Starting phenix.real_space_refine on Sat Mar 16 06:14:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/03_2024/7z0l_14427_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/03_2024/7z0l_14427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/03_2024/7z0l_14427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/03_2024/7z0l_14427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/03_2024/7z0l_14427_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/03_2024/7z0l_14427_trim.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 4478 2.51 5 N 1180 2.21 5 O 1349 1.98 5 H 6713 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13752 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4557 Classifications: {'peptide': 292} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 274} Chain: "B" Number of atoms: 5946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5946 Classifications: {'peptide': 370} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 342} Chain breaks: 5 Chain: "C" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3081 Classifications: {'peptide': 194} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 172} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.59, per 1000 atoms: 0.48 Number of scatterers: 13752 At special positions: 0 Unit cell: (87.98, 95.4, 144.16, 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 1349 8.00 N 1180 7.00 C 4478 6.00 H 6713 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 401 " - " ASN A 157 " " NAG A 402 " - " ASN A 225 " " NAG E 1 " - " ASN A 43 " " NAG F 1 " - " ASN A 61 " " NAG H 1 " - " ASN B 307 " " NAG I 1 " - " ASN C 46 " Time building additional restraints: 10.09 Conformation dependent library (CDL) restraints added in 1.6 seconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1628 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 16 sheets defined 20.9% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.541A pdb=" N GLY A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.893A pdb=" N MET A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 290 Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 319 through 332 Processing helix chain 'B' and resid 333 through 344 removed outlier: 3.587A pdb=" N GLN B 344 " --> pdb=" O GLY B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 377 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 399 removed outlier: 3.995A pdb=" N GLU B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 446 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.427A pdb=" N THR A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 39 removed outlier: 6.708A pdb=" N CYS A 103 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLY A 117 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU A 101 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR A 119 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 99 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 181 removed outlier: 6.659A pdb=" N LEU A 143 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N CYS A 134 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN A 145 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 132 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LYS A 219 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL A 136 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 168 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 230 removed outlier: 4.105A pdb=" N LEU A 226 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER A 241 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A 228 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS A 239 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 268 through 269 Processing sheet with id=AA8, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.995A pdb=" N ARG B 31 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB1, first strand: chain 'B' and resid 142 through 148 removed outlier: 4.839A pdb=" N HIS B 148 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLY B 133 " --> pdb=" O HIS B 