Starting phenix.real_space_refine on Fri Aug 9 06:28:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvq_16268/08_2024/8bvq_16268.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvq_16268/08_2024/8bvq_16268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvq_16268/08_2024/8bvq_16268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvq_16268/08_2024/8bvq_16268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvq_16268/08_2024/8bvq_16268.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvq_16268/08_2024/8bvq_16268.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2650 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 7486 2.51 5 N 2029 2.21 5 O 2328 1.98 5 H 11258 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 291": "OE1" <-> "OE2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A PHE 738": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 219": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 23133 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 12092 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 29, 'TRANS': 755} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 5337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 5337 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 11, 'TRANS': 352} Chain: "C" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 793 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain: "D" Number of atoms: 3478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3478 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 12, 'TRANS': 206} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1294 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 139 Classifications: {'peptide': 7} Modifications used: {'COO': 1, 'NH2NOTPRO': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'UX8:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 10.65, per 1000 atoms: 0.46 Number of scatterers: 23133 At special positions: 0 Unit cell: (122.84, 106.24, 134.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2328 8.00 N 2029 7.00 C 7486 6.00 H 11258 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.48 Conformation dependent library (CDL) restraints added in 2.3 seconds 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2774 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 18 sheets defined 22.5% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.542A pdb=" N MET A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.802A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 144 removed outlier: 3.768A pdb=" N ASP A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 216 through 233 removed outlier: 3.828A pdb=" N ARG A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.558A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.858A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.061A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.619A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.569A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 209 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 228 through 241 Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'E' and resid 51 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 80 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.749A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 5.667A pdb=" N ILE A 254 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 260 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 193 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.378A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.905A pdb=" N ALA A 375 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 2 through 5 removed outlier: 3.636A pdb=" N UX8 G 3 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 426 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR A 617 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 519 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.547A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 50 removed outlier: 4.204A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.026A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 100 through 101 removed outlier: 3.725A pdb=" N SER B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 122 through 124 removed outlier: 7.173A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.367A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.462A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.537A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.657A pdb=" N ALA B 307 " --> pdb=" O TRP B 317 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.730A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AB9, first strand: chain 'E' and resid 64 through 65 removed outlier: 4.559A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE E 74 " --> pdb=" O MET E 64 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR E 94 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1479 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: 8.43 Time building geometry restraints manager: 17.