Starting phenix.real_space_refine on Tue Feb 13 22:56:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6e_26364/02_2024/7u6e_26364_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6e_26364/02_2024/7u6e_26364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6e_26364/02_2024/7u6e_26364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6e_26364/02_2024/7u6e_26364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6e_26364/02_2024/7u6e_26364_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6e_26364/02_2024/7u6e_26364_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 60 5.16 5 C 5077 2.51 5 N 1357 2.21 5 O 1510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8004 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "B" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "E" Number of atoms: 4708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4708 Classifications: {'peptide': 584} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 555} Chain breaks: 2 Chain: "F" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2507 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 12, 'TRANS': 295} Chain breaks: 2 Chain: "G" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Unusual residues: {'HY1': 1} Classifications: {'peptide': 18, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 16, None: 1} Not linked: pdbres="HY1 G 0 " pdbres="SER G 1 " Chain: "H" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Unusual residues: {'HY1': 1} Classifications: {'peptide': 18, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 16, None: 1} Not linked: pdbres="HY1 H 0 " pdbres="SER H 1 " 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: "E" 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 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: 4.68, per 1000 atoms: 0.58 Number of scatterers: 8004 At special positions: 0 Unit cell: (117.307, 86.2133, 83.3866, 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 60 16.00 O 1510 8.00 N 1357 7.00 C 5077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.02 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=2.01 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.02 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS E 188 " distance=2.04 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.04 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.02 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.02 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.01 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.02 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.03 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.02 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 308 " distance=2.04 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 333 " distance=2.02 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS E 524 " - pdb=" SG CYS F 524 " distance=2.04 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.02 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.02 Simple disulfide: pdb=" SG CYS G 11 " - pdb=" SG CYS G 17 " distance=2.03 Simple disulfide: pdb=" SG CYS H 11 " - pdb=" SG CYS H 17 " distance=2.04 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=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN E 111 " " NAG E1001 " - " ASN E 25 " " NAG E1002 " - " ASN E 255 " " NAG E1003 " - " ASN E 418 " " NAG F1001 " - " ASN F 337 " " NAG F1002 " - " ASN F 397 " " NAG F1003 " - " ASN F 514 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.4 seconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 15 sheets defined 17.0% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 13 through 19 removed outlier: 3.903A pdb=" N TYR A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 removed outlier: 3.775A pdb=" N VAL B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 23 Processing helix chain 'E' and resid 43 through 46 No H-bonds generated for 'chain 'E' and resid 43 through 46' Processing helix chain 'E' and resid 72 through 75 No H-bonds generated for 'chain 'E' and resid 72 through 75' Processing helix chain 'E' and resid 133 through 136 No H-bonds generated for 'chain 'E' and resid 133 through 136' Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 315 through 317 No H-bonds generated for 'chain 'E' and resid 315 through 317' Processing helix chain 'E' and resid 324 through 330 removed outlier: 4.045A pdb=" N LEU E 330 " --> pdb=" O SER E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 358 Processing helix chain 'E' and resid 436 through 445 removed outlier: 3.787A pdb=" N MET E 442 " --> pdb=" O GLU E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 499 No H-bonds generated for 'chain 'E' and resid 497 