 0.135 6792 Z= 0.264 Angle : 0.646 10.952 9231 Z= 0.334 Chirality : 0.046 0.478 998 Planarity : 0.005 0.058 1181 Dihedral : 14.721 89.988 2631 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -0.76 (0.31), residues: 793 helix: 0.30 (0.30), residues: 344 sheet: -0.70 (0.66), residues: 59 loop : -1.18 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 478 HIS 0.004 0.001 HIS F 34 PHE 0.009 0.001 PHE F 369 TYR 0.010 0.001 TYR A 453 ARG 0.005 0.001 ARG A 357 *********************** 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 96 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.672 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2072 time to fit residues: 27.5254 Evaluate side-chains 79 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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: 1.9990 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 24 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6792 Z= 0.288 Angle : 0.660 10.492 9231 Z= 0.338 Chirality : 0.047 0.356 998 Planarity : 0.005 0.041 1181 Dihedral : 6.722 59.443 1097 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.00 % Allowed : 9.00 % Favored : 90.00 % 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: -0.78 (0.30), residues: 793 helix: 0.50 (0.29), residues: 344 sheet: -0.65 (0.65), residues: 60 loop : -1.44 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 473 HIS 0.005 0.002 HIS F 34 PHE 0.011 0.001 PHE F 369 TYR 0.018 0.002 TYR A 453 ARG 0.005 0.001 ARG F 306 *********************** 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 93 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.8786 (mp) cc_final: 0.8520 (mt) outliers start: 7 outliers final: 5 residues processed: 89 average time/residue: 0.1557 time to fit residues: 19.7861 Evaluate side-chains 86 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.0970 chunk 71 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6792 Z= 0.191 Angle : 0.582 10.235 9231 Z= 0.294 Chirality : 0.043 0.338 998 Planarity : 0.004 0.035 1181 Dihedral : 6.287 57.795 1097 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.71 % Allowed : 11.57 % Favored : 86.71 % 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: -0.59 (0.31), residues: 793 helix: 0.73 (0.30), residues: 340 sheet: -0.22 (0.73), residues: 50 loop : -1.43 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 473 HIS 0.004 0.001 HIS F 378 PHE 0.009 0.001 PHE F 369 TYR 0.012 0.001 TYR A 453 ARG 0.003 0.000 ARG F 306 *********************** 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 100 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 222 LEU cc_start: 0.8281 (tp) cc_final: 0.8048 (tt) REVERT: F 406 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6496 (mt-10) REVERT: F 600 LYS cc_start: 0.6442 (tppt) cc_final: 0.5497 (tmtt) outliers start: 12 outliers final: 6 residues processed: 97 average time/residue: 0.1763 time to fit residues: 24.3982 Evaluate side-chains 92 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 378 HIS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6792 Z= 0.209 Angle : 0.602 9.518 9231 Z= 0.299 Chirality : 0.044 0.332 998 Planarity : 0.004 0.034 1181 Dihedral : 6.149 56.903 1097 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.71 % Allowed : 14.57 % 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: -0.57 (0.30), residues: 793 helix: 0.76 (0.30), residues: 339 sheet: -0.14 (0.72), residues: 50 loop : -1.44 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 478 HIS 0.008 0.002 HIS F 265 PHE 0.009 0.001 PHE F 369 TYR 0.013 0.001 TYR A 453 ARG 0.003 0.000 ARG F 306 *********************** 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 97 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 406 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6504 (mt-10) REVERT: F 600 LYS cc_start: 0.6599 (tppt) cc_final: 0.5505 (tmtt) outliers start: 12 outliers final: 7 residues processed: 93 average time/residue: 0.1937 time to fit residues: 25.9462 Evaluate side-chains 92 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 378 HIS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 65 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6792 Z= 0.180 Angle : 0.580 10.072 9231 Z= 0.289 Chirality : 0.043 0.324 998 Planarity : 0.004 0.035 1181 Dihedral : 5.945 56.373 1097 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.00 % Allowed : 15.57 % Favored : 82.43 % 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: -0.50 (0.31), residues: 793 helix: 0.82 (0.30), residues: 340 sheet: -0.10 (0.72), residues: 50 loop : -1.40 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 478 HIS 0.008 0.001 HIS F 378 PHE 0.009 0.001 PHE F 504 TYR 0.011 0.001 TYR A 453 ARG 0.003 0.000 ARG F 306 *********************** 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 105 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 406 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6515 (mt-10) REVERT: F 449 THR cc_start: 0.7568 (OUTLIER) cc_final: 0.7248 (t) REVERT: F 600 LYS cc_start: 0.6553 (tppt) cc_final: 0.5539 (tmtt) outliers start: 14 outliers final: 7 residues processed: 102 average time/residue: 0.1705 time to fit residues: 24.1684 Evaluate side-chains 99 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 378 HIS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6792 Z= 0.209 Angle : 0.607 10.347 9231 Z= 0.300 Chirality : 0.044 0.321 998 Planarity : 0.004 0.036 1181 Dihedral : 5.878 56.722 1097 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.71 % Allowed : 16.43 % 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: -0.49 (0.31), residues: 793 helix: 0.84 (0.30), residues: 340 sheet: 0.02 (0.74), residues: 50 loop : -1.43 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 478 HIS 0.007 0.001 HIS F 378 PHE 0.012 0.001 PHE F 504 TYR 0.013 0.001 TYR A 453 ARG 0.004 0.000 ARG A 357 *********************** 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 108 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5708 (tt) REVERT: F 222 LEU cc_start: 0.8303 (tp) cc_final: 0.8038 (tt) REVERT: F 393 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7557 (mtt90) REVERT: F 406 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6637 (mt-10) REVERT: F 449 THR cc_start: 0.7508 (OUTLIER) cc_final: 0.7197 (t) REVERT: F 512 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6720 (t80) REVERT: F 600 LYS cc_start: 0.6569 (tppt) cc_final: 0.5525 (tmtt) outliers start: 19 outliers final: 8 residues processed: 103 average time/residue: 0.1635 time to fit residues: 23.5094 Evaluate side-chains 102 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 378 HIS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 473 TRP Chi-restraints excluded: chain F residue 512 PHE Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6792 Z= 0.351 Angle : 0.729 11.074 9231 Z= 0.364 Chirality : 0.051 0.530 998 Planarity : 0.004 0.042 1181 Dihedral : 6.566 58.965 1097 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.43 % Allowed : 16.43 % Favored : 81.14 % 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: -0.80 (0.30), residues: 793 helix: 0.63 (0.29), residues: 338 sheet: 0.55 (0.77), residues: 44 loop : -1.71 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 478 HIS 0.022 0.003 HIS F 378 PHE 0.016 0.002 PHE F 504 TYR 0.021 0.002 TYR A 453 ARG 0.006 0.001 ARG A 357 *********************** 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 109 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: F 222 LEU cc_start: 0.8537 (tp) cc_final: 0.8328 (tt) REVERT: F 406 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6826 (mt-10) REVERT: F 512 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.6826 (t80) REVERT: F 600 LYS cc_start: 0.6787 (tppt) cc_final: 0.5627 (tmtt) outliers start: 17 outliers final: 11 residues processed: 105 average time/residue: 0.1517 time to fit residues: 22.5486 Evaluate side-chains 99 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 378 HIS Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 473 TRP Chi-restraints excluded: chain F residue 508 ASN Chi-restraints excluded: chain F residue 512 PHE Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 0.0000 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN F 378 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6792 Z= 0.194 Angle : 0.640 11.034 9231 Z= 0.315 Chirality : 0.045 0.328 998 Planarity : 0.004 0.034 1181 Dihedral : 6.242 56.950 1097 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.71 % Allowed : 17.71 % Favored : 80.57 % 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: -0.61 (0.30), residues: 793 helix: 0.77 (0.30), residues: 340 sheet: 0.02 (0.72), residues: 50 loop : -1.54 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 478 HIS 0.011 0.001 HIS F 378 PHE 0.008 0.001 PHE F 327 TYR 0.013 0.001 TYR F 183 ARG 0.005 0.000 ARG A 357 *********************** 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 99 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: F 222 LEU cc_start: 0.8225 (tp) cc_final: 0.8003 (tt) REVERT: F 393 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.6996 (mtp85) REVERT: F 406 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6701 (mt-10) REVERT: F 512 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6680 (t80) REVERT: F 600 LYS cc_start: 0.6539 (tppt) cc_final: 0.5554 (tmtt) outliers start: 12 outliers final: 8 residues processed: 97 average time/residue: 0.1753 time to fit residues: 23.2340 Evaluate side-chains 92 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 378 HIS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 473 TRP Chi-restraints excluded: chain F residue 512 PHE Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6792 Z= 0.234 Angle : 0.660 11.025 9231 Z= 0.326 Chirality : 0.045 0.335 998 Planarity : 0.004 0.037 1181 Dihedral : 6.168 57.141 1097 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.71 % Allowed : 17.14 % Favored : 80.14 % 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: -0.57 (0.30), residues: 793 helix: 0.83 (0.30), residues: 339 sheet: 0.07 (0.73), residues: 50 loop : -1.54 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP F 478 HIS 0.004 0.001 HIS F 378 PHE 0.007 0.001 PHE F 327 TYR 0.018 0.001 TYR F 183 ARG 0.004 0.000 ARG A 357 *********************** 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 102 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: F 222 LEU cc_start: 0.8242 (tp) cc_final: 0.8026 (tt) REVERT: F 393 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7003 (mtp85) REVERT: F 406 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6726 (mt-10) REVERT: F 512 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6513 (t80) REVERT: F 600 LYS cc_start: 0.6562 (tppt) cc_final: 0.5581 (tmtt) outliers start: 19 outliers final: 9 residues processed: 98 average time/residue: 0.1634 time to fit residues: 22.4167 Evaluate side-chains 95 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 473 TRP Chi-restraints excluded: chain F residue 512 PHE Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.0000 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6792 Z= 0.199 Angle : 0.650 10.891 9231 Z= 0.321 Chirality : 0.044 0.304 998 Planarity : 0.004 0.034 1181 Dihedral : 6.051 56.321 1097 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.71 % Allowed : 17.71 % Favored : 80.57 % 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: -0.47 (0.30), residues: 793 helix: 0.90 (0.30), residues: 340 sheet: 0.07 (0.73), residues: 50 loop : -1.47 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP F 478 HIS 0.005 0.001 HIS F 345 PHE 0.008 0.001 PHE F 327 TYR 0.018 0.001 TYR F 183 ARG 0.004 0.000 ARG A 357 ********************** 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 99 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: F 222 LEU cc_start: 0.8158 (tp) cc_final: 0.7940 (tt) REVERT: F 393 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.6975 (mtp85) REVERT: F 406 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6725 (mt-10) REVERT: F 512 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6299 (t80) REVERT: F 600 LYS cc_start: 0.6475 (tppt) cc_final: 0.5570 (tmtt) outliers start: 12 outliers final: 7 residues processed: 96 average time/residue: 0.1622 time to fit residues: 21.7586 Evaluate side-chains 94 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 473 TRP Chi-restraints excluded: chain F residue 512 PHE Chi-restraints excluded: chain F residue 604 VAL 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: 1.9990 chunk 26 optimal weight: 0.0170 chunk 64 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN F 378 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.132462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122173 restraints weight = 13557.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123911 restraints weight = 9564.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.124958 restraints weight = 6607.397| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6792 Z= 0.218 Angle : 0.676 11.298 9231 Z= 0.332 Chirality : 0.049 0.617 998 Planarity : 0.004 0.035 1181 Dihedral : 6.354 58.563 1097 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.00 % Allowed : 18.29 % Favored : 79.71 % 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: -0.42 (0.31), residues: 793 helix: 0.92 (0.30), residues: 339 sheet: 0.08 (0.74), residues: 50 loop : -1.41 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP F 478 HIS 0.003 0.001 HIS F 34 PHE 0.008 0.001 PHE F 327 TYR 0.016 0.001 TYR F 183 ARG 0.004 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1643.44 seconds wall clock time: 31 minutes 4.73 seconds (1864.73 seconds total)