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11252 1.02 - 1.22: 5 1.22 - 1.42: 5149 1.42 - 1.61: 6924 1.61 - 1.81: 64 Bond restraints: 23394 Sorted by residual: bond pdb=" CB UX8 G 3 " pdb=" HB2 UX8 G 3 " ideal model delta sigma weight residual 0.970 1.243 -0.273 2.00e-02 2.50e+03 1.87e+02 bond pdb=" CZ3 UX8 G 3 " pdb=" HZ3 UX8 G 3 " ideal model delta sigma weight residual 0.930 1.132 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" CE3 UX8 G 3 " pdb=" HE3 UX8 G 3 " ideal model delta sigma weight residual 0.930 1.118 -0.188 2.00e-02 2.50e+03 8.84e+01 bond pdb=" CA UX8 G 3 " pdb=" C UX8 G 3 " ideal model delta sigma weight residual 1.525 1.334 0.191 2.10e-02 2.27e+03 8.24e+01 bond pdb=" CA UX8 G 3 " pdb=" CB UX8 G 3 " ideal model delta sigma weight residual 1.530 1.711 -0.181 2.00e-02 2.50e+03 8.21e+01 ... (remaining 23389 not shown) Histogram of bond angle deviations from ideal: 69.26 - 84.09: 3 84.09 - 98.93: 1 98.93 - 113.76: 27423 113.76 - 128.60: 14488 128.60 - 143.43: 78 Bond angle restraints: 41993 Sorted by residual: angle pdb=" CA UX8 G 3 " pdb=" C UX8 G 3 " pdb=" O UX8 G 3 " ideal model delta sigma weight residual 120.80 143.43 -22.63 1.70e+00 3.46e-01 1.77e+02 angle pdb=" C PRO A 684 " pdb=" CA PRO A 684 " pdb=" HA PRO A 684 " ideal model delta sigma weight residual 109.00 69.26 39.74 3.00e+00 1.11e-01 1.75e+02 angle pdb=" N PRO A 684 " pdb=" CA PRO A 684 " pdb=" HA PRO A 684 " ideal model delta sigma weight residual 110.00 74.86 35.14 3.00e+00 1.11e-01 1.37e+02 angle pdb=" CB PRO A 684 " pdb=" CA PRO A 684 " pdb=" HA PRO A 684 " ideal model delta sigma weight residual 109.00 76.06 32.94 3.00e+00 1.11e-01 1.21e+02 angle pdb=" CA UX8 G 3 " pdb=" C UX8 G 3 " pdb=" N THR G 4 " ideal model delta sigma weight residual 116.20 103.08 13.12 2.00e+00 2.50e-01 4.30e+01 ... (remaining 41988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 9778 17.75 - 35.50: 964 35.50 - 53.25: 289 53.25 - 71.00: 78 71.00 - 88.74: 11 Dihedral angle restraints: 11120 sinusoidal: 5963 harmonic: 5157 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual 93.00 151.79 -58.79 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CA ASP A 614 " pdb=" CB ASP A 614 " pdb=" CG ASP A 614 " pdb=" OD1 ASP A 614 " ideal model delta sinusoidal sigma weight residual -30.00 -84.40 54.40 1 2.00e+01 2.50e-03 1.00e+01 dihedral pdb=" CA ARG C 33 " pdb=" CB ARG C 33 " pdb=" CG ARG C 33 " pdb=" CD ARG C 33 " ideal model delta sinusoidal sigma weight residual 180.00 120.59 59.41 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 11117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1649 0.082 - 0.164: 145 0.164 - 0.246: 1 0.246 - 0.328: 0 0.328 - 0.409: 2 Chirality restraints: 1797 Sorted by residual: chirality pdb=" CB UX8 G 3 " pdb=" CA UX8 G 3 " pdb=" CG UX8 G 3 " pdb=" O9 UX8 G 3 " both_signs ideal model delta sigma weight residual False -2.38 -2.79 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA PRO A 684 " pdb=" N PRO A 684 " pdb=" C PRO A 684 " pdb=" CB PRO A 684 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA UX8 G 3 " pdb=" N UX8 G 3 " pdb=" C UX8 G 3 " pdb=" CB UX8 G 3 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 1794 not shown) Planarity restraints: 3599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 35 " -0.027 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO B 36 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 185 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C ASN A 185 " 0.026 2.00e-02 2.50e+03 pdb=" O ASN A 185 " -0.010 2.00e-02 2.50e+03 pdb=" N HIS A 186 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 31 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO D 32 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO D 32 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 32 " 0.018 5.00e-02 4.00e+02 ... (remaining 3596 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 514 2.12 - 2.74: 40715 2.74 - 3.36: 63818 3.36 - 3.98: 81734 3.98 - 4.60: 127390 Nonbonded interactions: 314171 Sorted by model distance: nonbonded pdb=" O HIS A 677 " pdb=" H THR A 692 " model vdw 1.503 2.450 nonbonded pdb=" OE1 GLU A 435 " pdb=" H GLU A 435 " model vdw 1.618 2.450 nonbonded pdb=" OG1 THR B 309 " pdb=" H VAL B 314 " model vdw 1.626 2.450 nonbonded pdb=" O LEU A 66 " pdb=" HG1 THR A 69 " model vdw 1.631 2.450 nonbonded pdb=" OD2 ASP A 362 " pdb="HH21 ARG A 366 " model vdw 1.635 2.450 ... (remaining 314166 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.350 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 68.080 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 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 : 0.004 0.191 12136 Z= 0.297 Angle : 0.551 22.631 16497 Z= 0.290 Chirality : 0.044 0.409 1797 Planarity : 0.003 0.040 2173 Dihedral : 16.055 88.745 4390 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.31 % Allowed : 23.46 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1503 helix: 2.48 (0.30), residues: 316 sheet: -0.90 (0.24), residues: 471 loop : -1.07 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 317 HIS 0.003 0.001 HIS A 677 PHE 0.015 0.001 PHE A 738 TYR 0.013 0.001 TYR D 184 ARG 0.005 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 1.952 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: D 183 GLU cc_start: 0.8235 (tp30) cc_final: 0.7579 (tt0) outliers start: 4 outliers final: 3 residues processed: 173 average time/residue: 0.4579 time to fit residues: 118.2625 Evaluate side-chains 165 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 808 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.0270 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.0457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12136 Z= 0.196 Angle : 0.499 5.949 16497 Z= 0.267 Chirality : 0.043 0.366 1797 Planarity : 0.004 0.052 2173 Dihedral : 4.302 59.750 1673 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.73 % Allowed : 21.81 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1503 helix: 2.21 (0.29), residues: 325 sheet: -0.84 (0.24), residues: 470 loop : -1.27 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 376 HIS 0.004 0.001 HIS A 280 PHE 0.010 0.001 PHE A 426 TYR 0.017 0.001 TYR D 184 ARG 0.005 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 1.877 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: A 243 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8536 (p) REVERT: A 501 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7282 (tt) REVERT: C 57 ILE cc_start: 0.8206 (pt) cc_final: 0.7959 (tp) REVERT: C 78 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7914 (mtpt) REVERT: D 183 GLU cc_start: 0.8287 (tp30) cc_final: 0.8013 (tt0) outliers start: 22 outliers final: 16 residues processed: 193 average time/residue: 0.4537 time to fit residues: 131.9105 Evaluate side-chains 183 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 573 ASN Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 0.3980 chunk 119 optimal weight: 0.0670 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 108 optimal weight: 0.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 12136 Z= 0.137 Angle : 0.474 6.232 16497 Z= 0.252 Chirality : 0.043 0.367 1797 Planarity : 0.003 0.039 2173 Dihedral : 4.218 59.695 1673 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.42 % Allowed : 21.97 % Favored : 76.61 % 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: -0.44 (0.22), residues: 1503 helix: 2.30 (0.29), residues: 332 sheet: -0.81 (0.24), residues: 471 loop : -1.18 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 376 HIS 0.004 0.001 HIS A 677 PHE 0.009 0.001 PHE A 426 TYR 0.014 0.001 TYR D 184 ARG 0.003 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.921 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. REVERT: A 243 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8492 (p) REVERT: C 57 ILE cc_start: 0.8214 (pt) cc_final: 0.7975 (tp) REVERT: C 78 LYS cc_start: 0.8071 (ttmt) cc_final: 0.7864 (mtpt) REVERT: D 183 GLU cc_start: 0.8243 (tp30) cc_final: 0.7593 (tt0) outliers start: 18 outliers final: 13 residues processed: 187 average time/residue: 0.4654 time to fit residues: 133.3859 Evaluate side-chains 174 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12136 Z= 0.201 Angle : 0.483 6.163 16497 Z= 0.257 Chirality : 0.043 0.367 1797 Planarity : 0.003 0.045 2173 Dihedral : 4.276 58.855 1673 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.60 % Allowed : 21.26 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1503 helix: 2.20 (0.29), residues: 332 sheet: -0.79 (0.24), residues: 475 loop : -1.26 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 776 HIS 0.004 0.001 HIS A 677 PHE 0.011 0.001 PHE A 426 TYR 0.016 0.001 TYR D 184 ARG 0.003 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 1.756 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. REVERT: A 243 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8534 (p) REVERT: C 57 ILE cc_start: 0.8270 (pt) cc_final: 0.8063 (tp) REVERT: D 183 GLU cc_start: 0.8321 (tp30) cc_final: 0.7644 (tt0) outliers start: 33 outliers final: 21 residues processed: 191 average time/residue: 0.4636 time to fit residues: 135.8842 Evaluate side-chains 181 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.0370 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 73 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 GLN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12136 Z= 0.263 Angle : 0.509 6.531 16497 Z= 0.273 Chirality : 0.043 0.364 1797 Planarity : 0.004 0.051 2173 Dihedral : 4.431 58.872 1673 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.68 % Allowed : 22.20 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.21), residues: 1503 helix: 2.10 (0.28), residues: 326 sheet: -0.86 (0.24), residues: 470 loop : -1.37 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 205 HIS 0.004 0.001 HIS A 677 PHE 0.013 0.001 PHE A 426 TYR 0.021 0.001 TYR D 80 ARG 0.003 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 1.645 