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 181 removed outlier: 6.068A pdb=" N TYR B 163 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 35 through 38 removed outlier: 4.542A pdb=" N LEU C 45 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C 87 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 74 through 77 Processing sheet with id=AB5, first strand: chain 'C' and resid 74 through 77 Processing sheet with id=AB6, first strand: chain 'C' and resid 127 through 135 removed outlier: 6.844A pdb=" N PHE C 129 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA C 147 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLN C 131 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN C 145 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU C 140 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 172 through 179 removed outlier: 4.396A pdb=" N PHE C 161 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N CYS C 159 " --> pdb=" O PRO C 176 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU C 178 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C 157 " --> pdb=" O LEU C 178 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 807 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: 4.95 Time building geometry restraints manager: 10.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6692 1.03 - 1.23: 28 1.23 - 1.42: 3032 1.42 - 1.62: 4150 1.62 - 1.82: 43 Bond restraints: 13945 Sorted by residual: bond pdb=" CB ASN A 131 " pdb=" CG ASN A 131 " ideal model delta sigma weight residual 1.516 1.419 0.097 2.50e-02 1.60e+03 1.50e+01 bond pdb=" CE1 HIS A 57 " pdb=" NE2 HIS A 57 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.09e+01 bond pdb=" CD2 HIS A 57 " pdb=" HD2 HIS A 57 " ideal model delta sigma weight residual 0.930 0.994 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" CG HIS A 57 " pdb=" ND1 HIS A 57 " ideal model delta sigma weight residual 1.378 1.409 -0.031 1.10e-02 8.26e+03 7.85e+00 bond pdb=" C1 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.66e+00 ... (remaining 13940 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.80: 439 106.80 - 113.69: 16406 113.69 - 120.58: 4241 120.58 - 127.48: 3896 127.48 - 134.37: 131 Bond angle restraints: 25113 Sorted by residual: angle pdb=" N ASN A 131 " pdb=" CA ASN A 131 " pdb=" CB ASN A 131 " ideal model delta sigma weight residual 112.63 104.51 8.12 1.61e+00 3.86e-01 2.55e+01 angle pdb=" CA TRP B 356 " pdb=" CB TRP B 356 " pdb=" CG TRP B 356 " ideal model delta sigma weight residual 113.60 120.83 -7.23 1.90e+00 2.77e-01 1.45e+01 angle pdb=" N VAL B 308 " pdb=" CA VAL B 308 " pdb=" C VAL B 308 " ideal model delta sigma weight residual 109.34 116.87 -7.53 2.08e+00 2.31e-01 1.31e+01 angle pdb=" CA ARG C 89 " pdb=" CB ARG C 89 " pdb=" CG ARG C 89 " ideal model delta sigma weight residual 114.10 120.49 -6.39 2.00e+00 2.50e-01 1.02e+01 angle pdb=" N GLN B 280 " pdb=" CA GLN B 280 " pdb=" C GLN B 280 " ideal model delta sigma weight residual 111.02 114.78 -3.76 1.22e+00 6.72e-01 9.49e+00 ... (remaining 25108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.19: 6341 23.19 - 46.37: 296 46.37 - 69.55: 155 69.55 - 92.74: 12 92.74 - 115.92: 17 Dihedral angle restraints: 6821 sinusoidal: 3814 harmonic: 3007 Sorted by residual: dihedral pdb=" CA LEU C 157 " pdb=" C LEU C 157 " pdb=" N ILE C 158 " pdb=" CA ILE C 158 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA PHE B 175 " pdb=" C PHE B 175 " pdb=" N ARG B 176 " pdb=" CA ARG B 176 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA LYS A 175 " pdb=" C LYS A 175 " pdb=" N HIS A 176 " pdb=" CA HIS A 176 " ideal model delta harmonic sigma weight residual 180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 6818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1075 0.124 - 0.247: 36 0.247 - 0.370: 0 0.370 - 0.494: 0 0.494 - 0.617: 2 Chirality restraints: 1113 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 307 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.51e+00 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 157 