through 499' Processing helix chain 'F' and resid 324 through 330 removed outlier: 4.613A pdb=" N GLU F 329 " --> pdb=" O THR F 325 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 359 removed outlier: 3.599A pdb=" N ASN F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 445 Processing helix chain 'F' and resid 497 through 499 No H-bonds generated for 'chain 'F' and resid 497 through 499' Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 691 through 713 Processing helix chain 'G' and resid 2 through 13 Processing helix chain 'H' and resid 2 through 12 Processing sheet with id= A, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.935A pdb=" N SER E 116 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL E 94 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG E 118 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N PHE E 96 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU E 120 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS E 144 " --> pdb=" O ILE E 119 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 231 through 233 Processing sheet with id= C, first strand: chain 'E' and resid 246 through 248 Processing sheet with id= D, first strand: chain 'E' and resid 278 through 280 Processing sheet with id= E, first strand: chain 'E' and resid 292 through 295 removed outlier: 4.660A pdb=" N LEU E 300 " --> pdb=" O ASN E 295 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 311 through 313 removed outlier: 6.630A pdb=" N VAL E 335 " --> pdb=" O CYS E 312 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 318 through 321 removed outlier: 6.676A pdb=" N SER E 339 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE E 321 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE E 341 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS E 425 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N TYR E 401 " --> pdb=" O LYS E 425 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE E 427 " --> pdb=" O TYR E 401 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU E 403 " --> pdb=" O PHE E 427 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N HIS E 429 " --> pdb=" O LEU E 403 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 477 through 480 removed outlier: 3.517A pdb=" N MET E 553 " --> pdb=" O ILE E 485 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 530 through 534 removed outlier: 6.552A pdb=" N LEU E 569 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE E 503 " --> pdb=" O LYS E 567 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS E 567 " --> pdb=" O PHE E 503 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU E 505 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE E 565 " --> pdb=" O LEU E 505 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR E 507 " --> pdb=" O ALA E 563 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA E 563 " --> pdb=" O TYR E 507 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLU E 509 " --> pdb=" O GLN E 561 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLN E 561 " --> pdb=" O GLU E 509 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 6 through 9 removed outlier: 7.534A pdb=" N CYS E 8 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE E 29 " --> pdb=" O CYS E 8 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 311 through 313 removed outlier: 6.453A pdb=" N VAL F 335 " --> pdb=" O CYS F 312 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 318 through 321 removed outlier: 6.624A pdb=" N SER F 339 " --> pdb=" O LYS F 319 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE F 321 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE F 341 " --> pdb=" O ILE F 321 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LYS F 425 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR F 401 " --> pdb=" O LYS F 425 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE F 427 " --> pdb=" O TYR F 401 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU F 403 " --> pdb=" O PHE F 427 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N HIS F 429 " --> pdb=" O LEU F 403 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 471 through 473 Processing sheet with id= N, first strand: chain 'F' and resid 550 through 553 Processing sheet with id= O, first strand: chain 'F' and resid 532 through 535 removed outlier: 6.717A pdb=" N LEU F 569 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE F 503 " --> pdb=" O LYS F 567 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS F 567 " --> pdb=" O PHE F 503 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU F 505 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE F 565 " --> pdb=" O LEU F 505 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR F 507 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA F 563 " --> pdb=" O TYR F 507 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1333 1.32 - 1.44: 2277 1.44 - 1.57: 4505 1.57 - 1.70: 0 1.70 - 1.83: 72 Bond restraints: 8187 Sorted by residual: bond pdb=" C1 NAG F1002 " pdb=" O5 NAG F1002 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1 NAG E1001 " pdb=" O5 NAG E1001 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" C1 NAG F1001 " pdb=" O5 NAG F1001 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" C1 NAG C 1 " pdb=" C2 NAG C 1 " ideal model delta sigma weight residual 1.532 1.499 0.033 2.00e-02 2.50e+03 2.77e+00 bond pdb=" CB ASN E 122 " pdb=" CG ASN E 122 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.14e+00 ... (remaining 8182 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.94: 175 105.94 - 112.97: 4347 112.97 - 120.00: 2861 120.00 - 127.03: 3584 127.03 - 134.06: 112 Bond angle restraints: 11079 Sorted by residual: angle pdb=" CA TRP E 559 " pdb=" CB TRP E 559 " pdb=" CG TRP E 559 " ideal model delta sigma weight residual 113.60 119.95 -6.35 1.90e+00 2.77e-01 1.12e+01 angle pdb=" N MET E 56 " pdb=" CA MET E 56 " pdb=" C MET E 56 " ideal model delta sigma weight residual 108.32 113.08 -4.76 1.64e+00 3.72e-01 8.42e+00 angle pdb=" N ILE F 388 " pdb=" CA ILE F 388 " pdb=" C ILE F 388 " ideal model delta sigma weight residual 108.17 104.16 4.01 1.40e+00 5.10e-01 8.20e+00 angle pdb=" C5 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" O4 NAG C 1 " ideal model delta sigma weight residual 111.70 103.34 8.36 3.00e+00 1.11e-01 7.76e+00 angle pdb=" N PHE E 382 " pdb=" CA PHE E 382 " pdb=" C PHE E 382 " ideal model delta sigma weight residual 109.96 105.83 4.13 1.49e+00 4.50e-01 7.69e+00 ... (remaining 11074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 4557 17.44 - 34.89: 373 34.89 - 52.33: 89 52.33 - 69.77: 21 69.77 - 87.22: 12 Dihedral angle restraints: 5052 sinusoidal: 2216 harmonic: 2836 Sorted by residual: dihedral pdb=" CB CYS E 192 " pdb=" SG CYS E 192 " pdb=" SG CYS E 201 " pdb=" CB CYS E 201 " ideal model delta sinusoidal sigma weight residual -86.00 -167.88 81.88 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS E 288 " pdb=" SG CYS E 288 " pdb=" SG CYS E 301 " pdb=" CB CYS E 301 " ideal model delta sinusoidal sigma weight residual -86.00 -164.61 78.61 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS H 11 " pdb=" SG CYS H 11 " pdb=" SG CYS H 17 " pdb=" CB CYS H 17 " ideal model delta sinusoidal sigma weight residual 93.00 166.66 -73.66 1 1.00e+01 1.00e-02 6.90e+01 ... (remaining 5049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 994 0.079 - 0.157: 208 0.157 - 0.236: 16 0.236 - 0.315: 2 0.315 - 0.394: 1 Chirality restraints: 1221 Sorted by residual: chirality pdb=" C1 NAG E1002 " pdb=" ND2 ASN E 255 " pdb=" C2 NAG E1002 " pdb=" O5 NAG E1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CB THR F 421 " pdb=" CA THR F 421 " pdb=" OG1 THR F 421 " pdb=" CG2 THR F 421 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG E1001 " pdb=" ND2 ASN E 25 " pdb=" C2 NAG E1001 " pdb=" O5 NAG E1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1218 not shown) Planarity restraints: 1423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 255 " 0.029 2.00e-02 2.50e+03 2.94e-02 1.08e+01 pdb=" CG ASN E 255 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN E 255 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN E 255 " -0.043 2.00e-02 2.50e+03 pdb=" C1 NAG E1002 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 717 " 0.216 9.50e-02 1.11e+02 9.76e-02 7.29e+00 pdb=" NE ARG F 717 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG F 717 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG F 717 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG F 717 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 345 " -0.212 9.50e-02 1.11e+02 9.56e-02 6.59e+00 pdb=" NE ARG F 345 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG F 345 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG F 345 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG F 345 " -0.002 2.00e-02 2.50e+03 ... (remaining 1420 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 425 2.72 - 3.26: 8268 3.26 - 3.81: 13863 3.81 - 4.35: 18393 4.35 - 4.90: 29632 Nonbonded interactions: 70581 Sorted by model distance: nonbonded pdb=" OE2 GLU E 211 " pdb=" ND2 ASN E 230 " model vdw 2.171 2.520 nonbonded pdb=" O3 NAG E1002 " pdb=" O7 NAG E1002 " model vdw 2.288 2.440 nonbonded pdb=" OE2 GLU E 120 " pdb=" NZ LYS E 121 " model vdw 2.310 2.520 nonbonded pdb=" OH TYR F 398 " pdb=" OD2 ASP F 456 " model vdw 2.328 2.440 nonbonded pdb=" OE2 GLU E 471 " pdb=" OH TYR E 492 " model vdw 2.357 2.440 ... (remaining 70576 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 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 5.490 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.210 Find NCS groups from input model: 0.210 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:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 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 : 0.008 0.066 8187 Z= 0.550 Angle : 0.914 9.183 11079 Z= 0.496 Chirality : 0.061 0.394 1221 Planarity : 0.008 0.098 1416 Dihedral : 14.187 87.215 3150 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 1.82 % Allowed : 8.29 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -2.19 (0.24), residues: 954 helix: -1.27 (0.37), residues: 182 sheet: -1.55 (0.42), residues: 148 loop : -1.53 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP F 414 HIS 0.012 0.002 HIS E 144 PHE 0.042 0.004 PHE E 89 TYR 0.025 0.004 TYR F 507 ARG 0.021 0.002 ARG F 717 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: E 299 LEU cc_start: 0.7723 (tp) cc_final: 0.7523 (tp) REVERT: E 483 ASP cc_start: 0.6432 (p0) cc_final: 0.6142 (p0) REVERT: E 505 LEU cc_start: 0.7781 (tt) cc_final: 0.7518 (tp) REVERT: E 553 MET cc_start: 0.7061 (mpp) cc_final: 0.6748 (mpp) REVERT: F 318 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6641 (tp30) REVERT: F 423 GLN cc_start: 0.8025 (tp40) cc_final: 0.7755 (tp-100) REVERT: F 579 TYR cc_start: 0.7289 (m-80) cc_final: 0.6999 (m-80) outliers start: 16 outliers final: 3 residues processed: 198 average time/residue: 1.1947 time to fit residues: 250.5690 Evaluate side-chains 99 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain F residue 412 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.0870 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 HIS E 343 ASN E 348 ASN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 ASN F 548 HIS F 561 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8187 Z= 0.324 Angle : 0.754 11.576 11079 Z= 0.394 Chirality : 0.050 0.364 1221 Planarity : 0.004 0.040 1416 Dihedral : 8.048 54.697 1237 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.52 % Allowed : 16.46 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.25), residues: 954 helix: -0.62 (0.38), residues: 175 sheet: -1.03 (0.41), residues: 165 loop : -1.44 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 559 HIS 0.007 0.001 HIS E 275 PHE 0.031 0.003 PHE E 482 TYR 0.018 0.002 TYR E 60 ARG 0.005 0.001 ARG F 554 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 108 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 110 MET cc_start: 0.7587 (mmp) cc_final: 0.6651 (mmt) REVERT: E 299 LEU cc_start: 0.8143 (tp) cc_final: 0.7753 (tp) REVERT: E 483 ASP cc_start: 0.6641 (p0) cc_final: 0.6417 (p0) REVERT: E 505 LEU cc_start: 0.8029 (tt) cc_final: 0.7821 (tp) REVERT: E 553 MET cc_start: 0.7003 (mpp) cc_final: 0.6653 (mpp) REVERT: F 318 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6518 (tp30) REVERT: F 417 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.7066 (t70) REVERT: F 579 TYR cc_start: 0.7423 (m-80) cc_final: 0.7046 (m-80) REVERT: F 706 GLU cc_start: 0.7264 (tt0) cc_final: 0.7061 (tt0) REVERT: G 8 GLN cc_start: 0.8233 (tm-30) cc_final: 0.8008 (pp30) outliers start: 31 outliers final: 7 residues processed: 130 average time/residue: 0.9399 time to fit residues: 131.7696 Evaluate side-chains 100 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 693 LEU Chi-restraints excluded: chain F residue 696 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 0.0000 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8187 Z= 0.331 Angle : 0.716 7.677 11079 Z= 0.370 Chirality : 0.049 0.355 1221 Planarity : 0.004 0.040 1416 Dihedral : 7.671 55.659 1235 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.75 % Allowed : 17.48 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.25), residues: 954 helix: -0.45 (0.39), residues: 176 sheet: -1.02 (0.40), residues: 174 loop : -1.58 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 559 HIS 0.006 0.002 HIS E 185 PHE 0.024 0.002 PHE E 89 TYR 0.020 0.002 TYR E 60 ARG 0.008 0.001 ARG E 498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 16 ASN cc_start: 0.5225 (p0) cc_final: 0.5016 (p0) REVERT: E 406 GLN cc_start: 0.7318 (mm-40) cc_final: 0.6924 (mm-40) REVERT: E 505 LEU cc_start: 0.8064 (tt) cc_final: 0.7861 (tp) REVERT: F 417 HIS cc_start: 0.7717 (OUTLIER) cc_final: 0.6613 (t70) REVERT: F 521 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: F 579 TYR cc_start: 0.7357 (m-80) cc_final: 0.6969 (m-80) REVERT: F 698 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6826 (tm-30) REVERT: G 8 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7837 (pp30) outliers start: 33 outliers final: 15 residues processed: 116 average time/residue: 0.9978 time to fit residues: 124.5435 Evaluate side-chains 96 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 201 CYS Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 521 GLN Chi-restraints excluded: chain F residue 535 ASP Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 696 LEU Chi-restraints excluded: chain H residue 2 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 0.0060 chunk 85 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8187 Z= 0.294 Angle : 0.679 13.119 11079 Z= 0.345 Chirality : 0.047 0.339 1221 Planarity : 0.004 0.045 1416 Dihedral : 7.201 49.207 1235 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.97 % Allowed : 18.84 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.25), residues: 954 helix: -0.43 (0.39), residues: 176 sheet: -1.10 (0.40), residues: 174 loop : -1.59 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 559 HIS 0.006 0.002 HIS E 263 PHE 0.019 0.002 PHE E 89 TYR 0.018 0.002 TYR E 60 ARG 0.011 0.001 ARG E 498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 94 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 355 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6920 (tp30) REVERT: E 406 GLN cc_start: 0.7399 (mm-40) cc_final: 0.6890 (mm-40) REVERT: E 483 ASP cc_start: 0.6601 (p0) cc_final: 0.6389 (p0) REVERT: F 417 HIS cc_start: 0.7838 (OUTLIER) cc_final: 0.6388 (t70) REVERT: F 442 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7436 (ttm) REVERT: F 579 TYR cc_start: 0.7302 (m-80) cc_final: 0.6909 (m-80) REVERT: F 698 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7004 (tm-30) outliers start: 35 outliers final: 14 residues processed: 118 average time/residue: 0.9793 time to fit residues: 124.7734 Evaluate side-chains 95 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 535 ASP Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 696 LEU Chi-restraints excluded: chain G residue 1 SER Chi-restraints excluded: chain H residue 2 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 46 optimal weight: 0.1980 chunk 81 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8187 Z= 0.220 Angle : 0.637 8.096 11079 Z= 0.324 Chirality : 0.045 0.311 1221 Planarity : 0.004 0.037 1416 Dihedral : 6.992 50.127 1234 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.84 % Allowed : 21.11 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.25), residues: 954 helix: -0.24 (0.40), residues: 175 sheet: -1.06 (0.41), residues: 169 loop : -1.52 (0.22), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 559 HIS 0.005 0.001 HIS E 185 PHE 0.016 0.002 PHE F 565 TYR 0.013 0.001 TYR E 60 ARG 0.006 0.000 ARG E 409 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 110 MET cc_start: 0.7367 (mmp) cc_final: 0.6416 (mmt) REVERT: E 270 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6516 (mpt180) REVERT: E 355 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6897 (tp30) REVERT: E 406 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6919 (mm-40) REVERT: F 318 GLU cc_start: 0.6688 (mm-30) cc_final: 0.6409 (mm-30) REVERT: F 417 HIS cc_start: 0.7853 (OUTLIER) cc_final: 0.6310 (t70) REVERT: F 442 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7769 (ttm) REVERT: F 579 TYR cc_start: 0.7241 (m-80) cc_final: 0.6896 (m-80) REVERT: F 698 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7158 (tm-30) outliers start: 25 outliers final: 12 residues processed: 100 average time/residue: 1.0100 time to fit residues: 108.8338 Evaluate side-chains 91 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 270 ARG Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain F residue 696 LEU Chi-restraints excluded: chain G residue 1 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 8187 Z= 0.365 Angle : 0.725 10.839 11079 Z= 0.368 Chirality : 0.049 0.346 1221 Planarity : 0.005 0.055 1416 Dihedral : 7.226 49.634 1234 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.20 % Allowed : 19.98 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.25), residues: 954 helix: -0.29 (0.40), residues: 175 sheet: -1.36 (0.42), residues: 159 loop : -1.61 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 559 HIS 0.006 0.002 HIS E 199 PHE 0.025 0.003 PHE E 89 TYR 0.021 0.002 TYR E 60 ARG 0.015 0.001 ARG E 498 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 85 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 188 CYS cc_start: 0.4785 (OUTLIER) cc_final: 0.4248 (p) REVERT: E 355 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6867 (tp30) REVERT: E 406 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7075 (mm-40) REVERT: F 350 LEU cc_start: 0.4100 (OUTLIER) cc_final: 0.3749 (tt) REVERT: F 417 HIS cc_start: 0.8038 (OUTLIER) cc_final: 0.6578 (t70) REVERT: F 442 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7472 (ttm) REVERT: F 501 LEU cc_start: 0.8238 (mp) cc_final: 0.7868 (mp) REVERT: F 579 TYR cc_start: 0.7248 (m-80) cc_final: 0.6930 (m-80) REVERT: F 698 GLU cc_start: 0.7338 (tm-30) cc_final: 0.7095 (tm-30) outliers start: 37 outliers final: 14 residues processed: 112 average time/residue: 1.0090 time to fit residues: 121.4373 Evaluate side-chains 99 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 44 GLU Chi-restraints excluded: chain E residue 188 CYS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 553 MET Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 535 ASP Chi-restraints excluded: chain F residue 578 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 521 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8187 Z= 0.264 Angle : 0.663 10.663 11079 Z= 0.338 Chirality : 0.046 0.319 1221 Planarity : 0.004 0.052 1416 Dihedral : 7.051 50.439 1234 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.63 % Allowed : 20.77 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.26), residues: 954 helix: -0.18 (0.41), residues: 175 sheet: -1.32 (0.42), residues: 157 loop : -1.56 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 559 HIS 0.004 0.001 HIS E 185 PHE 0.018 0.002 PHE F 572 TYR 0.014 0.001 TYR E 60 ARG 0.010 0.001 ARG E 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 85 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 188 CYS cc_start: 0.4731 (OUTLIER) cc_final: 0.4500 (p) REVERT: E 269 SER cc_start: 0.7373 (OUTLIER) cc_final: 0.6988 (p) REVERT: E 355 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6911 (tp30) REVERT: E 406 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7084 (mm-40) REVERT: F 350 LEU cc_start: 0.4090 (OUTLIER) cc_final: 0.3774 (tt) REVERT: F 417 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.6589 (t70) REVERT: F 442 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7508 (ttm) REVERT: F 501 LEU cc_start: 0.8225 (mp) cc_final: 0.7775 (mp) REVERT: F 579 TYR cc_start: 0.7185 (m-80) cc_final: 0.6918 (m-80) REVERT: F 698 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6863 (tm-30) outliers start: 32 outliers final: 12 residues processed: 109 average time/residue: 1.1182 time to fit residues: 130.6694 Evaluate side-chains 97 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 188 CYS Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 553 MET Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain G residue 1 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8187 Z= 0.271 Angle : 0.669 11.459 11079 Z= 0.340 Chirality : 0.046 0.317 1221 Planarity : 0.004 0.070 1416 Dihedral : 6.986 50.599 1234 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.52 % Allowed : 21.68 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.25), residues: 954 helix: -0.13 (0.41), residues: 175 sheet: -1.38 (0.42), residues: 157 loop : -1.60 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 559 HIS 0.004 0.001 HIS E 185 PHE 0.019 0.002 PHE E 89 TYR 0.015 0.001 TYR E 60 ARG 0.019 0.001 ARG E 498 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 87 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 188 CYS cc_start: 0.5116 (OUTLIER) cc_final: 0.4682 (p) REVERT: E 269 SER cc_start: 0.7370 (OUTLIER) cc_final: 0.6987 (p) REVERT: E 355 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: E 406 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7063 (mm-40) REVERT: E 467 SER cc_start: 0.4809 (OUTLIER) cc_final: 0.4313 (t) REVERT: F 350 LEU cc_start: 0.4113 (OUTLIER) cc_final: 0.3809 (tt) REVERT: F 417 HIS cc_start: 0.7964 (OUTLIER) cc_final: 0.6465 (t70) REVERT: F 442 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7512 (ttm) REVERT: F 501 LEU cc_start: 0.8201 (mp) cc_final: 0.7733 (mp) REVERT: F 579 TYR cc_start: 0.7186 (m-80) cc_final: 0.6900 (m-80) REVERT: F 698 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6986 (tm-30) outliers start: 31 outliers final: 14 residues processed: 110 average time/residue: 1.0435 time to fit residues: 123.2206 Evaluate side-chains 104 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 188 CYS Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 538 LEU Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 470 ASN Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 578 THR Chi-restraints excluded: chain G residue 1 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 66 optimal weight: 0.2980 chunk 25 optimal weight: 0.0470 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 0.0570 chunk 55 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8187 Z= 0.201 Angle : 0.636 12.176 11079 