Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 09:23:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v80_31785/04_2023/7v80_31785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v80_31785/04_2023/7v80_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_31785/04_2023/7v80_31785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v80_31785/04_2023/7v80_31785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v80_31785/04_2023/7v80_31785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v80_31785/04_2023/7v80_31785.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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 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 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 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 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 chiralities: 3 Time building chain proxies: 4.00, per 1000 atoms: 0.61 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: 2.77 Conformation dependent library (CDL) restraints added in 1.1 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: 0.34 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: 1.69 Time building geometry restraints manager: 2.91 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: 3473 18.00 - 36.00: 367 36.00 - 53.99: 64 53.99 - 71.99: 7 71.99 - 89.99: 10 Dihedral angle restraints: 3921 sinusoidal: 1582 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 3918 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: 2.270 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: 12.050 Check model and map are aligned: 0.130 Set scattering table: 0.060 Process input model: 21.070 Find NCS groups from input model: 0.180 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.590 ------------------------------------------------------------------------------- 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 : 14.996 89.988 2400 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 % 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 *********************** 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 : 0.805 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1823 time to fit residues: 24.1700 Evaluate side-chains 79 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1084 ------------------------------------------------------------------------------- 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: 0.7318 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 6792 Z= 0.286 Angle : 0.664 10.876 9231 Z= 0.339 Chirality : 0.047 0.321 998 Planarity : 0.005 0.041 1181 Dihedral : 4.954 22.122 866 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer Outliers : 1.00 % 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: -0.81 (0.30), residues: 793 helix: 0.47 (0.29), residues: 344 sheet: -0.64 (0.65), residues: 60 loop : -1.45 (0.32), residues: 389 *********************** 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 94 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 90 average time/residue: 0.1626 time to fit residues: 20.7912 Evaluate side-chains 87 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0619 time to fit residues: 1.6499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7335 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 6792 Z= 0.263 Angle : 0.643 10.507 9231 Z= 0.324 Chirality : 0.046 0.313 998 Planarity : 0.004 0.037 1181 Dihedral : 4.950 20.676 866 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 1.43 % 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: -0.78 (0.30), residues: 793 helix: 0.60 (0.29), residues: 339 sheet: -0.32 (0.72), residues: 50 loop : -1.56 (0.31), residues: 404 *********************** 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 91 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.704 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 89 average time/residue: 0.1534 time to fit residues: 19.7312 Evaluate side-chains 79 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.700 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0666 time to fit residues: 1.2028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7285 moved from start: 0.1481 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 : 0.597 9.235 9231 Z= 0.299 Chirality : 0.043 0.300 998 Planarity : 0.004 0.035 1181 Dihedral : 4.783 20.487 866 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 1.14 % 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: -0.62 (0.30), residues: 793 helix: 0.76 (0.30), residues: 339 sheet: -0.10 (0.73), residues: 50 loop : -1.51 (0.31), residues: 404 *********************** 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 94 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.822 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 92 average time/residue: 0.1616 time to fit residues: 21.3021 Evaluate side-chains 84 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0706 time to fit residues: 1.4861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 65 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.7268 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 6792 Z= 0.182 Angle : 0.593 10.486 9231 Z= 0.293 Chirality : 0.043 0.288 998 Planarity : 0.004 0.035 1181 Dihedral : 4.631 19.818 866 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 1.29 % 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: -0.52 (0.31), residues: 793 helix: 0.84 (0.30), residues: 340 sheet: -0.13 (0.72), residues: 50 loop : -1.46 (0.31), residues: 403 *********************** 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 93 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.769 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 93 average time/residue: 0.1491 time to fit residues: 20.1898 Evaluate side-chains 86 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0844 time to fit residues: 1.3891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.7286 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 6792 Z= 0.207 Angle : 0.620 10.335 9231 Z= 0.305 Chirality : 0.044 0.319 998 Planarity : 0.004 0.036 1181 Dihedral : 4.647 19.722 866 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 1.86 % 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: -0.52 (0.31), residues: 793 helix: 0.85 (0.30), residues: 340 sheet: -0.15 (0.71), residues: 50 loop : -1.47 (0.31), residues: 403 *********************** 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 98 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.793 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 0.1626 time to fit residues: 22.3020 Evaluate side-chains 90 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0676 time to fit residues: 1.9635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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: 0.7278 moved from start: 0.1823 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= 0.200 Angle : 0.620 10.617 9231 Z= 0.304 Chirality : 0.044 0.291 998 Planarity : 0.004 0.036 1181 Dihedral : 4.650 19.984 866 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 0.57 % 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: -0.50 (0.31), residues: 793 helix: 0.90 (0.30), residues: 340 sheet: -0.18 (0.71), residues: 50 loop : -1.47 (0.31), residues: 403 *********************** 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 88 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.874 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 87 average time/residue: 0.1705 time to fit residues: 21.2981 Evaluate side-chains 83 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0643 time to fit residues: 1.2068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 6792 Z= 0.251 Angle : 0.659 10.970 9231 Z= 0.325 Chirality : 0.045 0.333 998 Planarity : 0.004 0.038 1181 Dihedral : 4.809 20.994 866 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer Outliers : 1.00 % 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: -0.59 (0.30), residues: 793 helix: 0.84 (0.30), residues: 340 sheet: -0.17 (0.71), residues: 50 loop : -1.55 (0.31), residues: 403 *********************** 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 89 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.802 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 87 average time/residue: 0.1593 time to fit residues: 20.5591 Evaluate side-chains 82 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.724 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0960 time to fit residues: 1.7012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7311 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 6792 Z= 0.221 Angle : 0.662 13.151 9231 Z= 0.325 Chirality : 0.045 0.303 998 Planarity : 0.004 0.035 1181 Dihedral : 4.773 25.780 866 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 0.43 % 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: -0.55 (0.30), residues: 793 helix: 0.88 (0.30), residues: 340 sheet: -0.15 (0.73), residues: 50 loop : -1.54 (0.31), residues: 403 *********************** 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 88 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.805 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 87 average time/residue: 0.1532 time to fit residues: 19.6313 Evaluate side-chains 82 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 6792 Z= 0.208 Angle : 0.677 12.159 9231 Z= 0.331 Chirality : 0.048 0.582 998 Planarity : 0.004 0.034 1181 Dihedral : 4.832 30.216 866 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.96 (0.30), residues: 340 sheet: -0.22 (0.74), residues: 50 loop : -1.41 (0.31), residues: 403 ********************** 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 85 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.831 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1702 time to fit residues: 20.7399 Evaluate side-chains 81 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121567 restraints weight = 13648.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.123222 restraints weight = 9962.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124144 restraints weight = 6898.110| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 6792 Z= 0.218 Angle : 0.672 11.442 9231 Z= 0.329 Chirality : 0.047 0.517 998 Planarity : 0.004 0.035 1181 Dihedral : 4.801 27.125 866 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.29 % 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: -0.41 (0.31), residues: 793 helix: 0.95 (0.30), residues: 340 sheet: -0.21 (0.75), residues: 50 loop : -1.39 (0.31), residues: 403 =============================================================================== Job complete usr+sys time: 1502.25 seconds wall clock time: 28 minutes 4.15 seconds (1684.15 seconds total)