Starting phenix.real_space_refine on Fri Mar 15 01:51:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/03_2024/7oto_13063_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/03_2024/7oto_13063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/03_2024/7oto_13063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/03_2024/7oto_13063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/03_2024/7oto_13063_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oto_13063/03_2024/7oto_13063_updated.pdb" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.006 sd= 0.023 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 6472 2.51 5 N 1841 2.21 5 O 1961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 186": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B ARG 656": "NH1" <-> "NH2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 694": "OE1" <-> "OE2" Residue "B ARG 697": "NH1" <-> "NH2" Residue "B GLU 751": "OE1" <-> "OE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A ARG 108": "NH1" <-> "NH2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A GLU 540": "OE1" <-> "OE2" Residue "A GLU 646": "OE1" <-> "OE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A ARG 697": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10333 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4697 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 25, 'TRANS': 576} Chain breaks: 1 Chain: "A" Number of atoms: 5572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5572 Classifications: {'peptide': 711} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 679} Chain breaks: 3 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.15, per 1000 atoms: 0.60 Number of scatterers: 10333 At special positions: 0 Unit cell: (112.36, 121.9, 97.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 6 15.00 Mg 2 11.99 O 1961 8.00 N 1841 7.00 C 6472 6.00 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: 3.99 Conformation dependent library (CDL) restraints added in 1.9 seconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 10 sheets defined 48.7% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 187 through 190 Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 231 through 247 Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 318 through 330 Processing helix chain 'B' and resid 335 through 345 Proline residue: B 340 - end of helix Processing helix chain 'B' and resid 349 through 356 Processing helix chain 'B' and resid 362 through 384 Proline residue: B 376 - end of helix removed outlier: 3.811A pdb=" N THR B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 401 through 410 Processing helix chain 'B' and resid 431 through 440 Processing helix chain 'B' and resid 512 through 565 Proline residue: B 537 - end of helix removed outlier: 4.772A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ALA B 541 " --> pdb=" O PRO B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 591 removed outlier: 4.078A pdb=" N GLN B 590 " --> pdb=" O PRO B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 636 Processing helix chain 'B' and resid 669 through 683 Processing helix chain 'B' and resid 701 through 717 Processing helix chain 'B' and resid 732 through 738 Proline residue: B 736 - end of helix Processing helix chain 'B' and resid 772 through 779 Processing helix chain 'B' and resid 783 through 798 Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 41 through 51 removed outlier: 3.516A pdb=" N ALA A 47 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 removed outlier: 4.985A pdb=" N GLU A 77 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 231 through 248 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 318 through 331 Processing helix chain 'A' and resid 335 through 345 Proline residue: A 340 - end of helix removed outlier: 3.532A pdb=" N GLN A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 362 through 384 Proline residue: A 376 - end of helix removed outlier: 3.525A pdb=" N THR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 431 through 441 Processing helix chain 'A' and resid 513 through 565 Proline residue: A 537 - end of helix removed outlier: 4.953A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ALA A 541 " --> pdb=" O PRO A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 591 removed outlier: 3.808A pdb=" N GLN A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 636 removed outlier: 3.588A pdb=" N THR A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 683 Processing helix chain 'A' and resid 701 through 717 Processing helix chain 'A' and resid 730 through 738 Proline residue: A 736 - end of helix Processing helix chain 'A' and resid 772 through 779 Processing helix chain 'A' and resid 783 through 799 Processing sheet with id= A, first strand: chain 'B' and resid 132 through 138 removed outlier: 3.504A pdb=" N ARG B 154 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 178 through 181 Processing sheet with id= C, first strand: chain 'B' and resid 570 through 572 removed outlier: 6.683A pdb=" N VAL B 645 " --> pdb=" O THR B 571 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 644 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 762 through 764 removed outlier: 6.462A pdb=" N MET B 609 " --> pdb=" O ALA B 743 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL B 745 " --> pdb=" O MET B 609 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE B 611 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU B 747 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR B 613 " --> pdb=" O LEU B 747 