Starting phenix.real_space_refine on Sun Feb 18 12:57:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh2_12186/02_2024/7bh2_12186_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh2_12186/02_2024/7bh2_12186.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/7bh2_12186/02_2024/7bh2_12186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh2_12186/02_2024/7bh2_12186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh2_12186/02_2024/7bh2_12186_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh2_12186/02_2024/7bh2_12186_trim_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= 0.026 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: 10 Type Number sf(0) Gaussians K 2 8.98 5 P 1 5.49 5 Mg 1 5.21 5 S 62 5.16 5 Be 1 3.05 5 C 7004 2.51 5 N 1824 2.21 5 O 1979 1.98 5 F 3 1.80 5 H 11172 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 425": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 461": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 572": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 180": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22049 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8444 Classifications: {'peptide': 557} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 10201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 10201 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 647} Chain: "C" Number of atoms: 2879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2879 Classifications: {'peptide': 190} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 430 Classifications: {'peptide': 29} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 28} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 1, '9Y0': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 9.87, per 1000 atoms: 0.45 Number of scatterers: 22049 At special positions: 0 Unit cell: (75.53, 99.268, 176.956, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) K 2 19.00 S 62 16.00 P 1 15.00 Mg 1 11.99 F 3 9.00 O 1979 8.00 N 1824 7.00 C 7004 6.00 Be 1 4.00 H 11172 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.14 Conformation dependent library (CDL) restraints added in 2.4 seconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 8 sheets defined 55.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 Proline residue: A 22 - end of helix removed outlier: 3.821A pdb=" N SER A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 128 through 131 No H-bonds generated for 'chain 'A' and resid 128 through 131' Processing helix chain 'A' and resid 133 through 156 removed outlier: 3.540A pdb=" N ILE A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 192 removed outlier: 4.295A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 249 through 273 removed outlier: 3.652A pdb=" N PHE A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 278 through 304 removed outlier: 3.837A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 312 No H-bonds generated for 'chain 'A' and resid 309 through 312' Processing helix chain 'A' and resid 330 through 341 Processing helix chain 'A' and resid 356 through 367 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 378 through 398 Processing helix chain 'A' and resid 411 through 437 removed outlier: 4.623A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.527A pdb=" N ALA A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 507 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 524 through 548 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'B' and resid 11 through 25 Processing helix chain 'B' and resid 27 through 32 removed outlier: 5.587A pdb=" N ARG B 32 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 54 Processing helix chain 'B' and resid 62 through 87 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 216 through 245 removed outlier: 4.446A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 285 removed outlier: 4.153A pdb=" N LEU B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 398 through 408 Processing helix chain 'B' and resid 415 through 426 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 496 through 508 Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 555 through 594 removed outlier: 