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.35e+00 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.59e+00 ... (remaining 1110 not shown) Planarity restraints: 2034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 359 " -0.499 9.50e-02 1.11e+02 1.69e-01 4.83e+01 pdb=" NE ARG B 359 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG B 359 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 359 " 0.059 2.00e-02 2.50e+03 pdb=" NH2 ARG B 359 " 0.040 2.00e-02 2.50e+03 pdb="HH11 ARG B 359 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 359 " -0.040 2.00e-02 2.50e+03 pdb="HH21 ARG B 359 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 359 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 262 " 0.182 9.50e-02 1.11e+02 6.59e-02 1.87e+01 pdb=" NE ARG B 262 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 262 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 262 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 262 " -0.053 2.00e-02 2.50e+03 pdb="HH11 ARG B 262 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG B 262 " -0.010 2.00e-02 2.50e+03 pdb="HH21 ARG B 262 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 262 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 436 " 0.340 9.50e-02 1.11e+02 1.14e-01 1.68e+01 pdb=" NE ARG B 436 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 436 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 436 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG B 436 " -0.006 2.00e-02 2.50e+03 pdb="HH11 ARG B 436 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 436 " 0.021 2.00e-02 2.50e+03 pdb="HH21 ARG B 436 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 436 " 0.008 2.00e-02 2.50e+03 ... (remaining 2031 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 283 2.06 - 2.70: 20884 2.70 - 3.33: 39568 3.33 - 3.97: 49580 3.97 - 4.60: 77201 Nonbonded interactions: 187516 Sorted by model distance: nonbonded pdb=" H ALA B 203 " pdb=" OG SER B 213 " model vdw 1.426 1.850 nonbonded pdb=" O ALA B 203 " pdb=" H SER B 213 " model vdw 1.480 1.850 nonbonded pdb=" O PHE B 326 " pdb=" HG1 THR B 330 " model vdw 1.537 1.850 nonbonded pdb="HE22 GLN B 204 " pdb=" OD1 ASP B 208 " model vdw 1.556 1.850 nonbonded pdb=" O VAL B 201 " pdb=" H SER B 216 " model vdw 1.585 1.850 ... (remaining 187511 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 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.560 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: 0.200 Extract box with map and model: 2.680 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 44.900 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5111 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 0.097 7232 Z= 0.322 Angle : 0.947 8.123 9859 Z= 0.530 Chirality : 0.062 0.617 1113 Planarity : 0.013 0.191 1245 Dihedral : 15.673 115.924 2852 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.65 % Allowed : 4.78 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.67 (0.28), residues: 840 helix: -2.00 (0.36), residues: 137 sheet: 0.36 (0.28), residues: 298 loop : -0.37 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.005 TRP C 84 HIS 0.039 0.004 HIS A 57 PHE 0.022 0.003 PHE B 159 TYR 0.042 0.005 TYR B 282 ARG 0.020 0.004 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 210 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.7198 (t80) cc_final: 0.6910 (t80) REVERT: A 144 CYS cc_start: 0.9303 (m) cc_final: 0.8840 (m) REVERT: A 307 TYR cc_start: 0.8970 (m-80) cc_final: 0.8752 (m-80) REVERT: B 31 ARG cc_start: 0.7404 (tpm-80) cc_final: 0.6046 (mmm160) REVERT: B 93 VAL cc_start: 0.6175 (t) cc_final: 0.5938 (t) REVERT: B 264 GLU cc_start: 0.8546 (mm-30) cc_final: 0.7397 (mm-30) REVERT: B 430 LEU cc_start: 0.8846 (tp) cc_final: 0.8567 (tp) REVERT: B 440 ASP cc_start: 0.8177 (m-30) cc_final: 0.7706 (m-30) REVERT: C 60 VAL cc_start: 0.7699 (t) cc_final: 0.7320 (p) outliers start: 5 outliers final: 1 residues processed: 213 average time/residue: 0.5114 time to fit residues: 136.1227 Evaluate side-chains 163 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5181 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7232 Z= 0.239 Angle : 0.723 12.528 9859 Z= 0.365 Chirality : 0.045 0.221 1113 Planarity : 0.006 0.053 1245 Dihedral : 12.448 85.778 1181 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.33 % Allowed : 10.85 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.21 (0.28), residues: 840 helix: 0.13 (0.38), residues: 139 sheet: 0.34 (0.28), residues: 290 loop : 0.16 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 356 HIS 0.007 0.002 HIS C 63 PHE 0.020 0.002 PHE B 61 TYR 0.015 0.002 TYR B 303 ARG 0.008 0.001 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: A 129 PRO cc_start: 0.3540 (Cg_exo) cc_final: 0.3145 (Cg_endo) REVERT: B 31 ARG cc_start: 0.7372 (tpm-80) cc_final: 0.6046 (mmm160) REVERT: B 35 HIS cc_start: 0.3143 (p-80) cc_final: 0.2655 (p90) REVERT: B 102 MET cc_start: 0.3806 (mmm) cc_final: 0.3256 (mmm) REVERT: B 264 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7651 (mm-30) REVERT: B 440 ASP cc_start: 0.8285 (m-30) cc_final: 0.7804 (m-30) REVERT: C 60 VAL cc_start: 0.7436 (t) cc_final: 0.7173 (p) outliers start: 18 outliers final: 13 residues processed: 173 average time/residue: 0.5086 time to fit residues: 110.6721 Evaluate side-chains 167 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 78 GLN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 196 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5319 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7232 Z= 0.302 Angle : 0.740 10.855 9859 Z= 0.374 Chirality : 0.044 0.213 1113 Planarity : 0.006 0.050 1245 Dihedral : 9.891 68.342 1181 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.62 % Allowed : 11.50 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.12 (0.28), residues: 840 helix: 0.62 (0.39), residues: 140 sheet: -0.06 (0.29), residues: 281 loop : -0.21 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 356 HIS 0.011 0.002 HIS C 63 PHE 0.015 0.002 PHE B 159 TYR 0.021 0.003 TYR A 30 ARG 0.005 0.001 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 CYS cc_start: 0.9354 (m) cc_final: 0.8997 (t) REVERT: B 35 HIS cc_start: 0.3329 (p-80) cc_final: 0.2938 (p90) REVERT: B 205 ASP cc_start: -0.3947 (OUTLIER) cc_final: -0.4631 (t70) REVERT: B 264 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7647 (mm-30) REVERT: B 440 ASP cc_start: 0.8473 (m-30) cc_final: 0.7942 (m-30) REVERT: C 55 LEU cc_start: 0.7197 (mt) cc_final: 0.6864 (tp) REVERT: C 60 VAL cc_start: 0.7450 (t) cc_final: 0.7226 (p) outliers start: 28 outliers final: 23 residues processed: 166 average time/residue: 0.5050 time to fit residues: 105.3650 Evaluate side-chains 161 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 186 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 372 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5255 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7232 Z= 0.185 Angle : 0.641 7.761 9859 Z= 0.319 Chirality : 0.043 0.195 1113 Planarity : 0.005 0.044 1245 Dihedral : 8.554 63.279 1181 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.36 % Allowed : 13.05 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.26 (0.29), residues: 840 helix: 1.12 (0.40), residues: 140 sheet: 0.07 (0.30), residues: 273 loop : 0.06 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 356 HIS 0.009 0.002 HIS B 368 PHE 0.013 0.001 PHE B 286 TYR 0.016 0.002 TYR C 209 ARG 0.008 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 GLN cc_start: 0.0193 (OUTLIER) cc_final: -0.1695 (tt0) REVERT: B 208 ASP cc_start: 0.1773 (OUTLIER) cc_final: 0.0727 (t70) REVERT: B 264 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7703 (mm-30) REVERT: B 372 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8297 (mp-120) REVERT: B 387 LYS cc_start: 0.4237 (tppt) cc_final: 0.3796 (mppt) REVERT: B 440 ASP cc_start: 0.8580 (m-30) cc_final: 0.8166 (m-30) REVERT: C 55 LEU cc_start: 0.7175 (mt) cc_final: 0.6832 (tp) REVERT: C 60 VAL cc_start: 0.7440 (t) cc_final: 0.7226 (p) REVERT: C 96 ASP cc_start: 0.8143 (m-30) cc_final: 0.7717 (m-30) REVERT: C 118 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7553 (tp30) outliers start: 26 outliers final: 19 residues processed: 155 average time/residue: 0.5144 time to fit residues: 100.0853 Evaluate side-chains 158 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 196 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 20 optimal weight: 40.0000 chunk 27 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5330 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7232 Z= 0.246 Angle : 0.662 7.333 9859 Z= 0.337 Chirality : 0.042 0.174 1113 Planarity : 0.005 0.041 1245 Dihedral : 8.626 66.240 1181 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.13 % Allowed : 13.31 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.07 (0.29), residues: 840 helix: 0.94 (0.41), residues: 138 sheet: -0.13 (0.30), residues: 278 loop : 0.02 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 356 HIS 0.008 0.002 HIS A 71 PHE 0.010 0.002 PHE A 91 TYR 0.015 0.002 TYR C 209 ARG 0.005 0.001 ARG C 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8368 (t0) cc_final: 0.7825 (m-30) REVERT: B 204 GLN cc_start: 0.0974 (OUTLIER) cc_final: -0.0430 (tt0) REVERT: B 264 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7741 (mm-30) REVERT: B 289 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.7904 (t) REVERT: B 337 MET cc_start: 0.7376 (mtm) cc_final: 0.6986 (ptp) REVERT: B 359 ARG cc_start: 0.8335 (mtp180) cc_final: 0.7783 (mtp180) REVERT: B 387 LYS cc_start: 0.4319 (tppt) cc_final: 0.3903 (mppt) REVERT: B 440 ASP cc_start: 0.8652 (m-30) cc_final: 0.8258 (m-30) REVERT: C 55 LEU cc_start: 0.7220 (mt) cc_final: 0.6869 (tp) REVERT: C 60 VAL cc_start: 0.7436 (t) cc_final: 0.7216 (p) REVERT: C 96 ASP cc_start: 0.8372 (m-30) cc_final: 0.7752 (m-30) REVERT: C 118 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7524 (tp30) REVERT: C 136 GLU cc_start: 0.9039 (pm20) cc_final: 0.8826 (pm20) outliers start: 32 outliers final: 23 residues processed: 156 average time/residue: 0.5339 time to fit residues: 105.8076 Evaluate side-chains 161 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 372 GLN Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 196 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 48 optimal weight: 0.0040 chunk 20 optimal weight: 30.0000 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.0040 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 372 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5265 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7232 Z= 0.170 Angle : 0.613 7.079 9859 Z= 0.304 Chirality : 0.042 0.189 1113 Planarity : 0.005 0.055 1245 Dihedral : 8.303 64.797 1181 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.36 % Allowed : 14.08 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.35 (0.29), residues: 840 helix: 1.43 (0.41), residues: 137 sheet: -0.11 (0.29), residues: 285 loop : 0.24 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 356 HIS 0.007 0.001 HIS A 71 PHE 0.011 0.001 PHE B 334 TYR 0.016 0.002 TYR C 209 ARG 0.006 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8436 (t0) cc_final: 0.7859 (m-30) REVERT: B 204 GLN cc_start: 0.0949 (OUTLIER) cc_final: -0.0707 (tt0) REVERT: B 208 ASP cc_start: 0.1590 (OUTLIER) cc_final: 0.0850 (t70) REVERT: B 264 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7714 (mm-30) REVERT: B 337 MET cc_start: 0.7326 (mtm) cc_final: 0.6966 (ptp) REVERT: B 387 LYS cc_start: 0.4565 (tppt) cc_final: 0.4113 (mppt) REVERT: B 440 ASP cc_start: 0.8690 (m-30) cc_final: 0.8219 (m-30) REVERT: C 55 LEU cc_start: 0.7205 (mt) cc_final: 0.6851 (tp) REVERT: C 60 VAL cc_start: 0.7408 (t) cc_final: 0.7187 (p) outliers start: 26 outliers final: 20 residues processed: 147 average time/residue: 0.5201 time to fit residues: 96.0553 Evaluate side-chains 157 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 186 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 317 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5372 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7232 Z= 0.271 Angle : 