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 723 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE B 612 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE B 725 " --> pdb=" O ILE B 612 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 749 through 751 Processing sheet with id= F, first strand: chain 'A' and resid 55 through 58 removed outlier: 5.224A pdb=" N PHE A 40 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU A 29 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 112 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU A 94 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL A 110 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.325A pdb=" N LEU A 178 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ARG A 199 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TYR A 180 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 181 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLN A 138 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 601 through 603 removed outlier: 3.565A pdb=" N LYS A 644 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 762 through 764 removed outlier: 6.316A pdb=" N MET A 609 " --> pdb=" O ALA A 743 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL A 745 " --> pdb=" O MET A 609 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE A 611 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU A 747 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR A 723 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE A 612 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE A 725 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 749 through 752 498 hydrogen bonds defined for protein. 1398 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: 2.97 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1765 1.31 - 1.44: 2562 1.44 - 1.57: 6071 1.57 - 1.69: 10 1.69 - 1.82: 91 Bond restraints: 10499 Sorted by residual: bond pdb=" N3B ANP A1002 " pdb=" PG ANP A1002 " ideal model delta sigma weight residual 1.795 1.620 0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" N3B ANP B1002 " pdb=" PG ANP B1002 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.68e+01 bond pdb=" O3A ANP B1002 " pdb=" PB ANP B1002 " ideal model delta sigma weight residual 1.700 1.596 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O3A ANP A1002 " pdb=" PB ANP A1002 " ideal model delta sigma weight residual 1.700 1.600 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ILE A 66 " pdb=" CA ILE A 66 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.70e-03 1.69e+04 2.07e+01 ... (remaining 10494 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.08: 348 106.08 - 113.14: 5052 113.14 - 120.20: 5078 120.20 - 127.26: 3683 127.26 - 134.32: 66 Bond angle restraints: 14227 Sorted by residual: angle pdb=" CA GLY B 422 " pdb=" C GLY B 422 " pdb=" O GLY B 422 " ideal model delta sigma weight residual 122.45 117.11 5.34 7.20e-01 1.93e+00 5.50e+01 angle pdb=" CA PHE A 725 " pdb=" CB PHE A 725 " pdb=" CG PHE A 725 " ideal model delta sigma weight residual 113.80 120.50 -6.70 1.00e+00 1.00e+00 4.49e+01 angle pdb=" N PRO A 25 " pdb=" CA PRO A 25 " pdb=" C PRO A 25 " ideal model delta sigma weight residual 113.40 121.99 -8.59 1.34e+00 5.57e-01 4.11e+01 angle pdb=" CA SER B 604 " pdb=" C SER B 604 " pdb=" N PRO B 605 " ideal model delta sigma weight residual 117.68 122.22 -4.54 7.10e-01 1.98e+00 4.09e+01 angle pdb=" C PRO B 231 " pdb=" CA PRO B 231 " pdb=" CB PRO B 231 " ideal model delta sigma weight residual 113.06 102.93 10.13 1.59e+00 3.96e-01 4.06e+01 ... (remaining 14222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.08: 6265 32.08 - 64.17: 176 64.17 - 96.25: 32 96.25 - 128.34: 1 128.34 - 160.42: 1 Dihedral angle restraints: 6475 sinusoidal: 2676 harmonic: 3799 Sorted by residual: dihedral pdb=" O1A ANP B1002 " pdb=" O3A ANP B1002 " pdb=" PA ANP B1002 " pdb=" PB ANP B1002 " ideal model delta sinusoidal sigma weight residual 83.11 -77.31 160.42 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O1A ANP A1002 " pdb=" O3A ANP A1002 " pdb=" PA ANP A1002 " pdb=" PB ANP A1002 " ideal model delta sinusoidal sigma weight residual 83.11 -39.51 122.62 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C GLN B 248 " pdb=" N GLN B 248 " pdb=" CA GLN B 248 " pdb=" CB GLN B 248 " ideal model delta harmonic sigma weight residual -122.60 -113.29 -9.31 0 2.50e+00 1.60e-01 1.39e+01 ... (remaining 6472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 805 0.075 - 0.149: 540 0.149 - 0.224: 215 0.224 - 0.299: 68 0.299 - 0.373: 2 Chirality restraints: 1630 Sorted by residual: chirality pdb=" CB ILE B 258 " pdb=" CA ILE B 258 " pdb=" CG1 ILE B 258 " pdb=" CG2 ILE B 258 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C3' ANP A1002 " pdb=" C2' ANP A1002 " pdb=" C4' ANP A1002 " pdb=" O3' ANP A1002 " both_signs ideal model delta sigma weight residual False -2.36 -2.72 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA ILE B 258 " pdb=" N ILE B 258 " pdb=" C ILE B 258 " pdb=" CB ILE B 258 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1627 not shown) Planarity restraints: 1852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 268 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.23e+00 pdb=" C ILE B 268 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE B 268 " 0.017 2.00e-02 2.50e+03 pdb=" N MET B 269 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 675 " -0.011 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C THR B 675 " 0.041 2.00e-02 2.50e+03 pdb=" O THR B 675 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 