3.934A pdb=" N LEU B 558 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE B 559 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL B 562 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 571 " --> pdb=" O MET B 568 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 575 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 585 " --> pdb=" O ASN B 582 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 587 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE B 591 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 613 through 637 removed outlier: 4.197A pdb=" N ILE B 632 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Proline residue: B 633 - end of helix removed outlier: 3.605A pdb=" N LYS B 637 " --> pdb=" O PRO B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 679 removed outlier: 3.654A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 4 through 19 Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 92 through 108 removed outlier: 3.575A pdb=" N ALA C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 No H-bonds generated for 'chain 'C' and resid 118 through 121' Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'D' and resid 4 through 24 Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'B' and resid 106 through 108 Processing sheet with id= C, first strand: chain 'B' and resid 131 through 134 Processing sheet with id= D, first strand: chain 'B' and resid 151 through 153 Processing sheet with id= E, first strand: chain 'B' and resid 287 through 289 Processing sheet with id= F, first strand: chain 'B' and resid 321 through 323 removed outlier: 4.115A pdb=" N GLU B 321 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 373 through 375 Processing sheet with id= H, first strand: chain 'C' and resid 42 through 44 removed outlier: 4.098A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1575 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: 7.82 Time building geometry restraints manager: 18.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 11160 1.01 - 1.21: 14 1.21 - 1.41: 4309 1.41 - 1.61: 6635 1.61 - 1.81: 114 Bond restraints: 22232 Sorted by residual: bond pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " ideal model delta sigma weight residual 1.333 1.537 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" ND2 ASN B 624 " pdb="HD21 ASN B 624 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN B 624 " pdb="HD22 ASN B 624 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" BE BEF B 803 " pdb=" F3 BEF B 803 " ideal model delta sigma weight residual 1.476 1.363 0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" BE BEF B 803 " pdb=" F2 BEF B 803 " ideal model delta sigma weight residual 1.476 1.365 0.111 2.00e-02 2.50e+03 3.08e+01 ... (remaining 22227 not shown) Histogram of bond angle deviations from ideal: 94.29 - 105.05: 234 105.05 - 115.82: 28965 115.82 - 126.59: 10940 126.59 - 137.35: 157 137.35 - 148.12: 1 Bond angle restraints: 40297 Sorted by residual: angle pdb=" CD GLN B 528 " pdb=" NE2 GLN B 528 " pdb="HE22 GLN B 528 " ideal model delta sigma weight residual 120.00 148.12 -28.12 3.00e+00 1.11e-01 8.78e+01 angle pdb="HE21 GLN B 528 " pdb=" NE2 GLN B 528 " pdb="HE22 GLN B 528 " ideal model delta sigma weight residual 120.00 94.29 25.71 3.00e+00 1.11e-01 7.35e+01 angle pdb=" CD GLN B 528 " pdb=" NE2 GLN B 528 " pdb="HE21 GLN B 528 " ideal model delta sigma weight residual 120.00 96.55 23.45 3.00e+00 1.11e-01 6.11e+01 angle pdb=" C12 9Y0 B 801 " pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " ideal model delta sigma weight residual 127.16 112.40 14.76 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " pdb=" C15 9Y0 B 801 " ideal model delta sigma weight residual 127.64 113.67 13.97 3.00e+00 1.11e-01 2.17e+01 ... (remaining 40292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.37: 10046 34.37 - 68.73: 347 68.73 - 103.10: 9 103.10 - 137.46: 2 137.46 - 171.83: 1 Dihedral angle restraints: 10405 sinusoidal: 5729 harmonic: 4676 Sorted by residual: dihedral pdb=" N 9Y0 B 801 " pdb=" C3 9Y0 B 801 " pdb=" C4 9Y0 B 801 " pdb=" O1 9Y0 B 801 " ideal model delta sinusoidal sigma weight residual 297.35 125.52 171.83 