Z= 0.322 Chirality : 0.045 0.291 1221 Planarity : 0.004 0.056 1416 Dihedral : 6.678 51.173 1234 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.50 % Allowed : 23.04 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.25), residues: 954 helix: 0.05 (0.42), residues: 164 sheet: -1.27 (0.42), residues: 157 loop : -1.51 (0.22), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 559 HIS 0.004 0.001 HIS E 185 PHE 0.014 0.002 PHE F 565 TYR 0.011 0.001 TYR E 60 ARG 0.013 0.001 ARG E 409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 110 MET cc_start: 0.7321 (mmp) cc_final: 0.6340 (mmt) REVERT: E 188 CYS cc_start: 0.4594 (OUTLIER) cc_final: 0.4145 (p) REVERT: E 269 SER cc_start: 0.7278 (OUTLIER) cc_final: 0.6910 (p) REVERT: E 355 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7029 (tp30) REVERT: E 406 GLN cc_start: 0.7409 (mm-40) cc_final: 0.7027 (mm-40) REVERT: F 318 GLU cc_start: 0.6672 (mm-30) cc_final: 0.6331 (mm-30) REVERT: F 350 LEU cc_start: 0.4114 (OUTLIER) cc_final: 0.3858 (tt) REVERT: F 417 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.6419 (t70) REVERT: F 442 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7734 (ttm) REVERT: F 579 TYR cc_start: 0.7082 (m-80) cc_final: 0.6814 (m-80) REVERT: F 698 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6643 (tm-30) outliers start: 22 outliers final: 9 residues processed: 104 average time/residue: 1.1607 time to fit residues: 129.8696 Evaluate side-chains 95 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 188 CYS Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain G residue 1 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.0470 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8187 Z= 0.216 Angle : 0.638 11.307 11079 Z= 0.327 Chirality : 0.046 0.289 1221 Planarity : 0.004 0.062 1416 Dihedral : 6.608 51.103 1234 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.27 % Allowed : 23.95 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.25), residues: 954 helix: -0.13 (0.41), residues: 166 sheet: -1.26 (0.42), residues: 157 loop : -1.49 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 551 HIS 0.004 0.001 HIS E 185 PHE 0.014 0.002 PHE F 565 TYR 0.011 0.001 TYR E 60 ARG 0.013 0.001 ARG E 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.7797 (m-80) cc_final: 0.7556 (m-10) REVERT: E 110 MET cc_start: 0.7332 (mmp) cc_final: 0.6290 (mmt) REVERT: E 188 CYS cc_start: 0.4695 (OUTLIER) cc_final: 0.4265 (p) REVERT: E 250 ASP cc_start: 0.6308 (t0) cc_final: 0.6018 (t0) REVERT: E 269 SER cc_start: 0.7276 (OUTLIER) cc_final: 0.6909 (p) REVERT: E 355 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6980 (tp30) REVERT: E 406 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7010 (mm-40) REVERT: F 318 GLU cc_start: 0.6608 (mm-30) cc_final: 0.6300 (mm-30) REVERT: F 350 LEU cc_start: 0.4133 (OUTLIER) cc_final: 0.3886 (tt) REVERT: F 417 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.6444 (t70) REVERT: F 442 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7843 (ttm) REVERT: F 579 TYR cc_start: 0.7019 (m-80) cc_final: 0.6731 (m-80) REVERT: F 698 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6936 (tm-30) outliers start: 20 outliers final: 12 residues processed: 101 average time/residue: 1.1029 time to fit residues: 119.3365 Evaluate side-chains 99 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 188 CYS Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 269 SER Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 412 TRP Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 501 LEU Chi-restraints excluded: chain F residue 535 ASP Chi-restraints excluded: chain G residue 1 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 4 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.159411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.142759 restraints weight = 12775.002| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.02 r_work: 0.4102 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3972 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8187 Z= 0.214 Angle : 0.632 10.935 11079 Z= 0.323 Chirality : 0.045 0.286 1221 Planarity : 0.004 0.062 1416 Dihedral : 6.550 51.247 1234 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.50 % Allowed : 23.72 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.25), residues: 954 helix: -0.12 (0.41), residues: 166 sheet: -1.22 (0.42), residues: 157 loop : -1.51 (0.22), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 551 HIS 0.004 0.001 HIS E 185 PHE 0.015 0.002 PHE F 565 TYR 0.012 0.001 TYR E 60 ARG 0.013 0.001 ARG E 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3111.43 seconds wall clock time: 56 minutes 25.49 seconds (3385.49 seconds total)