676 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 213 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.38e+00 pdb=" C LEU B 213 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU B 213 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN B 214 " -0.014 2.00e-02 2.50e+03 ... (remaining 1849 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 4 2.42 - 3.04: 5563 3.04 - 3.66: 16012 3.66 - 4.28: 23125 4.28 - 4.90: 39236 Nonbonded interactions: 83940 Sorted by model distance: nonbonded pdb=" OG SER A 621 " pdb="MG MG A1001 " model vdw 1.799 2.170 nonbonded pdb=" OG SER B 621 " pdb="MG MG B1001 " model vdw 2.036 2.170 nonbonded pdb="MG MG A1001 " pdb=" O2B ANP A1002 " model vdw 2.128 2.170 nonbonded pdb="MG MG B1001 " pdb=" O1G ANP B1002 " model vdw 2.273 2.170 nonbonded pdb=" N ASP A 139 " pdb=" O ASP A 139 " model vdw 2.439 2.496 ... (remaining 83935 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: 0.170 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: 1.080 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.120 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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 : 0.013 0.175 10499 Z= 0.851 Angle : 1.836 14.147 14227 Z= 1.411 Chirality : 0.110 0.373 1630 Planarity : 0.006 0.034 1852 Dihedral : 15.716 160.421 4017 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % 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: 2.59 (0.21), residues: 1301 helix: 3.35 (0.17), residues: 662 sheet: 0.72 (0.39), residues: 159 loop : -0.34 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 202 HIS 0.010 0.002 HIS B 752 PHE 0.029 0.005 PHE B 532 TYR 0.035 0.003 TYR A 31 ARG 0.007 0.001 ARG B 607 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 147 THR cc_start: 0.8305 (t) cc_final: 0.8057 (m) REVERT: B 197 ARG cc_start: 0.7617 (mtp85) cc_final: 0.7328 (mtp180) REVERT: B 198 ARG cc_start: 0.7980 (mtm110) cc_final: 0.7511 (mtm-85) REVERT: B 201 LEU cc_start: 0.8205 (tp) cc_final: 0.7935 (mm) REVERT: B 205 GLU cc_start: 0.7437 (tt0) cc_final: 0.7155 (tt0) REVERT: B 229 ASN cc_start: 0.7428 (t0) cc_final: 0.7009 (p0) REVERT: B 242 GLN cc_start: 0.7209 (tp40) cc_final: 0.6973 (tm-30) REVERT: B 323 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7516 (mt-10) REVERT: B 355 LEU cc_start: 0.7836 (tp) cc_final: 0.7580 (tp) REVERT: B 373 GLN cc_start: 0.7608 (mt0) cc_final: 0.7377 (mm110) REVERT: B 386 ASP cc_start: 0.7722 (p0) cc_final: 0.7381 (p0) REVERT: B 402 GLU cc_start: 0.7532 (tp30) cc_final: 0.7264 (tp30) REVERT: B 535 LEU cc_start: 0.7229 (mt) cc_final: 0.6903 (mp) REVERT: B 566 ASN cc_start: 0.8095 (t0) cc_final: 0.7667 (t0) REVERT: B 640 VAL cc_start: 0.8618 (t) cc_final: 0.8350 (m) REVERT: B 656 ARG cc_start: 0.6896 (tpt90) cc_final: 0.6414 (tpt90) REVERT: B 692 MET cc_start: 0.8587 (mtp) cc_final: 0.8342 (mtt) REVERT: B 693 ASP cc_start: 0.8164 (t0) cc_final: 0.7802 (t0) REVERT: B 718 LYS cc_start: 0.8163 (mttm) cc_final: 0.7925 (ttmm) REVERT: A 52 ASP cc_start: 0.8157 (t0) cc_final: 0.7738 (t0) REVERT: A 96 ILE cc_start: 0.6907 (pt) cc_final: 0.6607 (mm) REVERT: A 122 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7628 (tp30) REVERT: A 130 ASP cc_start: 0.8327 (m-30) cc_final: 0.8018 (p0) REVERT: A 162 ASP cc_start: 0.7343 (m-30) cc_final: 0.6791 (t0) REVERT: A 166 MET cc_start: 0.7816 (tpt) cc_final: 0.7584 (tpp) REVERT: A 198 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.7853 (ttm-80) REVERT: A 225 PHE cc_start: 0.7779 (m-80) cc_final: 0.7426 (m-80) REVERT: A 240 LEU cc_start: 0.8064 (tp) cc_final: 0.7734 (tp) REVERT: A 283 LEU cc_start: 0.7896 (mt) cc_final: 0.7661 (mp) REVERT: A 296 ASP cc_start: 0.7792 (t0) cc_final: 0.7486 (t0) REVERT: A 355 LEU cc_start: 0.7303 (tp) cc_final: 0.6766 (tp) REVERT: A 417 VAL cc_start: 0.7812 (t) cc_final: 0.7495 (m) REVERT: A 566 ASN cc_start: 0.8189 (t0) cc_final: 0.7639 (t0) REVERT: A 651 ASP cc_start: 0.8132 (t70) cc_final: 0.7869 (t0) REVERT: A 661 ASP cc_start: 0.7631 (t0) cc_final: 0.7427 (t0) REVERT: A 662 ASP cc_start: 0.6550 (t0) cc_final: 0.6103 (p0) REVERT: A 667 ARG cc_start: 0.7674 (mmm-85) cc_final: 0.7258 (mmm-85) REVERT: A 692 MET cc_start: 0.8278 (mtm) cc_final: 0.8015 (mtp) REVERT: A 713 GLU cc_start: 0.7284 (tt0) cc_final: 0.7076 (tt0) REVERT: A 720 LYS cc_start: 0.7724 (mtpt) cc_final: 0.7509 (mtmm) REVERT: A 759 MET cc_start: 0.8355 (mmm) cc_final: 0.8075 (mmp) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.3256 time to fit residues: 148.0984 Evaluate side-chains 292 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 55 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.0570 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 GLN B 538 HIS B 734 GLN B 746 HIS B 752 HIS A 49 GLN A 74 HIS A 254 HIS A 264 GLN A 543 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10499 Z= 0.186 Angle : 0.572 7.289 14227 Z= 0.301 Chirality : 0.041 0.176 1630 Planarity : 0.004 0.039 1852 Dihedral : 8.637 165.452 1511 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.58 % Allowed : 13.56 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.22), residues: 1301 helix: 2.85 (0.19), residues: 671 sheet: 0.77 (0.38), residues: 181 loop : -0.68 (0.25), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 137 HIS 0.008 0.001 HIS A 74 PHE 0.015 0.002 PHE A 36 TYR 0.021 0.002 TYR A 31 ARG 0.008 0.001 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 290 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 LEU cc_start: 0.8403 (tp) cc_final: 0.8081 (mm) REVERT: B 205 GLU cc_start: 0.7262 (tt0) cc_final: 0.6946 (tt0) REVERT: B 229 ASN cc_start: 0.7564 (t0) cc_final: 0.6985 (p0) REVERT: B 269 MET cc_start: 0.8490 (mtm) cc_final: 0.8267 (mtp) REVERT: B 302 MET cc_start: 0.7030 (ptm) cc_final: 0.6737 (ptt) REVERT: B 373 GLN cc_start: 0.7406 (mt0) cc_final: 0.7195 (mm110) REVERT: B 566 ASN cc_start: 0.7988 (t0) cc_final: 0.7586 (t0) REVERT: B 609 MET cc_start: 0.7473 (ttt) cc_final: 0.7205 (ttt) REVERT: B 624 MET cc_start: 0.8265 (mtp) cc_final: 0.8009 (mtp) REVERT: B 640 VAL cc_start: 0.8478 (t) cc_final: 0.8060 (m) REVERT: B 692 MET cc_start: 0.8393 (mtp) cc_final: 0.8101 (mtt) REVERT: B 693 ASP cc_start: 0.8071 (t0) cc_final: 0.7856 (t70) REVERT: B 723 THR cc_start: 0.8021 (m) cc_final: 0.7743 (p) REVERT: B 739 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.6414 (ttm) REVERT: A 36 PHE cc_start: 0.7332 (m-10) cc_final: 0.7121 (m-10) REVERT: A 52 ASP cc_start: 0.8002 (t0) cc_final: 0.7079 (t0) REVERT: A 107 GLU cc_start: 0.7263 (tt0) cc_final: 0.6778 (tm-30) REVERT: A 126 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.7030 (tt0) REVERT: A 133 LEU cc_start: 0.8230 (tp) cc_final: 0.8020 (tp) REVERT: A 157 LEU cc_start: 0.7573 (tt) cc_final: 0.7025 (tp) REVERT: A 198 ARG cc_start: 0.8381 (ttm-80) cc_final: 0.7967 (ttm-80) REVERT: A 225 PHE cc_start: 0.7821 (m-80) cc_final: 0.7501 (m-80) REVERT: A 240 LEU cc_start: 0.7925 (tp) cc_final: 0.7551 (tp) REVERT: A 242 GLN cc_start: 0.8050 (tp40) cc_final: 0.7787 (tp40) REVERT: A 296 ASP cc_start: 0.7405 (t0) cc_final: 0.7151 (t0) REVERT: A 355 LEU cc_start: 0.7330 (tp) cc_final: 0.6829 (tp) REVERT: A 565 LEU cc_start: 0.8019 (mt) cc_final: 0.7450 (mt) REVERT: A 566 ASN cc_start: 0.8106 (t0) cc_final: 0.7447 (t0) REVERT: A 633 MET cc_start: 0.7639 (mtp) cc_final: 0.7408 (mtm) REVERT: A 651 ASP cc_start: 0.8247 (t70) cc_final: 0.7990 (t0) REVERT: A 662 ASP cc_start: 0.6409 (t0) cc_final: 0.5847 (t0) REVERT: A 692 MET cc_start: 0.8068 (mtm) cc_final: 0.7821 (mtp) REVERT: A 720 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7496 (mtmm) REVERT: A 751 GLU cc_start: 0.7513 (pm20) cc_final: 0.7262 (pm20) REVERT: A 759 MET cc_start: 0.8291 (mmm) cc_final: 0.7957 (mmp) REVERT: A 778 LEU cc_start: 0.7683 (tp) cc_final: 0.7299 (mp) outliers start: 28 outliers final: 15 residues processed: 303 average time/residue: 0.2896 time to fit residues: 114.0197 Evaluate side-chains 275 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 258 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 99 optimal weight: 0.2980 chunk 81 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN B 602 ASN A 254 HIS A 616 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10499 Z= 0.265 Angle : 0.572 7.577 14227 Z= 0.296 Chirality : 0.042 0.273 1630 Planarity : 0.005 0.044 1852 Dihedral : 7.471 155.319 1511 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.60 % Allowed : 15.77 % Favored : 80.63 % 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: 1.59 (0.22), residues: 1301 helix: 2.43 (0.19), residues: 670 sheet: 0.55 (0.37), residues: 192 loop : -0.92 (0.25), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 137 HIS 0.006 0.002 HIS A 370 PHE 0.014 0.002 PHE B 758 TYR 0.019 0.002 TYR A 635 ARG 0.007 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 267 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7726 (ttm170) cc_final: 0.7502 (ttm170) REVERT: B 179 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7713 (mt) REVERT: B 201 LEU cc_start: 0.8503 (tp) cc_final: 0.8179 (mm) REVERT: B 205 GLU cc_start: 0.7427 (tt0) cc_final: 0.7110 (tt0) REVERT: B 229 ASN cc_start: 0.7620 (t0) cc_final: 0.6973 (p0) REVERT: B 242 GLN cc_start: 0.7046 (mm-40) cc_final: 0.6541 (tm-30) REVERT: B 302 MET cc_start: 0.7170 (ptm) cc_final: 0.6879 (ptt) REVERT: B 363 ARG cc_start: 0.7470 (mtt180) cc_final: 0.7262 (mtt180) REVERT: B 373 GLN cc_start: 0.7506 (mt0) cc_final: 0.7247 (mm110) REVERT: B 640 VAL cc_start: 0.8511 (t) cc_final: 0.8185 (m) REVERT: B 662 ASP cc_start: 0.7286 (m-30) cc_final: 0.7019 (p0) REVERT: B 667 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7288 (mtm-85) REVERT: B 692 MET cc_start: 0.8352 (mtp) cc_final: 0.8123 (mtt) REVERT: B 693 ASP cc_start: 0.8005 (t0) cc_final: 0.7792 (t70) REVERT: B 723 THR cc_start: 0.7957 (m) cc_final: 0.7620 (p) REVERT: B 738 LYS cc_start: 0.8382 (mtmm) cc_final: 0.8088 (mtmm) REVERT: B 748 ASP cc_start: 0.7796 (m-30) cc_final: 0.7301 (m-30) REVERT: B 784 GLU cc_start: 0.7252 (tp30) cc_final: 0.6946 (tp30) REVERT: A 107 GLU cc_start: 0.7723 (tt0) cc_final: 0.7092 (tm-30) REVERT: A 126 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7289 (tt0) REVERT: A 130 ASP cc_start: 0.8325 (m-30) cc_final: 0.8029 (t0) REVERT: A 163 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6495 (ttm110) REVERT: A 166 MET cc_start: 0.7249 (tpp) cc_final: 0.6771 (tpp) REVERT: A 198 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.7922 (ttm-80) REVERT: A 296 ASP cc_start: 0.7430 (t0) cc_final: 0.7114 (t0) REVERT: A 355 LEU cc_start: 0.7403 (tp) cc_final: 0.7021 (tp) REVERT: A 566 ASN cc_start: 0.8101 (t0) cc_final: 0.7472 (t0) REVERT: A 571 THR cc_start: 0.8411 (p) cc_final: 0.8206 (p) REVERT: A 692 MET cc_start: 0.8067 (mtm) cc_final: 0.7851 (mtp) REVERT: A 720 LYS cc_start: 0.7730 (mtpt) cc_final: 0.7491 (mtmm) REVERT: A 751 GLU cc_start: 0.7587 (pm20) cc_final: 0.7242 (pm20) REVERT: A 759 MET cc_start: 0.8162 (mmm) cc_final: 0.7887 (mmp) REVERT: A 778 LEU cc_start: 0.7823 (tp) cc_final: 0.7582 (tt) outliers start: 39 outliers final: 25 residues processed: 287 average time/residue: 0.3143 time to fit residues: 115.9106 Evaluate side-chains 278 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 250 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 5.9990 chunk 89 optimal weight: 0.2980 chunk 61 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 744 ASN A 248 GLN A 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10499 Z= 0.219 Angle : 0.525 8.729 14227 Z= 0.272 Chirality : 0.040 0.193 1630 Planarity : 0.004 0.038 1852 Dihedral : 7.216 155.290 1511 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.41 % Allowed : 18.08 % Favored : 78.51 % 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: 1.49 (0.23), residues: 1301 helix: 2.39 (0.20), residues: 662 sheet: 0.51 (0.37), residues: 198 loop : -1.01 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 137 HIS 0.005 0.001 HIS A 74 PHE 0.016 0.002 PHE A 36 TYR 0.017 0.002 TYR B 635 ARG 0.005 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 265 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7706 (ttm170) cc_final: 0.7486 (ttm170) REVERT: B 179 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7721 (mt) REVERT: B 201 LEU cc_start: 0.8486 (tp) cc_final: 0.7740 (mm) REVERT: B 205 GLU cc_start: 0.7494 (tt0) cc_final: 0.7091 (mp0) REVERT: B 229 ASN cc_start: 0.7592 (t0) cc_final: 0.6930 (p0) REVERT: B 302 MET cc_start: 0.7124 (ptm) cc_final: 0.6813 (ptt) REVERT: B 373 GLN cc_start: 0.7510 (mt0) cc_final: 0.7247 (mm110) REVERT: B 565 LEU cc_start: 0.7948 (mt) cc_final: 0.7715 (mt) REVERT: B 579 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7709 (mtm180) REVERT: B 723 THR cc_start: 0.7922 (m) cc_final: 0.7528 (p) REVERT: B 738 LYS cc_start: 0.8366 (mtmm) cc_final: 0.8142 (mtmm) REVERT: B 742 VAL cc_start: 0.8358 (t) cc_final: 0.7897 (m) REVERT: B 748 ASP cc_start: 0.7837 (m-30) cc_final: 0.7342 (m-30) REVERT: B 784 GLU cc_start: 0.7208 (tp30) cc_final: 0.6903 (tp30) REVERT: A 83 LEU cc_start: 0.7051 (mt) cc_final: 0.6844 (mp) REVERT: A 107 GLU cc_start: 0.7808 (tt0) cc_final: 0.7164 (tm-30) REVERT: A 130 ASP cc_start: 0.8327 (m-30) cc_final: 0.8045 (t0) REVERT: A 166 MET cc_start: 0.7417 (tpp) cc_final: 0.7052 (tpp) REVERT: A 198 ARG cc_start: 0.8458 (ttm-80) cc_final: 0.7895 (ttm-80) REVERT: A 355 LEU cc_start: 0.7331 (tp) cc_final: 0.6951 (tp) REVERT: A 566 ASN cc_start: 0.8063 (t0) cc_final: 0.7431 (t0) REVERT: A 571 THR cc_start: 0.8416 (p) cc_final: 0.8204 (p) REVERT: A 692 MET cc_start: 0.8069 (mtm) cc_final: 0.7850 (mtp) REVERT: A 693 ASP cc_start: 0.8409 (t0) cc_final: 0.8073 (t0) REVERT: A 720 LYS cc_start: 0.7707 (mtpt) cc_final: 0.7452 (mtmm) REVERT: A 751 GLU cc_start: 0.7505 (pm20) cc_final: 0.7124 (pm20) REVERT: A 759 MET cc_start: 0.8055 (mmm) cc_final: 0.7801 (mmp) REVERT: A 778 LEU cc_start: 0.7835 (tp) cc_final: 0.7618 (tt) outliers start: 37 outliers final: 28 residues processed: 280 average time/residue: 0.3006 time to fit residues: 108.8224 Evaluate side-chains 284 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 254 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 0.0010 chunk 87 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 31 optimal weight: 0.0770 overall best weight: 1.8150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10499 Z= 0.199 Angle : 0.518 9.883 14227 Z= 0.266 Chirality : 0.039 0.160 1630 Planarity : 0.004 0.039 1852 Dihedral : 7.056 154.427 1511 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.85 % Rotamer: Outliers : 3.41 % Allowed : 18.08 % Favored : 78.51 % 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: 1.57 (0.23), residues: 1301 helix: 2.45 (0.20), residues: 658 sheet: 0.49 (0.38), residues: 194 loop : -0.89 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 137 HIS 0.005 0.001 HIS A 254 PHE 0.011 0.002 PHE A 654 TYR 0.017 0.001 TYR B 635 ARG 0.006 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 269 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 179 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7713 (mt) REVERT: B 201 LEU cc_start: 0.8512 (tp) cc_final: 0.7685 (mm) REVERT: B 205 GLU cc_start: 0.7527 (tt0) cc_final: 0.7210 (mp0) REVERT: B 229 ASN cc_start: 0.7523 (t0) cc_final: 0.6956 (p0) REVERT: B 242 GLN cc_start: 0.7631 (tp40) cc_final: 0.7346 (tm-30) REVERT: B 302 MET cc_start: 0.7088 (ptm) cc_final: 0.6773 (ptt) REVERT: B 373 GLN cc_start: 0.7516 (mt0) cc_final: 0.7247 (mm110) REVERT: B 579 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7750 (mtm180) REVERT: B 640 VAL cc_start: 0.8520 (t) cc_final: 0.8093 (m) REVERT: B 723 THR cc_start: 0.7917 (m) cc_final: 0.7567 (p) REVERT: B 738 LYS cc_start: 0.8371 (mtmm) cc_final: 0.8148 (mtmm) REVERT: B 742 VAL cc_start: 0.8355 (t) cc_final: 0.7882 (m) REVERT: B 748 ASP cc_start: 0.7876 (m-30) cc_final: 0.7359 (m-30) REVERT: B 784 GLU cc_start: 0.7194 (tp30) cc_final: 0.6883 (tp30) REVERT: A 83 LEU cc_start: 0.7048 (mt) cc_final: 0.6846 (mp) REVERT: A 107 GLU cc_start: 0.7893 (tt0) cc_final: 0.7256 (tm-30) REVERT: A 130 ASP cc_start: 0.8346 (m-30) cc_final: 0.8061 (t0) REVERT: A 166 MET cc_start: 0.7404 (tpp) cc_final: 0.7068 (tpp) REVERT: A 198 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.7738 (ttm-80) REVERT: A 355 LEU cc_start: 0.7279 (tp) cc_final: 0.6894 (tp) REVERT: A 566 ASN cc_start: 0.8034 (t0) cc_final: 0.7440 (t0) REVERT: A 571 THR cc_start: 0.8407 (p) cc_final: 0.8184 (p) REVERT: A 662 ASP cc_start: 0.6672 (m-30) cc_final: 0.5778 (p0) REVERT: A 667 ARG cc_start: 0.7500 (mtp85) cc_final: 0.6748 (mmm-85) REVERT: A 671 MET cc_start: 0.7753 (mmm) cc_final: 0.7502 (mmm) REVERT: A 692 MET cc_start: 0.8072 (mtm) cc_final: 0.7861 (mtp) REVERT: A 720 LYS cc_start: 0.7707 (mtpt) cc_final: 0.7464 (mtmm) REVERT: A 751 GLU cc_start: 0.7473 (pm20) cc_final: 0.7072 (pm20) REVERT: A 759 MET cc_start: 0.7987 (mmm) cc_final: 0.7732 (mmt) REVERT: A 778 LEU cc_start: 0.7857 (tp) cc_final: 0.7656 (tt) REVERT: A 783 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7835 (mmtm) outliers start: 37 outliers final: 31 residues processed: 286 average time/residue: 0.2791 time to fit residues: 104.5218 Evaluate side-chains 293 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 260 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 25 optimal weight: 0.0570 chunk 74 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 0.0770 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.2260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 344 GLN A 590 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10499 Z= 0.164 Angle : 0.491 7.893 14227 Z= 0.254 Chirality : 0.038 0.143 1630 Planarity : 0.004 0.039 1852 Dihedral : 6.961 154.166 1511 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.00 % Favored : 97.92 % Rotamer: Outliers : 4.06 % Allowed : 18.54 % Favored : 77.40 % 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: 1.57 (0.23), residues: 1301 helix: 2.45 (0.20), residues: 664 sheet: 0.51 (0.38), residues: 189 loop : -0.94 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 137 HIS 0.007 0.001 HIS A 254 PHE 0.012 0.001 PHE B 532 TYR 0.017 0.001 TYR B 635 ARG 0.006 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 268 time to evaluate : 1.267 Fit side-chains REVERT: B 154 ARG cc_start: 0.7661 (ttm170) cc_final: 0.7302 (ttm-80) REVERT: B 179 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7698 (mt) REVERT: B 182 GLU cc_start: 0.7126 (tp30) cc_final: 0.6427 (mm-30) REVERT: B 198 ARG cc_start: 0.8180 (mtm110) cc_final: 0.7967 (mtp180) REVERT: B 201 LEU cc_start: 0.8520 (tp) cc_final: 0.7706 (mm) REVERT: B 205 GLU cc_start: 0.7541 (tt0) cc_final: 0.7234 (mp0) REVERT: B 229 ASN cc_start: 0.7512 (t0) cc_final: 0.6968 (p0) REVERT: B 242 GLN cc_start: 0.7662 (tp40) cc_final: 0.7361 (tm-30) REVERT: B 302 MET cc_start: 0.7026 (ptm) cc_final: 0.6713 (ptt) REVERT: B 373 GLN cc_start: 0.7525 (mt0) cc_final: 0.7251 (mm110) REVERT: B 579 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7772 (mtm180) REVERT: B 640 VAL cc_start: 0.8512 (t) cc_final: 0.8079 (m) REVERT: B 723 THR cc_start: 0.7894 (m) cc_final: 0.7542 (p) REVERT: B 738 LYS cc_start: 0.8375 (mtmm) cc_final: 0.8002 (mtmm) REVERT: B 742 VAL cc_start: 0.8340 (t) cc_final: 0.7871 (m) REVERT: B 748 ASP cc_start: 0.7827 (m-30) cc_final: 0.7333 (m-30) REVERT: B 784 GLU cc_start: 0.7160 (tp30) cc_final: 0.6851 (tp30) REVERT: A 107 GLU cc_start: 0.7897 (tt0) cc_final: 0.7259 (tm-30) REVERT: A 130 ASP cc_start: 0.8350 (m-30) cc_final: 0.8068 (t0) REVERT: A 166 MET cc_start: 0.7410 (tpp) cc_final: 0.7102 (tpp) REVERT: A 186 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7371 (mp0) REVERT: A 198 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.8147 (ttm-80) REVERT: A 355 LEU cc_start: 0.7220 (tp) cc_final: 0.6839 (tp) REVERT: A 566 ASN cc_start: 0.7994 (t0) cc_final: 0.7458 (t0) REVERT: A 571 THR cc_start: 0.8378 (p) cc_final: 0.8150 (p) REVERT: A 662 ASP cc_start: 0.6640 (m-30) cc_final: 0.5738 (p0) REVERT: A 671 MET cc_start: 0.7722 (mmm) cc_final: 0.7501 (mmm) REVERT: A 692 MET cc_start: 0.8051 (mtm) cc_final: 0.7849 (mtp) REVERT: A 693 ASP cc_start: 0.8258 (t0) cc_final: 0.7982 (t0) REVERT: A 720 LYS cc_start: 0.7723 (mtpt) cc_final: 0.7487 (mtmm) outliers start: 44 outliers final: 32 residues processed: 289 average time/residue: 0.2887 time to fit residues: 109.4923 Evaluate side-chains 296 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 262 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10499 Z= 0.409 Angle : 0.624 9.552 14227 Z= 0.318 Chirality : 0.044 0.167 1630 Planarity : 0.005 0.046 1852 Dihedral : 7.167 152.127 1511 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.31 % Favored : 97.62 % Rotamer: Outliers : 3.69 % Allowed : 18.82 % Favored : 77.49 % 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: 1.07 (0.23), residues: 1301 helix: 1.96 (0.20), residues: 659 sheet: 0.44 (0.38), residues: 190 loop : -1.08 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 137 HIS 0.009 0.002 HIS A 585 PHE 0.017 0.002 PHE A 30 TYR 0.021 0.002 TYR B 635 ARG 0.006 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 275 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7713 (ttm170) cc_final: 0.7232 (ttm-80) REVERT: B 179 LEU cc_start: 0.7997 (mt) cc_final: 0.7674 (mt) REVERT: B 201 LEU cc_start: 0.8599 (tp) cc_final: 0.7642 (mm) REVERT: B 205 GLU cc_start: 0.7690 (tt0) cc_final: 0.7286 (mp0) REVERT: B 229 ASN cc_start: 0.7621 (t0) cc_final: 0.6972 (p0) REVERT: B 242 GLN cc_start: 0.7617 (tp40) cc_final: 0.7352 (tm-30) REVERT: B 373 GLN cc_start: 0.7534 (mt0) cc_final: 0.7257 (mm110) REVERT: B 579 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7696 (mtm180) REVERT: B 640 VAL cc_start: 0.8548 (t) cc_final: 0.8112 (m) REVERT: B 723 THR cc_start: 0.7828 (m) cc_final: 0.7435 (p) REVERT: B 734 GLN cc_start: 0.8034 (mt0) cc_final: 0.7827 (mt0) REVERT: B 738 LYS cc_start: 0.8389 (mtmm) cc_final: 0.8143 (mtmm) REVERT: B 742 VAL cc_start: 0.8380 (t) cc_final: 0.7938 (m) REVERT: B 748 ASP cc_start: 0.8144 (m-30) cc_final: 0.7667 (m-30) REVERT: B 784 GLU cc_start: 0.7339 (tp30) cc_final: 0.7005 (tp30) REVERT: A 130 ASP cc_start: 0.8377 (m-30) cc_final: 0.8077 (t0) REVERT: A 166 MET cc_start: 0.7416 (tpp) cc_final: 0.7109 (tpp) REVERT: A 186 