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " pdb=" C15 9Y0 B 801 " pdb=" C16 9Y0 B 801 " ideal model delta sinusoidal sigma weight residual 127.88 -8.28 136.16 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" CA LEU A 124 " pdb=" C LEU A 124 " pdb=" N SER A 125 " pdb=" CA SER A 125 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 10402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1240 0.045 - 0.089: 440 0.089 - 0.134: 109 0.134 - 0.179: 15 0.179 - 0.223: 3 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CB THR B 677 " pdb=" CA THR B 677 " pdb=" OG1 THR B 677 " pdb=" CG2 THR B 677 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB ILE B 388 " pdb=" CA ILE B 388 " pdb=" CG1 ILE B 388 " pdb=" CG2 ILE B 388 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CA PHE A 543 " pdb=" N PHE A 543 " pdb=" C PHE A 543 " pdb=" CB PHE A 543 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 1804 not shown) Planarity restraints: 3285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 9Y0 B 801 " 0.148 2.00e-02 2.50e+03 3.29e-01 1.08e+03 pdb=" C13 9Y0 B 801 " -0.431 2.00e-02 2.50e+03 pdb=" C14 9Y0 B 801 " 0.446 2.00e-02 2.50e+03 pdb=" C15 9Y0 B 801 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 528 " -0.050 2.00e-02 2.50e+03 9.01e-02 1.22e+02 pdb=" CD GLN B 528 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN B 528 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 GLN B 528 " 0.155 2.00e-02 2.50e+03 pdb="HE21 GLN B 528 " 0.037 2.00e-02 2.50e+03 pdb="HE22 GLN B 528 " -0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 408 " -0.040 2.00e-02 2.50e+03 6.64e-02 6.61e+01 pdb=" CG ASN B 408 " 0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN B 408 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 408 " -0.111 2.00e-02 2.50e+03 pdb="HD21 ASN B 408 " -0.009 2.00e-02 2.50e+03 pdb="HD22 ASN B 408 " 0.074 2.00e-02 2.50e+03 ... (remaining 3282 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.32: 5739 2.32 - 3.02: 61462 3.02 - 3.73: 80564 3.73 - 4.43: 126531 4.43 - 5.14: 198954 Nonbonded interactions: 473250 Sorted by model distance: nonbonded pdb=" O ASP B 329 " pdb=" H THR B 332 " model vdw 1.614 1.850 nonbonded pdb="HH22 ARG B 281 " pdb=" OE1 GLN B 567 " model vdw 1.619 1.850 nonbonded pdb="HH12 ARG B 475 " pdb=" OE1 GLU B 493 " model vdw 1.644 1.850 nonbonded pdb=" O VAL A 329 " pdb=" HG SER A 333 " model vdw 1.653 1.850 nonbonded pdb=" OD1 ASN B 387 " pdb="HH12 ARG B 394 " model vdw 1.679 1.850 ... (remaining 473245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.660 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: 0.330 Extract box with map and model: 8.140 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 74.360 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 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 : 0.009 0.204 11060 Z= 0.569 Angle : 0.852 14.760 15039 Z= 0.444 Chirality : 0.048 0.223 1807 Planarity : 0.010 0.329 1906 Dihedral : 13.527 171.828 3952 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.18 % Allowed : 8.55 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.19), residues: 1442 helix: -0.73 (0.16), residues: 844 sheet: -3.92 (0.37), residues: 106 loop : -3.16 (0.23), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 240 HIS 0.004 0.001 HIS A 242 PHE 0.033 0.003 PHE A 109 TYR 0.026 0.003 TYR B 657 ARG 0.007 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.7302 (mmt) cc_final: 0.6908 (mpt) REVERT: A 55 ARG cc_start: 0.7229 (ttp-110) cc_final: 0.6141 (ptt-90) REVERT: A 112 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8113 (t0) REVERT: A 116 ARG cc_start: 0.7806 (mtp-110) cc_final: 0.7320 (ptm-80) REVERT: A 205 ASN cc_start: 0.7642 (p0) cc_final: 0.7131 (p0) REVERT: A 274 MET cc_start: 0.8441 (mmt) cc_final: 0.8197 (mmt) REVERT: A 408 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8371 (tttm) REVERT: B 138 ASP cc_start: 0.7451 (m-30) cc_final: 0.7040 (t70) REVERT: B 302 ASP cc_start: 0.7756 (m-30) cc_final: 0.7540 (m-30) REVERT: B 321 GLU cc_start: 0.6462 (mt-10) cc_final: 0.5769 (pt0) REVERT: B 331 LYS cc_start: 0.7665 (tttt) cc_final: 0.7199 (ttpp) REVERT: B 383 MET cc_start: 0.8766 (ptp) cc_final: 