Starting phenix.real_space_refine on Sat Aug 3 10:42:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/08_2024/8u1m_41817.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/08_2024/8u1m_41817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/08_2024/8u1m_41817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/08_2024/8u1m_41817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/08_2024/8u1m_41817.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/08_2024/8u1m_41817.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 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 28 5.16 5 C 4988 2.51 5 N 1318 2.21 5 O 1540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 420": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7882 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3789 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 10, 'TRANS': 452} Chain breaks: 2 Chain: "B" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4029 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 11, 'TRANS': 482} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.82, per 1000 atoms: 0.61 Number of scatterers: 7882 At special positions: 0 Unit cell: (90.948, 110.682, 108.108, 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 28 16.00 P 6 15.00 Mg 2 11.99 O 1540 8.00 N 1318 7.00 C 4988 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: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1814 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 40.1% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.849A pdb=" N MET A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 61 removed outlier: 4.083A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.790A pdb=" N SER A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.586A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.570A pdb=" N ALA A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU A 191 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.853A pdb=" N LEU A 400 " --> pdb=" O GLN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 443 removed outlier: 6.932A pdb=" N LYS A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 452 removed outlier: 3.747A pdb=" N ALA A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 474 Processing helix chain 'A' and resid 516 through 524 Processing helix chain 'B' and resid 20 through 32 removed outlier: 4.353A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 60 removed outlier: 4.018A pdb=" N ARG B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 43 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 108 through 117 removed outlier: 4.115A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 138 removed outlier: 3.633A pdb=" N TYR B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 138 " --> pdb=" O SER B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.912A pdb=" N LEU B 342 " --> pdb=" O PRO B 339 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 343 " --> pdb=" O PHE B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 343' Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.244A pdb=" N LEU B 368 " --> pdb=" O ASN B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 396 through 421 removed outlier: 3.887A pdb=" N GLU B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASP B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 443 removed outlier: 6.599A pdb=" N LYS B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 454 Processing helix chain 'B' and resid 468 through 474 Processing helix chain 'B' and resid 489 through 495 removed outlier: 3.920A pdb=" N VAL B 493 " --> pdb=" O ASN B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.873A pdb=" N ARG B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL B 502 " --> pdb=" O PHE B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 521 removed outlier: 3.690A pdb=" N VAL B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 4.326A pdb=" N ARG B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 278 removed outlier: 6.674A pdb=" N ILE A 73 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N THR A 216 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE A 75 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N GLU A 218 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 85 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 179 " --> pdb=" O ASP A 88 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 178 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 143 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 147 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 168 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 13 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.794A pdb=" N ILE A 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 322 removed outlier: 6.351A pdb=" N VAL A 334 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL A 317 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A 332 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS A 319 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA A 330 " --> pdb=" O HIS A 319 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N SER A 321 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 328 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 380 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 382 " --> pdb=" O TYR A 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 485 Processing sheet with id=AA7, first strand: chain 'B' and resid 316 through 322 removed outlier: 4.413A pdb=" N ALA B 316 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 320 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 377 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AA9, first strand: chain 'B' and resid 510 through 512 removed outlier: 7.449A pdb=" N TYR B 483 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N MET B 512 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE B 485 " --> pdb=" O MET B 512 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 482 " --> pdb=" O VAL B 533 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2483 1.34 - 1.45: 1081 1.45 - 1.57: 4405 1.57 - 1.69: 4 1.69 - 1.81: 48 Bond restraints: 8021 Sorted by residual: bond pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " ideal model delta sigma weight residual 1.443 1.217 0.226 1.00e-02 1.00e+04 5.12e+02 bond pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 1.443 1.221 0.222 1.00e-02 1.00e+04 4.92e+02 bond pdb=" C3' ATP B 801 " pdb=" O3' ATP B 801 " ideal model delta sigma weight residual 1.423 1.370 0.053 1.10e-02 8.26e+03 2.36e+01 bond pdb=" C4' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.444 1.397 0.047 1.10e-02 8.26e+03 1.81e+01 bond pdb=" C1' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.416 1.361 0.055 1.30e-02 5.92e+03 1.79e+01 ... (remaining 8016 not shown) Histogram of bond angle deviations from ideal: 80.37 - 95.41: 7 95.41 - 110.46: 1868 110.46 - 125.50: 8835 125.50 - 140.54: 83 140.54 - 155.59: 2 Bond angle restraints: 10795 Sorted by residual: angle pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 121.27 155.59 -34.32 1.00e+00 1.00e+00 1.18e+03 angle pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 121.27 155.25 -33.98 1.00e+00 1.00e+00 1.15e+03 angle pdb=" C3' ATP B 801 " pdb=" C4' ATP B 801 " pdb=" C5' ATP B 801 " ideal model delta sigma weight residual 115.19 83.50 31.69 1.76e+00 3.23e-01 3.24e+02 angle pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " ideal model delta sigma weight residual 115.19 84.32 30.87 1.76e+00 3.23e-01 3.08e+02 angle pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 108.83 140.19 -31.36 2.33e+00 1.85e-01 1.82e+02 ... (remaining 10790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4276 17.98 - 35.95: 516 35.95 - 53.93: 112 53.93 - 71.91: 22 71.91 - 89.88: 10 Dihedral angle restraints: 4936 sinusoidal: 2122 harmonic: 2814 Sorted by residual: dihedral pdb=" CA MET B 512 " pdb=" C MET B 512 " pdb=" N THR B 513 " pdb=" CA THR B 513 " ideal model delta harmonic sigma weight residual -180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA MET A 25 " pdb=" C MET A 25 " pdb=" N SER A 26 " pdb=" CA SER A 26 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA TYR A 456 " pdb=" C TYR A 456 " pdb=" N HIS A 457 " pdb=" CA HIS A 457 " ideal model delta harmonic sigma weight residual 180.00 161.52 18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 4933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1117 0.094 - 0.188: 52 0.188 - 0.282: 4 0.282 - 0.376: 0 0.376 - 0.471: 2 Chirality restraints: 1175 Sorted by residual: chirality pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O4' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.96 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" C4' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" C5' ATP B 801 " pdb=" O4' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.96 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" C3' ATP A 801 " pdb=" C2' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" O3' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1172 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 311 " -0.014 2.00e-02 2.50e+03 1.70e-02 7.19e+00 pdb=" CG TRP A 311 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 311 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 311 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 311 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 311 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 311 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 311 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 311 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 311 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 211 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 212 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 177 " -0.136 9.50e-02 1.11e+02 6.11e-02 2.39e+00 pdb=" NE ARG A 177 