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7362 (mp0) REVERT: A 198 ARG cc_start: 0.8454 (ttm-80) cc_final: 0.7756 (ttm-80) REVERT: A 355 LEU cc_start: 0.7373 (tp) cc_final: 0.7026 (tp) REVERT: A 566 ASN cc_start: 0.8013 (t0) cc_final: 0.7448 (t0) REVERT: A 571 THR cc_start: 0.8522 (p) cc_final: 0.8298 (p) REVERT: A 662 ASP cc_start: 0.6920 (m-30) cc_final: 0.5969 (p0) REVERT: A 693 ASP cc_start: 0.8422 (t0) cc_final: 0.8089 (t0) REVERT: A 720 LYS cc_start: 0.7736 (mtpt) cc_final: 0.7498 (mtmm) outliers start: 40 outliers final: 34 residues processed: 296 average time/residue: 0.2956 time to fit residues: 114.9029 Evaluate side-chains 299 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 264 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 644 LYS Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 647 ILE Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.0070 chunk 50 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 ASN B 602 ASN A 248 GLN A 254 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10499 Z= 0.264 Angle : 0.557 9.125 14227 Z= 0.284 Chirality : 0.041 0.208 1630 Planarity : 0.004 0.047 1852 Dihedral : 7.125 152.693 1511 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.61 % Favored : 97.31 % Rotamer: Outliers : 3.23 % Allowed : 19.93 % Favored : 76.85 % 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: 1.15 (0.23), residues: 1301 helix: 2.06 (0.20), residues: 659 sheet: 0.31 (0.36), residues: 205 loop : -1.05 (0.26), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 137 HIS 0.006 0.001 HIS A 254 PHE 0.028 0.002 PHE A 36 TYR 0.020 0.002 TYR B 635 ARG 0.007 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 272 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7710 (ttm170) cc_final: 0.7221 (ttm-80) REVERT: B 179 LEU cc_start: 0.8006 (mt) cc_final: 0.7760 (mt) REVERT: B 201 LEU cc_start: 0.8564 (tp) cc_final: 0.7625 (mm) REVERT: B 204 PHE cc_start: 0.7610 (m-80) cc_final: 0.7322 (m-80) REVERT: B 205 GLU cc_start: 0.7635 (tt0) cc_final: 0.7279 (mp0) REVERT: B 229 ASN cc_start: 0.7567 (t0) cc_final: 0.6956 (p0) REVERT: B 242 GLN cc_start: 0.7650 (tp40) cc_final: 0.7376 (tm-30) REVERT: B 373 GLN cc_start: 0.7521 (mt0) cc_final: 0.7243 (mm110) REVERT: B 579 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7709 (mtm180) REVERT: B 635 TYR cc_start: 0.8008 (m-80) cc_final: 0.7670 (m-80) REVERT: B 640 VAL cc_start: 0.8531 (t) cc_final: 0.8101 (m) REVERT: B 656 ARG cc_start: 0.6869 (tpt90) cc_final: 0.6304 (tpt90) REVERT: B 723 THR cc_start: 0.7837 (m) cc_final: 0.7482 (p) REVERT: B 734 GLN cc_start: 0.8062 (mt0) cc_final: 0.7845 (mt0) REVERT: B 738 LYS cc_start: 0.8288 (mtmm) cc_final: 0.8042 (mtmm) REVERT: B 742 VAL cc_start: 0.8381 (t) cc_final: 0.7936 (m) REVERT: B 748 ASP cc_start: 0.8155 (m-30) cc_final: 0.7687 (m-30) REVERT: B 784 GLU cc_start: 0.7274 (tp30) cc_final: 0.6933 (tp30) REVERT: A 130 ASP cc_start: 0.8378 (m-30) cc_final: 0.8088 (t0) REVERT: A 166 MET cc_start: 0.7409 (tpp) cc_final: 0.7112 (tpp) REVERT: A 186 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7313 (mp0) REVERT: A 198 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.7708 (ttm-80) REVERT: A 355 LEU cc_start: 0.7267 (tp) cc_final: 0.6909 (tp) REVERT: A 403 LEU cc_start: 0.6571 (mm) cc_final: 0.6347 (mp) REVERT: A 566 ASN cc_start: 0.7994 (t0) cc_final: 0.7426 (t0) REVERT: A 571 THR cc_start: 0.8503 (p) cc_final: 0.8264 (p) REVERT: A 662 ASP cc_start: 0.6799 (m-30) cc_final: 0.5884 (p0) REVERT: A 693 ASP cc_start: 0.8461 (t0) cc_final: 0.8113 (t0) REVERT: A 720 LYS cc_start: 0.7730 (mtpt) cc_final: 0.7494 (mtmm) REVERT: A 751 GLU cc_start: 0.7375 (pm20) cc_final: 0.7094 (pm20) outliers start: 35 outliers final: 30 residues processed: 291 average time/residue: 0.2987 time to fit residues: 113.9115 Evaluate side-chains 299 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 268 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 579 ARG Chi-restraints excluded: chain B residue 644 LYS Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 124 optimal weight: 0.0670 overall best weight: 3.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 GLN B 557 ASN A 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10499 Z= 0.347 Angle : 0.608 9.603 14227 Z= 0.308 Chirality : 0.043 0.224 1630 Planarity : 0.005 0.050 1852 Dihedral : 7.181 151.437 1511 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 3.32 % Allowed : 20.20 % Favored : 76.48 % 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: 0.95 (0.23), residues: 1301 helix: 1.90 (0.20), residues: 654 sheet: 0.32 (0.38), residues: 189 loop : -1.11 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 137 HIS 0.008 0.002 HIS A 585 PHE 0.015 0.002 PHE A 204 TYR 0.018 0.002 TYR B 635 ARG 0.007 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 268 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7723 (ttm170) cc_final: 0.7224 (ttm-80) REVERT: B 179 LEU cc_start: 0.8004 (mt) cc_final: 0.7759 (mt) REVERT: B 201 LEU cc_start: 0.8573 (tp) cc_final: 0.7813 (tp) REVERT: B 204 PHE cc_start: 0.7653 (m-80) cc_final: 0.7351 (m-80) REVERT: B 205 GLU cc_start: 0.7642 (tt0) cc_final: 0.7295 (mp0) REVERT: B 229 ASN cc_start: 0.7542 (t0) cc_final: 0.6911 (p0) REVERT: B 242 GLN cc_start: 0.7761 (tp40) cc_final: 0.7455 (tm-30) REVERT: B 373 GLN cc_start: 0.7524 (mt0) cc_final: 0.7252 (mm110) REVERT: B 640 VAL cc_start: 0.8531 (t) cc_final: 0.8098 (m) REVERT: B 656 ARG cc_start: 0.6901 (tpt90) cc_final: 0.6336 (tpt90) REVERT: B 723 THR cc_start: 0.7822 (m) cc_final: 0.7451 (p) REVERT: B 734 GLN cc_start: 