0.8529 (ptt) REVERT: B 679 CYS cc_start: 0.7015 (m) cc_final: 0.6728 (m) REVERT: C 164 GLN cc_start: 0.8083 (tp-100) cc_final: 0.7609 (mt0) REVERT: C 169 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8259 (mptt) REVERT: C 190 GLU cc_start: 0.6955 (mp0) cc_final: 0.6722 (mm-30) REVERT: D 1 MET cc_start: 0.5471 (mtm) cc_final: 0.4895 (mtm) outliers start: 2 outliers final: 1 residues processed: 138 average time/residue: 2.4589 time to fit residues: 369.7034 Evaluate side-chains 110 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 112 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.0770 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 0.0980 chunk 68 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 129 optimal weight: 0.0370 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN A 252 ASN B 408 ASN B 426 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11060 Z= 0.159 Angle : 0.534 4.964 15039 Z= 0.282 Chirality : 0.037 0.140 1807 Planarity : 0.005 0.063 1906 Dihedral : 8.822 139.987 1573 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.97 % Allowed : 10.66 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1442 helix: 0.46 (0.17), residues: 847 sheet: -3.39 (0.40), residues: 106 loop : -2.35 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.003 0.001 HIS B 404 PHE 0.013 0.001 PHE A 109 TYR 0.021 0.001 TYR A 381 ARG 0.003 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.7184 (mmt) cc_final: 0.6968 (mpt) REVERT: A 55 ARG cc_start: 0.7218 (ttp-110) cc_final: 0.6169 (ptt-90) REVERT: A 205 ASN cc_start: 0.7305 (p0) cc_final: 0.6880 (p0) REVERT: A 274 MET cc_start: 0.8364 (mmt) cc_final: 0.8137 (mmt) REVERT: A 408 LYS cc_start: 0.8684 (ttpt) cc_final: 0.8409 (tttm) REVERT: B 102 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8103 (ttmm) REVERT: B 138 ASP cc_start: 0.7284 (m-30) cc_final: 0.6846 (t0) REVERT: B 265 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7932 (m) REVERT: B 321 GLU cc_start: 0.5882 (mt-10) cc_final: 0.5138 (pt0) REVERT: B 331 LYS cc_start: 0.7666 (tttt) cc_final: 0.7196 (ttpp) REVERT: B 383 MET cc_start: 0.8644 (ptp) cc_final: 0.8406 (ptt) REVERT: B 438 ARG cc_start: 0.7290 (ptt180) cc_final: 0.7038 (ptt90) REVERT: B 655 TRP cc_start: 0.7325 (m100) cc_final: 0.6871 (t-100) REVERT: C 164 GLN cc_start: 0.8004 (tp-100) cc_final: 0.7591 (mt0) REVERT: C 169 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8212 (mptt) REVERT: D 1 MET cc_start: 0.5338 (mtm) cc_final: 0.4840 (mtm) outliers start: 11 outliers final: 6 residues processed: 127 average time/residue: 2.2460 time to fit residues: 313.9401 Evaluate side-chains 115 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain C residue 149 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 0.0370 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS B 426 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11060 Z= 0.200 Angle : 0.511 5.407 15039 Z= 0.269 Chirality : 0.038 0.144 1807 Planarity : 0.004 0.050 1906 Dihedral : 7.984 89.999 1571 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.23 % Allowed : 11.28 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1442 helix: 0.80 (0.17), residues: 847 sheet: -3.02 (0.43), residues: 106 loop : -2.15 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 71 HIS 0.003 0.001 HIS A 85 PHE 0.015 0.001 PHE A 109 TYR 0.023 0.001 TYR A 381 ARG 0.008 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7209 (ttp-110) cc_final: 0.6049 (ptt-90) REVERT: A 205 ASN cc_start: 0.7369 (p0) cc_final: 0.6953 (p0) REVERT: A 274 MET cc_start: 0.8316 (mmt) cc_final: 0.8083 (mmt) REVERT: A 408 LYS cc_start: 0.8677 (ttpt) cc_final: 0.8395 (tttm) REVERT: B 102 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8125 (ttmm) REVERT: B 138 ASP cc_start: 0.7341 (m-30) cc_final: 0.6887 (t0) REVERT: B 321 GLU cc_start: 0.5925 (mt-10) cc_final: 0.5361 (pt0) REVERT: B 331 LYS cc_start: 0.7671 (tttt) cc_final: 0.7210 (ttpp) REVERT: B 438 ARG cc_start: 0.7368 (ptt180) cc_final: 0.7151 (ptt90) REVERT: C 164 GLN cc_start: 0.8005 (tp-100) cc_final: 0.7600 (mt0) REVERT: C 169 LYS cc_start: 0.8658 (ttmm) cc_final: 0.8206 (mptt) REVERT: D 1 MET cc_start: 0.5351 (mtm) cc_final: 0.4840 (mtm) outliers start: 14 outliers final: 11 residues processed: 117 average time/residue: 2.2668 time to fit residues: 292.8559 Evaluate side-chains 117 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 149 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 37 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: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11060 Z= 0.227 Angle : 0.505 5.258 15039 Z= 0.266 Chirality : 0.038 0.140 1807 Planarity : 0.004 0.047 1906 Dihedral : 7.402 76.300 1571 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.15 % Allowed : 11.45 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1442 helix: 0.97 (0.18), residues: 839 sheet: -2.91 (0.45), residues: 106 loop : -2.02 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 71 HIS 0.003 0.001 HIS A 85 PHE 0.014 0.001 PHE A 109 TYR 0.021 0.001 TYR A 381 ARG 0.007 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7175 (ttp-110) cc_final: 0.6013 (ptt-90) REVERT: A 205 ASN cc_start: 0.7368 (p0) cc_final: 0.6986 (p0) REVERT: A 274 MET cc_start: 0.8409 (mmt) cc_final: 0.8168 (mmt) REVERT: A 408 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8390 (tttm) REVERT: B 102 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8137 (ttmm) REVERT: B 138 ASP cc_start: 0.7299 (m-30) cc_final: 0.6920 (t0) REVERT: B 321 GLU cc_start: 0.5901 (mt-10) cc_final: 0.5326 (pt0) REVERT: B 331 LYS cc_start: 0.7673 (tttt) cc_final: 0.7211 (ttpp) REVERT: B 438 ARG cc_start: 0.7333 (ppt170) cc_final: 0.7122 (ptt90) REVERT: C 164 GLN cc_start: 0.8032 (tp-100) cc_final: 0.7599 (mt0) REVERT: C 169 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8205 (mptt) REVERT: D 1 MET cc_start: 0.5355 (mtm) cc_final: 0.4838 (mtm) outliers start: 13 outliers final: 10 residues processed: 114 average time/residue: 2.3339 time to fit residues: 292.1312 Evaluate side-chains 116 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 149 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 124 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11060 Z= 0.249 Angle : 0.512 5.403 15039 Z= 0.269 Chirality : 0.038 0.140 1807 Planarity : 0.004 0.043 1906 Dihedral : 7.092 74.831 1569 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.32 % Allowed : 11.98 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1442 helix: 0.99 (0.18), residues: 848 sheet: -2.83 (0.45), residues: 106 loop : -1.97 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 59 HIS 0.003 0.001 HIS A 85 PHE 0.013 0.001 PHE A 109 TYR 0.022 0.001 TYR A 381 ARG 0.003 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7155 (ttp-110) cc_final: 0.5989 (ptt-90) REVERT: A 205 ASN cc_start: 0.7401 (p0) cc_final: 0.7003 (p0) REVERT: A 274 MET cc_start: 0.8403 (mmt) cc_final: 0.8113 (mmt) REVERT: A 408 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8405 (tttm) REVERT: B 102 LYS cc_start: 0.8478 (ttmt) cc_final: 0.8123 (ttmm) REVERT: B 138 ASP cc_start: 0.7319 (m-30) cc_final: 0.6947 (t0) REVERT: B 321 GLU cc_start: 0.5929 (mt-10) cc_final: 0.5344 (pt0) REVERT: B 331 LYS cc_start: 0.7648 (tttt) cc_final: 0.7180 (ttpp) REVERT: C 164 GLN cc_start: 0.8091 (tp-100) cc_final: 0.7616 (mt0) REVERT: C 169 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8204 (mptt) REVERT: D 1 MET cc_start: 0.5362 (mtm) cc_final: 0.4844 (mtm) outliers start: 15 outliers final: 13 residues processed: 112 average time/residue: 2.3413 time to fit residues: 287.7723 Evaluate side-chains 118 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 149 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN B 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11060 Z= 0.208 Angle : 0.494 5.186 15039 Z= 0.259 Chirality : 0.038 0.139 1807 Planarity : 0.004 0.043 1906 Dihedral : 6.663 72.827 1569 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.32 % Allowed : 12.42 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1442 helix: 1.11 (0.18), residues: 847 sheet: -2.70 (0.46), residues: 106 loop : -1.87 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 31 HIS 0.003 0.001 HIS A 85 PHE 0.012 0.001 PHE B 64 TYR 0.021 0.001 TYR A 381 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7146 (ttp-110) cc_final: 0.6085 (ptt90) REVERT: A 205 ASN cc_start: 0.7350 (p0) cc_final: 0.6959 (p0) REVERT: A 274 MET cc_start: 0.8380 (mmt) cc_final: 0.8116 (mmt) REVERT: A 408 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8431 (tttm) REVERT: A 557 SER cc_start: 0.8321 (t) cc_final: 0.7945 (p) REVERT: B 102 LYS cc_start: 0.8462 (ttmt) cc_final: 0.8117 (ttmm) REVERT: B 138 ASP cc_start: 0.7281 (m-30) cc_final: 0.6924 (t0) REVERT: B 321 GLU cc_start: 0.5908 (mt-10) cc_final: 0.5325 (pt0) REVERT: B 331 LYS cc_start: 0.7641 (tttt) cc_final: 0.7172 (ttpp) REVERT: C 164 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7533 (mt0) REVERT: C 169 LYS cc_start: 0.8644 (ttmm) cc_final: 0.8192 (mptt) REVERT: D 1 MET cc_start: 0.5226 (mtm) cc_final: 0.4689 (mtm) outliers start: 15 outliers final: 10 residues processed: 116 average time/residue: 2.3048 time to fit residues: 297.2488 Evaluate side-chains 115 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain C residue 111 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11060 Z= 0.260 Angle : 0.511 5.440 15039 Z= 0.268 Chirality : 0.038 0.140 1807 Planarity : 0.004 0.065 1906 Dihedral : 6.575 73.749 1569 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.50 % Allowed : 12.16 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.22), residues: 1442 helix: 1.08 (0.18), residues: 849 sheet: -2.68 (0.46), residues: 106 loop : -1.88 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 31 HIS 0.003 0.001 HIS A 85 PHE 0.012 0.001 PHE A 109 TYR 0.022 0.002 TYR A 381 ARG 0.010 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7109 (ttp-110) cc_final: 0.5991 (ptt90) REVERT: A 205 ASN cc_start: 0.7427 (p0) cc_final: 0.7013 (p0) REVERT: A 274 MET cc_start: 0.8398 (mmt) cc_final: 0.8135 (mmt) REVERT: A 557 SER cc_start: 0.8338 (t) cc_final: 0.7955 (p) REVERT: B 102 LYS cc_start: 0.8572 (ttmt) cc_final: 0.8218 (ttmm) REVERT: B 138 ASP cc_start: 0.7319 (m-30) cc_final: 0.6953 (t0) REVERT: B 321 GLU cc_start: 0.5930 (mt-10) cc_final: 0.5337 (pt0) REVERT: B 331 LYS cc_start: 0.7630 (tttt) cc_final: 0.7153 (ttpp) REVERT: C 164 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7508 (mt0) REVERT: C 169 LYS cc_start: 0.8652 (ttmm) cc_final: 0.8214 (mptt) REVERT: D 1 MET cc_start: 0.5234 (mtm) cc_final: 0.4694 (mtm) outliers start: 17 outliers final: 13 residues processed: 116 average time/residue: 2.1235 time to fit residues: 272.3318 Evaluate side-chains 117 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 111 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 0.0770 chunk 93 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11060 Z= 0.185 Angle : 0.487 5.178 15039 Z= 0.254 Chirality : 0.037 0.138 1807 Planarity : 0.004 0.065 1906 Dihedral : 6.371 71.685 1569 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.23 % Allowed : 12.86 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1442 helix: 1.23 (0.18), residues: 848 sheet: -2.54 (0.47), residues: 106 loop : -1.79 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 31 HIS 0.003 0.000 HIS A 85 PHE 0.011 0.001 PHE A 109 TYR 0.021 0.001 TYR A 381 ARG 0.010 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7103 (ttp-110) cc_final: 0.6060 (ptt90) REVERT: A 205 ASN cc_start: 0.7332 (p0) cc_final: 0.6936 (p0) REVERT: A 274 MET cc_start: 0.8364 (mmt) cc_final: 0.8116 (mmt) REVERT: A 557 SER cc_start: 0.8320 (t) cc_final: 0.7938 (p) REVERT: B 102 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8209 (ttmm) REVERT: B 138 ASP cc_start: 0.7277 (m-30) cc_final: 0.6939 (t0) REVERT: B 321 GLU cc_start: 0.5903 (mt-10) cc_final: 0.5320 (pt0) REVERT: B 331 LYS cc_start: 0.7602 (tttt) cc_final: 0.7111 (ttpp) REVERT: B 383 MET cc_start: 0.8052 (ptt) cc_final: 0.7802 (ptt) REVERT: C 164 GLN cc_start: 0.8119 (tp-100) cc_final: 0.7499 (mt0) REVERT: C 169 LYS cc_start: 0.8625 (ttmm) cc_final: 0.8198 (mppt) REVERT: D 1 MET cc_start: 0.5240 (mtm) cc_final: 0.4663 (mtm) outliers start: 14 outliers final: 11 residues processed: 118 average time/residue: 2.0995 time to fit residues: 274.9597 Evaluate side-chains 115 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 111 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11060 Z= 0.225 Angle : 0.501 5.351 15039 Z= 0.262 Chirality : 0.038 0.138 1807 Planarity : 0.004 0.073 1906 Dihedral : 6.361 72.310 1569 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.32 % Allowed : 13.13 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1442 helix: 1.20 (0.18), residues: 851 sheet: -2.49 (0.47), residues: 106 loop : -1.87 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 31 HIS 0.003 0.001 HIS A 85 PHE 0.011 0.001 PHE B 64 TYR 0.021 0.001 TYR A 381 ARG 0.011 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7107 (ttp-110) cc_final: 0.6062 (ptt90) REVERT: A 205 ASN cc_start: 0.7386 (p0) cc_final: 0.6977 (p0) REVERT: A 274 MET cc_start: 0.8424 (mmt) cc_final: 0.8192 (mmt) REVERT: A 557 SER cc_start: 0.8315 (t) cc_final: 0.7922 (p) REVERT: B 102 LYS cc_start: 0.8583 (ttmt) cc_final: 0.8213 (ttmm) REVERT: B 138 ASP cc_start: 0.7296 (m-30) cc_final: 0.6952 (t0) REVERT: B 321 GLU cc_start: 0.5930 (mt-10) cc_final: 0.5313 (pt0) REVERT: B 331 LYS cc_start: 0.7608 (tttt) cc_final: 0.7115 (ttpp) REVERT: B 383 MET cc_start: 0.8082 (ptt) cc_final: 0.7822 (ptt) REVERT: B 515 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7298 (ttt) REVERT: C 164 GLN cc_start: 0.8105 (tp-100) cc_final: 0.7506 (mt0) REVERT: C 169 LYS cc_start: 0.8644 (ttmm) cc_final: 0.8204 (mptt) REVERT: D 1 MET cc_start: 0.5243 (mtm) cc_final: 0.4663 (mtm) outliers start: 15 outliers final: 11 residues processed: 114 average time/residue: 2.1353 time to fit residues: 269.0758 Evaluate side-chains 115 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 131 optimal weight: 0.3980 chunk 113 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11060 Z= 0.188 Angle : 0.489 5.215 15039 Z= 0.254 Chirality : 0.037 0.138 1807 Planarity : 0.004 0.074 1906 Dihedral : 6.245 71.393 1569 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.06 % Allowed : 13.39 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1442 helix: 1.28 (0.18), residues: 853 sheet: -2.40 (0.47), residues: 106 loop : -1.80 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 31 HIS 0.003 0.000 HIS A 85 PHE 0.011 0.001 PHE B 64 TYR 0.021 0.001 TYR A 381 ARG 0.013 0.000 ARG A 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.575 Fit side-chains revert: symmetry clash REVERT: A 55 ARG cc_start: 0.7123 (ttp-110) cc_final: 0.6063 (ptt90) REVERT: A 205 ASN cc_start: 0.7376 (p0) cc_final: 0.6960 (p0) REVERT: A 274 MET cc_start: 0.8418 (mmt) cc_final: 0.8197 (mmt) REVERT: A 557 SER cc_start: 0.8335 (t) cc_final: 0.7918 (p) REVERT: B 102 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8222 (ttmm) REVERT: B 138 ASP cc_start: 0.7267 (m-30) cc_final: 0.6937 (t0) REVERT: B 321 GLU cc_start: 0.5914 (mt-10) cc_final: 0.5302 (pt0) REVERT: B 331 LYS cc_start: 0.7600 (tttt) cc_final: 0.7109 (ttpp) REVERT: B 383 MET cc_start: 0.8047 (ptt) cc_final: 0.7791 (ptt) REVERT: C 164 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7525 (mt0) REVERT: C 169 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8191 (mptt) REVERT: D 1 MET cc_start: 0.5238 (mtm) cc_final: 0.4659 (mtm) outliers start: 12 outliers final: 10 residues processed: 113 average time/residue: 2.1505 time to fit residues: 269.3800 Evaluate side-chains 114 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 194 ASN Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.121692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.089873 restraints weight = 37861.837| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.12 r_work: 0.2932 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11060 Z= 0.212 Angle : 0.498 5.318 15039 Z= 0.259 Chirality : 0.038 0.137 1807 Planarity : 0.004 0.058 1906 Dihedral : 6.238 71.919 1569 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.97 % Allowed : 13.57 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1442 helix: 1.28 (0.18), residues: 853 sheet: -2.35 (0.48), residues: 106 loop : -1.82 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 31 HIS 0.003 0.001 HIS A 85 PHE 0.011 0.001 PHE B 64 TYR 0.021 0.001 TYR A 381 ARG 0.009 0.000 ARG A 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6718.88 seconds wall clock time: 118 minutes 41.47 seconds (7121.47 seconds total)