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 177 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 177 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 177 " -0.007 2.00e-02 2.50e+03 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 69 2.40 - 3.03: 4825 3.03 - 3.65: 13142 3.65 - 4.28: 19190 4.28 - 4.90: 29932 Nonbonded interactions: 67158 Sorted by model distance: nonbonded pdb=" CB SER B 159 " pdb=" CD1 PHE B 165 " model vdw 1.781 3.740 nonbonded pdb=" O2G ATP A 801 " pdb="MG MG A 802 " model vdw 1.938 2.170 nonbonded pdb=" O3A ATP B 801 " pdb="MG MG B 802 " model vdw 1.967 2.170 nonbonded pdb=" O2B ATP A 801 " pdb="MG MG A 802 " model vdw 1.971 2.170 nonbonded pdb=" O2A ATP A 801 " pdb="MG MG A 802 " model vdw 2.028 2.170 ... (remaining 67153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 10 through 490 or resid 507 through 530 or resid 801 throu \ gh 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.280 Find NCS groups from input model: 0.290 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 : 0.005 0.226 8021 Z= 0.405 Angle : 1.167 34.316 10795 Z= 0.717 Chirality : 0.048 0.471 1175 Planarity : 0.004 0.061 1374 Dihedral : 16.519 89.885 3122 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.35 % Allowed : 18.79 % Favored : 80.86 % 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: -1.18 (0.27), residues: 947 helix: 0.01 (0.30), residues: 313 sheet: -1.23 (0.42), residues: 156 loop : -1.10 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 311 HIS 0.007 0.001 HIS A 314 PHE 0.010 0.001 PHE A 208 TYR 0.015 0.002 TYR A 372 ARG 0.006 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.5009 (mmt) cc_final: 0.4370 (mmt) REVERT: B 362 MET cc_start: 0.4810 (tpt) cc_final: 0.4181 (tpp) REVERT: B 475 MET cc_start: 0.4829 (mtm) cc_final: 0.4611 (ptp) outliers start: 3 outliers final: 0 residues processed: 36 average time/residue: 0.3059 time to fit residues: 16.5515 Evaluate side-chains 31 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 5.9990 chunk 72 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN A 446 ASN B 150 ASN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN B 406 ASN B 431 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8021 Z= 0.315 Angle : 0.691 7.831 10795 Z= 0.371 Chirality : 0.044 0.163 1175 Planarity : 0.004 0.046 1374 Dihedral : 10.541 88.615 1110 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.67 % Allowed : 18.56 % Favored : 78.77 % 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: -1.43 (0.27), residues: 947 helix: -0.00 (0.29), residues: 320 sheet: -1.52 (0.40), residues: 162 loop : -1.36 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 311 HIS 0.009 0.002 HIS A 314 PHE 0.012 0.002 PHE A 84 TYR 0.017 0.002 TYR B 519 ARG 0.006 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 31 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8923 (ppp) cc_final: 0.8566 (ppp) REVERT: B 84 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7038 (t80) REVERT: B 300 TYR cc_start: 0.2386 (OUTLIER) cc_final: 0.2174 (m-10) outliers start: 23 outliers final: 11 residues processed: 52 average time/residue: 0.1722 time to fit residues: 13.6610 Evaluate side-chains 44 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 31 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 507 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 69 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8021 Z= 0.157 Angle : 0.559 6.625 10795 Z= 0.303 Chirality : 0.042 0.150 1175 Planarity : 0.003 0.038 1374 Dihedral : 9.837 82.807 1110 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.90 % Allowed : 16.71 % Favored : 80.39 % 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: -1.22 (0.27), residues: 947 helix: 0.22 (0.30), residues: 321 sheet: -1.53 (0.40), residues: 161 loop : -1.22 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 311 HIS 0.006 0.001 HIS A 314 PHE 0.010 0.001 PHE B 303 TYR 0.018 0.001 TYR A 372 ARG 0.002 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 32 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8961 (ppp) cc_final: 0.8687 (ppp) REVERT: B 362 MET cc_start: 0.4809 (tpt) cc_final: 0.3833 (tpp) REVERT: B 421 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8252 (p0) REVERT: B 512 MET cc_start: 0.4905 (ppp) cc_final: 0.4597 (ppp) outliers start: 25 outliers final: 12 residues processed: 56 average time/residue: 0.1772 time to fit residues: 15.1436 Evaluate side-chains 47 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 34 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 507 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 44 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 479 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8021 Z= 0.265 Angle : 0.633 9.084 10795 Z= 0.334 Chirality : 0.042 0.153 1175 Planarity : 0.004 0.048 1374 Dihedral : 10.208 86.148 1110 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.06 % Allowed : 17.17 % Favored : 78.77 % 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: -1.26 (0.27), residues: 947 helix: 0.25 (0.30), residues: 317 sheet: -1.64 (0.40), residues: 163 loop : -1.24 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 311 HIS 0.005 0.001 HIS A 441 PHE 0.010 0.001 PHE A 84 TYR 0.016 0.002 TYR A 300 ARG 0.005 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 34 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8894 (ppp) cc_final: 0.8516 (ppp) REVERT: B 156 MET cc_start: 0.4786 (tpp) cc_final: 0.4579 (mmm) REVERT: B 300 TYR cc_start: 0.2051 (OUTLIER) cc_final: 0.1611 (m-10) outliers start: 35 outliers final: 19 residues processed: 66 average time/residue: 0.1758 time to fit residues: 17.0490 Evaluate side-chains 53 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 33 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8021 Z= 0.213 Angle : 0.626 14.704 10795 Z= 0.324 Chirality : 0.042 0.147 1175 Planarity : 0.003 0.047 1374 Dihedral : 9.937 85.856 1110 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.36 % Allowed : 17.98 % Favored : 78.65 % 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: -1.31 (0.27), residues: 947 helix: 0.27 (0.30), residues: 323 sheet: -1.70 (0.40), residues: 166 loop : -1.32 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 311 HIS 0.006 0.001 HIS A 314 PHE 0.021 0.001 PHE B 333 TYR 0.016 0.002 TYR A 372 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 33 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8900 (ppp) cc_final: 0.8516 (ppp) REVERT: B 125 MET cc_start: 0.6372 (pmm) cc_final: 0.5910 (pmm) REVERT: B 156 MET cc_start: 0.4653 (tpp) cc_final: 0.4421 (mmm) outliers start: 29 outliers final: 22 residues processed: 59 average time/residue: 0.1992 time to fit residues: 16.9843 Evaluate side-chains 55 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 33 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8021 Z= 0.293 Angle : 0.686 10.423 10795 Z= 0.356 Chirality : 0.043 0.158 1175 Planarity : 0.004 0.049 1374 Dihedral : 10.131 87.234 1110 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.83 % Allowed : 18.56 % Favored : 77.61 % 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: -1.47 (0.27), residues: 947 helix: 0.11 (0.29), residues: 323 sheet: -1.91 (0.39), residues: 170 loop : -1.32 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 311 HIS 0.008 0.002 HIS A 314 PHE 0.012 0.001 PHE B 333 TYR 0.015 0.002 TYR B 471 ARG 0.006 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 33 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8360 (t0) REVERT: A 125 MET cc_start: 0.8567 (mmm) cc_final: 0.8247 (mmm) REVERT: A 156 MET cc_start: 0.8896 (ppp) cc_final: 0.8528 (ppp) REVERT: A 393 MET cc_start: 0.8764 (mpp) cc_final: 0.8494 (mmm) REVERT: B 156 MET cc_start: 0.4718 (tpp) cc_final: 0.4456 (mmm) REVERT: B 300 TYR cc_start: 0.1927 (OUTLIER) cc_final: 0.1672 (m-10) REVERT: B 362 MET cc_start: 0.5064 (tpt) cc_final: 0.4271 (tpp) outliers start: 33 outliers final: 24 residues processed: 63 average time/residue: 0.2060 time to fit residues: 19.2708 Evaluate side-chains 57 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 31 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8021 Z= 0.244 Angle : 0.659 14.335 10795 Z= 0.340 Chirality : 0.043 0.163 1175 Planarity : 0.004 0.050 1374 Dihedral : 9.853 86.208 1110 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.83 % Allowed : 20.19 % Favored : 75.99 % 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: -1.47 (0.27), residues: 947 helix: 0.17 (0.30), residues: 320 sheet: -1.94 (0.39), residues: 166 loop : -1.37 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 311 HIS 0.008 0.001 HIS A 314 PHE 0.016 0.001 PHE B 333 TYR 0.016 0.002 TYR A 372 ARG 0.005 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 32 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8923 (ppp) cc_final: 0.8507 (ppp) REVERT: B 125 MET cc_start: 0.6431 (pmm) cc_final: 0.5913 (pmm) REVERT: B 156 MET cc_start: 0.4672 (tpp) cc_final: 0.4410 (mmm) REVERT: B 300 TYR cc_start: 0.1830 (OUTLIER) cc_final: 0.1588 (m-10) REVERT: B 362 MET cc_start: 0.4873 (tpt) cc_final: 0.4231 (tpp) REVERT: B 421 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8445 (p0) outliers start: 33 outliers final: 27 residues processed: 63 average time/residue: 0.1943 time to fit residues: 17.6217 Evaluate side-chains 60 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 31 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 525 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8021 Z= 0.210 Angle : 0.642 12.324 10795 Z= 0.330 Chirality : 0.042 0.169 1175 Planarity : 0.003 0.043 1374 Dihedral : 9.675 87.743 1110 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.25 % Allowed : 21.23 % Favored : 75.52 % 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: -1.42 (0.27), residues: 947 helix: 0.24 (0.30), residues: 320 sheet: -1.96 (0.39), residues: 166 loop : -1.34 