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. REVERT: A 243 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8541 (p) REVERT: C 57 ILE cc_start: 0.8315 (pt) cc_final: 0.8113 (tp) outliers start: 34 outliers final: 27 residues processed: 190 average time/residue: 0.4297 time to fit residues: 122.9921 Evaluate side-chains 183 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.0020 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12136 Z= 0.208 Angle : 0.492 6.631 16497 Z= 0.263 Chirality : 0.043 0.366 1797 Planarity : 0.003 0.054 2173 Dihedral : 4.394 59.131 1673 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.52 % Allowed : 22.52 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.21), residues: 1503 helix: 2.14 (0.28), residues: 326 sheet: -0.86 (0.24), residues: 470 loop : -1.36 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 376 HIS 0.002 0.001 HIS A 533 PHE 0.011 0.001 PHE A 426 TYR 0.015 0.001 TYR D 184 ARG 0.003 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 1.740 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. REVERT: A 243 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8534 (p) REVERT: D 225 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7848 (mtp) outliers start: 32 outliers final: 28 residues processed: 186 average time/residue: 0.4340 time to fit residues: 122.6641 Evaluate side-chains 187 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 0.4980 chunk 104 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12136 Z= 0.243 Angle : 0.503 6.529 16497 Z= 0.269 Chirality : 0.043 0.365 1797 Planarity : 0.004 0.054 2173 Dihedral : 4.434 58.509 1673 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.07 % Allowed : 22.28 % Favored : 74.65 % 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: -0.72 (0.21), residues: 1503 helix: 2.08 (0.28), residues: 326 sheet: -0.90 (0.24), residues: 476 loop : -1.39 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 205 HIS 0.003 0.001 HIS A 533 PHE 0.011 0.001 PHE A 426 TYR 0.016 0.001 TYR D 184 ARG 0.003 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 163 time to evaluate : 1.786 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. REVERT: A 243 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8536 (p) REVERT: D 225 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7797 (mtp) outliers start: 39 outliers final: 32 residues processed: 192 average time/residue: 0.4490 time to fit residues: 131.9159 Evaluate side-chains 191 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.0370 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 12136 Z= 0.157 Angle : 0.478 6.760 16497 Z= 0.254 Chirality : 0.043 0.367 1797 Planarity : 0.003 0.053 2173 Dihedral : 4.309 58.782 1673 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.19 % Favored : 95.74 % Rotamer: Outliers : 2.28 % Allowed : 22.83 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1503 helix: 2.34 (0.29), residues: 326 sheet: -0.82 (0.24), residues: 470 loop : -1.28 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 376 HIS 0.002 0.001 HIS B 347 PHE 0.009 0.001 PHE A 426 TYR 0.018 0.001 TYR D 80 ARG 0.003 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 2.102 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 243 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8534 (p) REVERT: D 183 GLU cc_start: 0.8293 (tp30) cc_final: 0.7622 (tt0) outliers start: 29 outliers final: 22 residues processed: 188 average time/residue: 0.4469 time to fit residues: 127.8038 Evaluate side-chains 181 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 125 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12136 Z= 0.252 Angle : 0.505 6.784 16497 Z= 0.270 Chirality : 0.043 0.365 1797 Planarity : 0.004 0.055 2173 Dihedral : 4.394 57.932 1673 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.44 % Allowed : 23.07 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.22), residues: 1503 helix: 2.20 (0.29), residues: 326 sheet: -0.88 (0.24), residues: 476 loop : -1.33 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 205 HIS 0.003 0.001 HIS A 533 PHE 0.011 0.001 PHE A 791 TYR 0.016 0.001 TYR D 184 ARG 0.003 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3006 Ramachandran restraints generated. 1503 Oldfield, 0 Emsley, 1503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. Residue THR 328 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "SER E 111 " (corrupted residue). Skipping it. Residue LYS 5 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 1.432 Fit side-chains TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER D 242 " (corrupted residue). Skipping it. REVERT: A 243 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8534 (p) outliers start: 31 outliers final: 28 residues processed: 182 average time/residue: 0.4379 time to fit residues: 123.4020 Evaluate side-chains 185 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 28 TYR Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.0270 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: