Starting phenix.real_space_refine (version: dev) on Sat Feb 18 11:11:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6e_26364/02_2023/7u6e_26364_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6e_26364/02_2023/7u6e_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_2023/7u6e_26364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6e_26364/02_2023/7u6e_26364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6e_26364/02_2023/7u6e_26364_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6e_26364/02_2023/7u6e_26364_updated.pdb" } resolution = 3.0 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= 0.000 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 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-4877/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 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 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 chiralities: 3 Time building chain proxies: 5.06, per 1000 atoms: 0.63 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: 3.44 Conformation dependent library (CDL) restraints added in 1.1 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: 0.89 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: 2.32 Time building geometry restraints manager: 3.57 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=" 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 bond pdb=" C1 NAG F1002 " pdb=" O5 NAG F1002 " ideal model delta sigma weight residual 1.426 1.472 -0.046 3.20e-02 9.77e+02 2.03e+00 bond pdb=" CB CYS E 212 " pdb=" SG CYS E 212 " ideal model delta sigma weight residual 1.808 1.761 0.047 3.30e-02 9.18e+02 2.00e+00 bond pdb=" CB VAL E 117 " pdb=" CG1 VAL E 117 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.94e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.426 1.382 0.044 3.20e-02 9.77e+02 1.89e+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=" C1 NAG C 2 " pdb=" O5 NAG C 2 " pdb=" C5 NAG C 2 " ideal model delta sigma weight residual 113.34 118.74 -5.40 1.74e+00 3.30e-01 9.62e+00 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 109.25 103.34 5.91 2.08e+00 2.31e-01 8.05e+00 ... (remaining 11074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 4458 17.44 - 34.89: 362 34.89 - 52.33: 81 52.33 - 69.77: 19 69.77 - 87.22: 12 Dihedral angle restraints: 4932 sinusoidal: 2096 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 4929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 996 0.079 - 0.157: 206 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 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. 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: 1.560 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: 5.420 Check model and map are aligned: 0.120 Process input model: 24.350 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 0.053 8187 Z= 0.541 Angle : 0.899 9.183 11079 Z= 0.498 Chirality : 0.061 0.394 1221 Planarity : 0.008 0.098 1416 Dihedral : 14.055 87.215 3030 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 % 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 *********************** 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 : 0.989 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 198 average time/residue: 1.2031 time to fit residues: 252.2560 Evaluate side-chains 94 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.2386 time to fit residues: 1.6313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.7400 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 8187 Z= 0.311 Angle : 0.740 12.372 11079 Z= 0.392 Chirality : 0.050 0.370 1221 Planarity : 0.004 0.047 1416 Dihedral : 6.549 40.149 1112 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 3.97 % 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: -0.68 (0.38), residues: 176 sheet: -0.98 (0.41), residues: 165 loop : -1.44 (0.22), residues: 613 *********************** 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 140 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 105 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 7 residues processed: 127 average time/residue: 0.9418 time to fit residues: 129.1249 Evaluate side-chains 97 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 0.1621 time to fit residues: 2.4245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 0.0170 chunk 26 optimal weight: 0.0370 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 84 optimal weight: 0.0010 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 overall best weight: 0.3102 ------------------------------------------------------------------------------- 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 E 348 ASN ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8187 Z= 0.211 Angle : 0.642 6.513 11079 Z= 0.337 Chirality : 0.046 0.322 1221 Planarity : 0.004 0.040 1416 Dihedral : 6.052 37.556 1112 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 3.63 % 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: -1.56 (0.25), residues: 954 helix: -0.32 (0.40), residues: 170 sheet: -0.79 (0.41), residues: 175 loop : -1.35 (0.23), residues: 609 *********************** 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 124 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 9 residues processed: 113 average time/residue: 0.9956 time to fit residues: 121.3061 Evaluate side-chains 90 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.1321 time to fit residues: 1.9469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.0470 chunk 64 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 57 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 ** 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: 0.7387 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 8187 Z= 0.236 Angle : 0.625 7.331 11079 Z= 0.326 Chirality : 0.046 0.333 1221 Planarity : 0.004 0.042 1416 Dihedral : 5.753 34.525 1112 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 3.63 % 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: -1.58 (0.25), residues: 954 helix: -0.34 (0.40), residues: 166 sheet: -0.83 (0.41), residues: 169 loop : -1.35 (0.23), residues: 619 *********************** 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 119 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 87 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 13 residues processed: 105 average time/residue: 0.9609 time to fit residues: 109.1596 Evaluate side-chains 92 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.1465 time to fit residues: 2.3668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 0 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7441 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 8187 Z= 0.318 Angle : 0.664 9.942 11079 Z= 0.342 Chirality : 0.047 0.347 1221 Planarity : 0.004 0.049 1416 Dihedral : 