0.8140 (mt0) cc_final: 0.7917 (mt0) REVERT: B 738 LYS cc_start: 0.8309 (mtmm) cc_final: 0.8061 (mtmm) REVERT: B 742 VAL cc_start: 0.8378 (t) cc_final: 0.7932 (m) REVERT: B 748 ASP cc_start: 0.8197 (m-30) cc_final: 0.7742 (m-30) REVERT: B 784 GLU cc_start: 0.7367 (tp30) cc_final: 0.7012 (tp30) REVERT: A 130 ASP cc_start: 0.8392 (m-30) cc_final: 0.8096 (t0) REVERT: A 166 MET cc_start: 0.7420 (tpp) cc_final: 0.7125 (tpp) REVERT: A 198 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.7652 (ttm-80) REVERT: A 355 LEU cc_start: 0.7310 (tp) cc_final: 0.6955 (tp) REVERT: A 403 LEU cc_start: 0.6593 (mm) cc_final: 0.6370 (mp) REVERT: A 566 ASN cc_start: 0.7981 (t0) cc_final: 0.7450 (t0) REVERT: A 571 THR cc_start: 0.8527 (p) cc_final: 0.8300 (p) REVERT: A 662 ASP cc_start: 0.6902 (m-30) cc_final: 0.5985 (p0) REVERT: A 693 ASP cc_start: 0.8402 (t0) cc_final: 0.8048 (t0) REVERT: A 720 LYS cc_start: 0.7708 (mtpt) cc_final: 0.7457 (mtmm) REVERT: A 751 GLU cc_start: 0.7381 (pm20) cc_final: 0.7094 (pm20) outliers start: 36 outliers final: 32 residues processed: 288 average time/residue: 0.3016 time to fit residues: 112.6467 Evaluate side-chains 298 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 266 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 120 optimal weight: 0.0870 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 0.0670 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 ASN A 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10499 Z= 0.162 Angle : 0.529 8.688 14227 Z= 0.270 Chirality : 0.039 0.166 1630 Planarity : 0.004 0.046 1852 Dihedral : 6.946 152.026 1511 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.15 % Favored : 97.77 % Rotamer: Outliers : 2.40 % Allowed : 21.40 % Favored : 76.20 % 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: 1.28 (0.23), residues: 1301 helix: 2.24 (0.20), residues: 658 sheet: 0.27 (0.39), residues: 182 loop : -1.00 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 137 HIS 0.006 0.001 HIS A 254 PHE 0.011 0.001 PHE B 532 TYR 0.015 0.001 TYR A 41 ARG 0.007 0.000 ARG A 579 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 275 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 154 ARG cc_start: 0.7676 (ttm170) cc_final: 0.7179 (ttm-80) REVERT: B 179 LEU cc_start: 0.7992 (mt) cc_final: 0.7740 (mt) REVERT: B 201 LEU cc_start: 0.8566 (tp) cc_final: 0.7697 (mm) REVERT: B 204 PHE cc_start: 0.7474 (m-80) cc_final: 0.7226 (m-80) REVERT: B 205 GLU cc_start: 0.7526 (tt0) cc_final: 0.7286 (mp0) REVERT: B 229 ASN cc_start: 0.7463 (t0) cc_final: 0.6837 (p0) REVERT: B 242 GLN cc_start: 0.7639 (tp40) cc_final: 0.7352 (tm-30) REVERT: B 261 GLU cc_start: 0.7677 (tp30) cc_final: 0.7201 (tp30) REVERT: B 373 GLN cc_start: 0.7508 (mt0) cc_final: 0.7243 (mm110) REVERT: B 557 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7731 (t0) REVERT: B 624 MET cc_start: 0.8111 (mtp) cc_final: 0.7862 (mtm) REVERT: B 635 TYR cc_start: 0.7946 (m-80) cc_final: 0.7607 (m-80) REVERT: B 640 VAL cc_start: 0.8483 (t) cc_final: 0.8059 (m) REVERT: B 656 ARG cc_start: 0.6896 (tpt90) cc_final: 0.6364 (tpt90) REVERT: B 723 THR cc_start: 0.7828 (m) cc_final: 0.7572 (p) REVERT: B 734 GLN cc_start: 0.8027 (mt0) cc_final: 0.7654 (mt0) REVERT: B 738 LYS cc_start: 0.8297 (mtmm) cc_final: 0.7920 (mtmm) REVERT: B 742 VAL cc_start: 0.8349 (t) cc_final: 0.7857 (m) REVERT: B 748 ASP cc_start: 0.8038 (m-30) cc_final: 0.7615 (m-30) REVERT: B 784 GLU cc_start: 0.7195 (tp30) cc_final: 0.6891 (tp30) REVERT: A 130 ASP cc_start: 0.8391 (m-30) cc_final: 0.8086 (t0) REVERT: A 166 MET cc_start: 0.7434 (tpp) cc_final: 0.7141 (tpp) REVERT: A 186 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7289 (mp0) REVERT: A 198 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.7667 (ttm-80) REVERT: A 242 GLN cc_start: 0.7988 (tp40) cc_final: 0.7601 (tp40) REVERT: A 355 LEU cc_start: 0.7142 (tp) cc_final: 0.6781 (tp) REVERT: A 566 ASN cc_start: 0.7907 (t0) cc_final: 0.7409 (t0) REVERT: A 693 ASP cc_start: 0.8412 (t0) cc_final: 0.8062 (t0) REVERT: A 695 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8023 (pt) REVERT: A 720 LYS cc_start: 0.7649 (mtpt) cc_final: 0.7394 (mtmm) REVERT: A 748 ASP cc_start: 0.7272 (p0) cc_final: 0.6854 (p0) REVERT: A 751 GLU cc_start: 0.7287 (pm20) cc_final: 0.7012 (pm20) outliers start: 26 outliers final: 21 residues processed: 287 average time/residue: 0.3045 time to fit residues: 114.2304 Evaluate side-chains 291 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 268 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 28 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 ASN B 744 ASN A 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112064 restraints weight = 19498.389| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.38 r_work: 0.3254 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10499 Z= 0.215 Angle : 0.546 8.704 14227 Z= 0.277 Chirality : 0.039 0.184 1630 Planarity : 0.004 0.045 1852 Dihedral : 6.940 151.223 1511 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 2.40 % Allowed : 21.49 % Favored : 76.11 % 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: 1.25 (0.23), residues: 1301 helix: 2.22 (0.20), residues: 660 sheet: 0.28 (0.39), residues: 180 loop : -1.04 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 137 HIS 0.006 0.001 HIS A 254 PHE 0.013 0.001 PHE A 654 TYR 0.016 0.001 TYR A 41 ARG 0.007 0.000 ARG A 579 =============================================================================== Job complete usr+sys time: 2791.25 seconds wall clock time: 50 minutes 26.27 seconds (3026.27 seconds total)