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 311 HIS 0.007 0.001 HIS A 314 PHE 0.019 0.001 PHE B 333 TYR 0.017 0.002 TYR A 372 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 32 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8923 (ppp) cc_final: 0.8538 (ppp) REVERT: A 393 MET cc_start: 0.8791 (mpp) cc_final: 0.8513 (mmm) REVERT: B 125 MET cc_start: 0.6538 (pmm) cc_final: 0.6074 (pmm) REVERT: B 156 MET cc_start: 0.4583 (tpp) cc_final: 0.4333 (mmm) REVERT: B 362 MET cc_start: 0.4773 (tpt) cc_final: 0.4561 (mmt) REVERT: B 421 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8450 (p0) REVERT: B 512 MET cc_start: 0.5276 (ppp) cc_final: 0.5006 (ppp) outliers start: 28 outliers final: 23 residues processed: 59 average time/residue: 0.1836 time to fit residues: 15.7043 Evaluate side-chains 55 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 31 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 525 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 26 optimal weight: 0.0570 chunk 77 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8021 Z= 0.196 Angle : 0.627 12.958 10795 Z= 0.324 Chirality : 0.042 0.150 1175 Planarity : 0.003 0.045 1374 Dihedral : 9.576 88.084 1110 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.02 % Allowed : 21.58 % Favored : 75.41 % 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: -1.33 (0.27), residues: 947 helix: 0.34 (0.30), residues: 320 sheet: -1.89 (0.39), residues: 164 loop : -1.32 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 311 HIS 0.007 0.001 HIS A 314 PHE 0.025 0.001 PHE B 17 TYR 0.018 0.002 TYR A 372 ARG 0.004 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 32 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8913 (ppp) cc_final: 0.8527 (ppp) REVERT: A 393 MET cc_start: 0.8841 (mpp) cc_final: 0.8575 (mmm) REVERT: B 125 MET cc_start: 0.6518 (pmm) cc_final: 0.6061 (pmm) REVERT: B 156 MET cc_start: 0.4533 (tpp) cc_final: 0.4277 (mmm) REVERT: B 512 MET cc_start: 0.5173 (ppp) cc_final: 0.4924 (ppp) outliers start: 26 outliers final: 24 residues processed: 57 average time/residue: 0.1631 time to fit residues: 14.1856 Evaluate side-chains 55 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 31 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 525 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 75 optimal weight: 0.0040 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 HIS B 441 HIS ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8021 Z= 0.159 Angle : 0.616 11.534 10795 Z= 0.318 Chirality : 0.043 0.156 1175 Planarity : 0.003 0.035 1374 Dihedral : 9.235 89.919 1110 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.32 % Allowed : 22.04 % Favored : 75.64 % 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 (0.28), residues: 947 helix: 0.43 (0.30), residues: 321 sheet: -1.77 (0.39), residues: 166 loop : -1.18 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 311 HIS 0.005 0.001 HIS A 314 PHE 0.019 0.001 PHE B 17 TYR 0.020 0.002 TYR A 275 ARG 0.004 0.000 ARG B 348 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 33 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: -0.0452 (mtp) cc_final: -0.0791 (mtt) REVERT: A 156 MET cc_start: 0.8889 (ppp) cc_final: 0.8553 (ppp) REVERT: A 393 MET cc_start: 0.8846 (mpp) cc_final: 0.8546 (mmm) REVERT: B 125 MET cc_start: 0.6634 (pmm) cc_final: 0.6261 (pmm) REVERT: B 156 MET cc_start: 0.4444 (tpp) cc_final: 0.4220 (mmm) REVERT: B 475 MET cc_start: 0.4070 (mtt) cc_final: 0.3780 (ptp) REVERT: B 512 MET cc_start: 0.4830 (ppp) cc_final: 0.4459 (ppp) outliers start: 20 outliers final: 15 residues processed: 53 average time/residue: 0.1913 time to fit residues: 15.0057 Evaluate side-chains 47 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 32 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 525 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 0.0050 chunk 20 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.043627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.035708 restraints weight = 94336.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.036491 restraints weight = 67926.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.037050 restraints weight = 53718.348| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8021 Z= 0.162 Angle : 0.607 11.074 10795 Z= 0.312 Chirality : 0.042 0.139 1175 Planarity : 0.003 0.035 1374 Dihedral : 9.207 88.204 1110 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.20 % Allowed : 22.16 % Favored : 75.64 % 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: -1.02 (0.28), residues: 947 helix: 0.52 (0.30), residues: 315 sheet: -1.70 (0.41), residues: 158 loop : -1.08 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 311 HIS 0.006 0.001 HIS A 314 PHE 0.018 0.001 PHE B 17 TYR 0.020 0.002 TYR A 275 ARG 0.003 0.000 ARG A 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1590.99 seconds wall clock time: 29 minutes 28.65 seconds (1768.65 seconds total)