Starting phenix.real_space_refine on Fri Jul 19 12:27:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/07_2024/8u1m_41817_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/07_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_41817/07_2024/8u1m_41817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/07_2024/8u1m_41817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/07_2024/8u1m_41817_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1m_41817/07_2024/8u1m_41817_neut.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-5388/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: 4.83, 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: 3.34 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: 0.96 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: 2.27 Time building geometry restraints manager: 3.56 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 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: 0.840 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.060 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.400 ------------------------------------------------------------------------------- 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 : 1.008 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: 0.2258 time to fit residues: 11.9335 Evaluate side-chains 31 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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: 3.9990 chunk 72 optimal weight: 30.0000 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN A 446 ASN B 118 GLN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 345 ASN B 406 ASN B 431 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1443 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= 0.291 Angle : 0.662 7.478 10795 Z= 0.355 Chirality : 0.043 0.160 1175 Planarity : 0.004 0.077 1374 Dihedral : 10.546 78.826 1110 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 30.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.71 % Allowed : 17.98 % Favored : 78.31 % 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: -1.38 (0.27), residues: 947 helix: -0.06 (0.29), residues: 322 sheet: -1.44 (0.40), residues: 162 loop : -1.27 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 311 HIS 0.008 0.002 HIS A 314 PHE 0.011 0.002 PHE A 84 TYR 0.018 0.002 TYR B 519 ARG 0.009 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 64 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 32 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8905 (ppp) cc_final: 0.8580 (ppp) REVERT: B 84 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.6977 (t80) REVERT: B 125 MET cc_start: 0.6358 (pmm) cc_final: 0.6138 (pmm) REVERT: B 300 TYR cc_start: 0.2554 (OUTLIER) cc_final: 0.2319 (m-10) outliers start: 32 outliers final: 13 residues processed: 61 average time/residue: 0.1770 time to fit residues: 16.0425 Evaluate side-chains 45 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 30 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 208 PHE Chi-restraints excluded: chain A residue 221 ARG 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 31 THR Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 188 ASP 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: 10.0000 chunk 23 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8021 Z= 0.241 Angle : 0.607 7.113 10795 Z= 0.326 Chirality : 0.042 0.155 1175 Planarity : 0.004 0.075 1374 Dihedral : 10.237 88.850 1110 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 27.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.83 % Allowed : 18.68 % 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: -1.41 (0.27), residues: 947 helix: 0.02 (0.29), residues: 320 sheet: -1.49 (0.41), residues: 160 loop : -1.36 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 311 HIS 0.005 0.001 HIS A 314 PHE 0.010 0.001 PHE A 208 TYR 0.014 0.002 TYR A 300 ARG 0.009 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 66 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 33 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.1507 (mmt) cc_final: 0.1109 (mmt) REVERT: A 156 MET cc_start: 0.8927 (ppp) cc_final: 0.8369 (ppp) REVERT: B 125 MET cc_start: 0.6562 (pmm) cc_final: 0.6311 (pmm) REVERT: B 300 TYR cc_start: 0.2496 (OUTLIER) cc_final: 0.2236 (m-10) outliers start: 33 outliers final: 17 residues processed: 63 average time/residue: 0.1779 time to fit residues: 16.8123 Evaluate side-chains 50 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 32 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 276 THR Chi-restraints excluded: chain A residue 376 ILE 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 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 354 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN B 118 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8021 Z= 0.381 Angle : 0.754 8.281 10795 Z= 0.396 Chirality : 0.044 0.151 1175 Planarity : 0.005 0.085 1374 Dihedral : 10.558 86.009 1110 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 38.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.68 % Allowed : 19.95 % Favored : 74.36 % 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: -1.71 (0.27), residues: 947 helix: -0.26 (0.29), residues: 323 sheet: -1.90 (0.40), residues: 161 loop : -1.42 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 311 HIS 0.008 0.002 HIS B 184 PHE 0.014 0.002 PHE A 84 TYR 0.018 0.003 TYR A 300 ARG 0.010 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 78 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 29 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.2009 (mmt) cc_final: 0.1442 (mmt) REVERT: A 156 MET cc_start: 0.8826 (ppp) cc_final: 0.8398 (ppp) REVERT: B 84 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7278 (t80) REVERT: B 300 TYR cc_start: 0.2886 (OUTLIER) cc_final: 0.2397 (m-10) REVERT: B 362 MET cc_start: 0.4547 (OUTLIER) cc_final: 0.4184 (tpt) REVERT: B 429 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7223 (t80) REVERT: B 512 MET cc_start: 0.5662 (ppp) cc_final: 0.5413 (ppp) outliers start: 49 outliers final: 26 residues processed: 75 average time/residue: 0.1834 time to fit residues: 19.9381 Evaluate side-chains 60 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 30 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 ILE 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 216 THR Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 40 LEU 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 151 ASP Chi-restraints excluded: chain B residue 188 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 304 TYR Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 429 TYR 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: 4.9990 chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8021 Z= 0.177 Angle : 0.613 13.104 10795 Z= 0.321 Chirality : 0.042 0.149 1175 Planarity : 0.004 0.071 1374 Dihedral : 9.919 88.264 1110 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.25 % Allowed : 21.35 % 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: -1.40 (0.27), residues: 947 helix: 0.09 (0.30), residues: 328 sheet: -1.82 (0.40), residues: 160 loop : -1.28 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 311 HIS 0.005 0.001 HIS A 314 PHE 0.014 0.001 PHE B 333 TYR 0.019 0.002 TYR A 372 ARG 0.008 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 63 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 35 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8845 (ppp) cc_final: 0.8559 (ppp) REVERT: B 300 TYR cc_start: 0.2035 (OUTLIER) cc_final: 0.1700 (m-10) REVERT: B 362 MET cc_start: 0.4629 (OUTLIER) cc_final: 0.4392 (tpp) outliers start: 28 outliers final: 19 residues processed: 59 average time/residue: 0.1829 time to fit residues: 16.0092 Evaluate side-chains 53 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 32 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 216 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 31 THR 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 354 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 493 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: 10.0000 chunk 82 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 128 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7359 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8021 Z= 0.350 Angle : 0.743 13.875 10795 Z= 0.383 Chirality : 0.044 0.150 1175 Planarity : 0.004 0.082 1374 Dihedral : 10.362 87.349 1110 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 37.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 5.34 % Allowed : 21.00 % Favored : 73.67 % 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: -1.64 (0.27), residues: 947 helix: -0.17 (0.29), residues: 327 sheet: -2.00 (0.40), residues: 160 loop : -1.35 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 311 HIS 0.008 0.002 HIS B 184 PHE 0.014 0.002 PHE B 333 TYR 0.023 0.002 TYR A 275 ARG 0.010 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 77 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 31 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8748 (ppp) cc_final: 0.8463 (ppp) REVERT: A 173 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7240 (tm-30) REVERT: B 128 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: B 300 TYR cc_start: 0.2464 (OUTLIER) cc_final: 0.2174 (m-10) REVERT: B 362 MET cc_start: 0.4533 (OUTLIER) cc_final: 0.3932 (tpp) REVERT: B 512 MET cc_start: 0.5768 (ppp) cc_final: 0.5385 (ppp) outliers start: 46 outliers final: 29 residues processed: 73 average time/residue: 0.1928 time to fit residues: 20.0489 Evaluate side-chains 63 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 30 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 31 THR 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 122 ASP Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 188 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 304 TYR Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 362 MET 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 518 GLU Chi-restraints excluded: chain B residue 525 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** 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: 0.7393 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8021 Z= 0.403 Angle : 0.794 12.956 10795 Z= 0.410 Chirality : 0.045 0.153 1175 Planarity : 0.005 0.086 1374 Dihedral : 10.421 88.128 1110 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 41.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 5.34 % Allowed : 21.35 % Favored : 73.32 % 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: -1.94 (0.26), residues: 947 helix: -0.45 (0.28), residues: 324 sheet: -2.13 (0.39), residues: 160 loop : -1.51 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP A 311 HIS 0.009 0.002 HIS A 314 PHE 0.015 0.002 PHE B 129 TYR 0.019 0.003 TYR A 275 ARG 0.010 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 75 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 29 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8773 (ppp) cc_final: 0.8561 (ppp) REVERT: A 173 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: B 300 TYR cc_start: 0.2647 (OUTLIER) cc_final: 0.2341 (m-10) REVERT: B 362 MET cc_start: 0.4496 (OUTLIER) cc_final: 0.4014 (tpp) REVERT: B 512 MET cc_start: 0.5978 (ppp) cc_final: 0.4890 (ppp) outliers start: 46 outliers final: 31 residues processed: 72 average time/residue: 0.1838 time to fit residues: 19.3428 Evaluate side-chains 63 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 29 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 31 THR 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 122 ASP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 188 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 304 TYR Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 350 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 362 MET 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 518 GLU 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: 7.9990 chunk 27 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8021 Z= 0.178 Angle : 0.631 12.214 10795 Z= 0.327 Chirality : 0.043 0.184 1175 