5.883 34.114 1112 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 3.63 % 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: -1.62 (0.26), residues: 954 helix: -0.27 (0.40), residues: 169 sheet: -1.10 (0.42), residues: 159 loop : -1.34 (0.23), residues: 626 *********************** 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 118 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 86 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 13 residues processed: 106 average time/residue: 1.0745 time to fit residues: 122.9609 Evaluate side-chains 96 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.2186 time to fit residues: 2.4101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7434 moved from start: 0.3779 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= 0.270 Angle : 0.632 10.222 11079 Z= 0.329 Chirality : 0.046 0.331 1221 Planarity : 0.004 0.052 1416 Dihedral : 5.813 33.622 1112 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 3.29 % 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: -1.70 (0.25), residues: 954 helix: -0.30 (0.41), residues: 165 sheet: -1.20 (0.42), residues: 157 loop : -1.38 (0.22), residues: 632 *********************** 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 113 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 84 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 105 average time/residue: 1.0185 time to fit residues: 115.0705 Evaluate side-chains 92 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.2292 time to fit residues: 1.7791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 0.0270 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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: 0.7429 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 8187 Z= 0.250 Angle : 0.621 10.694 11079 Z= 0.321 Chirality : 0.046 0.315 1221 Planarity : 0.004 0.050 1416 Dihedral : 5.706 33.244 1112 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 3.29 % 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: -1.66 (0.26), residues: 954 helix: -0.19 (0.42), residues: 165 sheet: -1.22 (0.42), residues: 157 loop : -1.36 (0.23), residues: 632 *********************** 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 116 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 87 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 110 average time/residue: 1.0819 time to fit residues: 127.9203 Evaluate side-chains 91 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.1775 time to fit residues: 2.0398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 86 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.1980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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: 0.7419 moved from start: 0.4042 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= 0.226 Angle : 0.646 11.299 11079 Z= 0.331 Chirality : 0.045 0.320 1221 Planarity : 0.004 0.076 1416 Dihedral : 5.618 32.179 1112 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 2.72 % 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: -1.64 (0.26), residues: 954 helix: -0.15 (0.42), residues: 165 sheet: -1.23 (0.42), residues: 157 loop : -1.36 (0.23), residues: 632 *********************** 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 109 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 104 average time/residue: 1.1123 time to fit residues: 123.9299 Evaluate side-chains 95 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.2297 time to fit residues: 1.9108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 66 optimal weight: 0.0670 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 ** E 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 8187 Z= 0.275 Angle : 0.687 13.411 11079 Z= 0.351 Chirality : 0.047 0.317 1221 Planarity : 0.004 0.062 1416 Dihedral : 5.651 31.233 1112 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 2.38 % 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: -1.70 (0.26), residues: 954 helix: -0.17 (0.42), residues: 165 sheet: -1.27 (0.42), residues: 157 loop : -1.41 (0.23), residues: 632 *********************** 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 104 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 101 average time/residue: 1.1677 time to fit residues: 126.3848 Evaluate side-chains 96 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.2491 time to fit residues: 2.0511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 74 optimal weight: 0.0670 chunk 7 optimal weight: 0.3980 chunk 57 optimal weight: 0.0970 chunk 45 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 22 optimal weight: 0.0470 overall best weight: 0.1392 ------------------------------------------------------------------------------- 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: 0.7361 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8187 Z= 0.177 Angle : 0.631 12.570 11079 Z= 0.321 Chirality : 0.045 0.339 1221 Planarity : 0.004 0.089 1416 Dihedral : 5.338 30.822 1112 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 1.70 % 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: -1.51 (0.26), residues: 954 helix: -0.02 (0.42), residues: 164 sheet: -1.02 (0.43), residues: 157 loop : -1.31 (0.23), residues: 633 ********************** 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 107 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 105 average time/residue: 1.0196 time to fit residues: 115.3381 Evaluate side-chains 92 residues out of total 881 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1458 time to fit residues: 1.5463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 20 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 4 optimal weight: 0.0770 chunk 53 optimal weight: 0.6980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 ** E 417 HIS ** 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 = 0.4423 r_free = 0.4423 target = 0.160241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.143797 restraints weight = 12721.285| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.02 r_work: 0.4116 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3984 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 8187 Z= 0.246 Angle : 0.681 14.407 11079 Z= 0.349 Chirality : 0.046 0.325 1221 Planarity : 0.004 0.062 1416 Dihedral : 5.394 30.784 1112 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 1.93 % 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: -1.61 (0.25), residues: 954 helix: -0.24 (0.40), residues: 165 sheet: -1.10 (0.42), residues: 157 loop : -1.33 (0.23), residues: 632 =============================================================================== Job complete usr+sys time: 3008.21 seconds wall clock time: 54 minutes 33.51 seconds (3273.51 seconds total)