Planarity : 0.004 0.069 1374 Dihedral : 9.570 86.964 1110 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.36 % Allowed : 23.90 % Favored : 72.74 % 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: -1.44 (0.27), residues: 947 helix: 0.14 (0.30), residues: 319 sheet: -1.86 (0.41), residues: 155 loop : -1.36 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 311 HIS 0.006 0.001 HIS A 314 PHE 0.018 0.001 PHE B 333 TYR 0.019 0.001 TYR A 372 ARG 0.007 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 63 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 34 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.3002 (mmt) cc_final: 0.2579 (mmm) REVERT: B 300 TYR cc_start: 0.1906 (OUTLIER) cc_final: 0.1591 (m-10) REVERT: B 362 MET cc_start: 0.4107 (OUTLIER) cc_final: 0.3849 (tpp) REVERT: B 475 MET cc_start: 0.4186 (mtt) cc_final: 0.3821 (ptp) REVERT: B 512 MET cc_start: 0.5517 (OUTLIER) cc_final: 0.5309 (ppp) outliers start: 29 outliers final: 19 residues processed: 59 average time/residue: 0.1928 time to fit residues: 16.8427 Evaluate side-chains 55 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 33 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 31 THR 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 362 MET 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 512 MET 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: 8.9990 chunk 87 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 ASN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7404 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 8021 Z= 0.428 Angle : 0.815 12.805 10795 Z= 0.421 Chirality : 0.046 0.230 1175 Planarity : 0.005 0.083 1374 Dihedral : 10.356 87.672 1110 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 42.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.71 % Allowed : 24.48 % Favored : 71.81 % 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: -1.86 (0.26), residues: 947 helix: -0.36 (0.28), residues: 316 sheet: -2.20 (0.39), residues: 153 loop : -1.44 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP A 311 HIS 0.009 0.002 HIS A 314 PHE 0.031 0.002 PHE B 17 TYR 0.032 0.003 TYR A 275 ARG 0.009 0.001 ARG A 177 *********************** 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 64 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 32 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: B 24 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8950 (mt) REVERT: B 300 TYR cc_start: 0.2501 (OUTLIER) cc_final: 0.2227 (m-10) REVERT: B 362 MET cc_start: 0.4378 (OUTLIER) cc_final: 0.4042 (tpt) REVERT: B 512 MET cc_start: 0.6125 (ppp) cc_final: 0.5080 (ppp) outliers start: 32 outliers final: 24 residues processed: 61 average time/residue: 0.1771 time to fit residues: 16.4286 Evaluate side-chains 57 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 30 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 363 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 31 THR 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 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 309 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 362 MET 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: 10.0000 chunk 94 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 75 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8021 Z= 0.206 Angle : 0.668 12.085 10795 Z= 0.343 Chirality : 0.044 0.174 1175 Planarity : 0.004 0.077 1374 Dihedral : 9.739 88.117 1110 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 29.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.78 % Allowed : 25.41 % Favored : 71.81 % 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: -1.55 (0.27), residues: 947 helix: -0.08 (0.29), residues: 320 sheet: -1.90 (0.42), residues: 145 loop : -1.35 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 311 HIS 0.006 0.001 HIS A 314 PHE 0.023 0.002 PHE B 333 TYR 0.024 0.002 TYR A 275 ARG 0.008 0.001 ARG A 177 ********************** 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 57 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 33 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8920 (mp) REVERT: B 300 TYR cc_start: 0.2018 (OUTLIER) cc_final: 0.1794 (m-10) REVERT: B 362 MET cc_start: 0.4139 (OUTLIER) cc_final: 0.3920 (mmt) REVERT: B 512 MET cc_start: 0.5912 (ppp) cc_final: 0.5590 (ppp) outliers start: 24 outliers final: 21 residues processed: 55 average time/residue: 0.1846 time to fit residues: 15.0589 Evaluate side-chains 57 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 33 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 108 SER 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 309 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 362 MET 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 69 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 77 optimal weight: 0.0170 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 66 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** 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 = 0.3947 r_free = 0.3947 target = 0.042886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.035272 restraints weight = 95464.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.036068 restraints weight = 68616.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.036601 restraints weight = 53894.760| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8021 Z= 0.156 Angle : 0.635 11.758 10795 Z= 0.323 Chirality : 0.042 0.149 1175 Planarity : 0.003 0.054 1374 Dihedral : 9.196 87.428 1110 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.20 % Allowed : 26.10 % Favored : 71.69 % 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 (0.28), residues: 947 helix: 0.05 (0.29), residues: 327 sheet: -1.87 (0.40), residues: 159 loop : -1.27 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP A 311 HIS 0.004 0.001 HIS B 314 PHE 0.023 0.002 PHE B 333 TYR 0.019 0.001 TYR A 275 ARG 0.005 0.000 ARG A 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1596.27 seconds wall clock time: 29 minutes 57.10 seconds (1797.10 seconds total)