0.659 7.583 9859 Z= 0.334 Chirality : 0.042 0.164 1113 Planarity : 0.005 0.044 1245 Dihedral : 8.448 65.730 1181 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.88 % Allowed : 13.95 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.08 (0.29), residues: 840 helix: 1.27 (0.41), residues: 138 sheet: -0.35 (0.30), residues: 277 loop : 0.07 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 356 HIS 0.009 0.002 HIS C 63 PHE 0.014 0.002 PHE C 92 TYR 0.021 0.002 TYR C 209 ARG 0.007 0.001 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.7499 (mpp) cc_final: 0.7173 (mmp) REVERT: B 39 TYR cc_start: 0.1387 (t80) cc_final: 0.0596 (t80) REVERT: B 204 GLN cc_start: 0.1075 (OUTLIER) cc_final: -0.0432 (tt0) REVERT: B 208 ASP cc_start: 0.1867 (OUTLIER) cc_final: 0.1045 (t70) REVERT: B 264 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7756 (mm-30) REVERT: B 289 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.7949 (t) REVERT: B 337 MET cc_start: 0.7412 (mtm) cc_final: 0.7041 (ptp) REVERT: B 387 LYS cc_start: 0.4805 (tppt) cc_final: 0.4394 (mppt) REVERT: B 440 ASP cc_start: 0.8706 (m-30) cc_final: 0.8350 (m-30) REVERT: C 55 LEU cc_start: 0.7254 (mt) cc_final: 0.6886 (tp) REVERT: C 60 VAL cc_start: 0.7416 (t) cc_final: 0.7175 (p) REVERT: C 96 ASP cc_start: 0.8383 (m-30) cc_final: 0.7827 (m-30) REVERT: C 118 GLU cc_start: 0.7452 (tp30) cc_final: 0.7203 (mm-30) outliers start: 30 outliers final: 23 residues processed: 152 average time/residue: 0.5087 time to fit residues: 97.7168 Evaluate side-chains 156 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 186 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 0.0060 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5303 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7232 Z= 0.170 Angle : 0.599 6.937 9859 Z= 0.298 Chirality : 0.042 0.180 1113 Planarity : 0.005 0.065 1245 Dihedral : 8.130 63.645 1181 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.36 % Allowed : 14.86 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.30 (0.30), residues: 840 helix: 1.57 (0.41), residues: 137 sheet: -0.26 (0.29), residues: 277 loop : 0.22 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 356 HIS 0.006 0.001 HIS A 71 PHE 0.011 0.001 PHE B 334 TYR 0.014 0.001 TYR C 209 ARG 0.009 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8305 (t0) cc_final: 0.7743 (m-30) REVERT: B 39 TYR cc_start: 0.1282 (t80) cc_final: 0.1052 (t80) REVERT: B 204 GLN cc_start: 0.1197 (OUTLIER) cc_final: -0.0600 (tt0) REVERT: B 208 ASP cc_start: 0.1835 (OUTLIER) cc_final: 0.1009 (t70) REVERT: B 264 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 289 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.7855 (t) REVERT: B 337 MET cc_start: 0.7324 (mtm) cc_final: 0.7010 (ptp) REVERT: B 387 LYS cc_start: 0.4801 (tppt) cc_final: 0.4414 (mppt) REVERT: B 440 ASP cc_start: 0.8738 (m-30) cc_final: 0.8330 (m-30) REVERT: C 55 LEU cc_start: 0.7324 (mt) cc_final: 0.6926 (tp) REVERT: C 60 VAL cc_start: 0.7446 (t) cc_final: 0.7211 (p) outliers start: 26 outliers final: 22 residues processed: 150 average time/residue: 0.5108 time to fit residues: 96.7818 Evaluate side-chains 161 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 186 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 59 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5374 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7232 Z= 0.221 Angle : 0.628 7.281 9859 Z= 0.315 Chirality : 0.042 0.162 1113 Planarity : 0.005 0.054 1245 Dihedral : 8.152 63.368 1181 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.75 % Allowed : 14.47 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.11 (0.30), residues: 840 helix: 1.44 (0.41), residues: 137 sheet: -0.43 (0.29), residues: 290 loop : 0.14 (0.34), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 356 HIS 0.008 0.001 HIS A 71 PHE 0.014 0.002 PHE B 96 TYR 0.017 0.002 TYR C 209 ARG 0.006 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8308 (t0) cc_final: 0.7714 (m-30) REVERT: B 39 TYR cc_start: 0.1673 (t80) cc_final: 0.1449 (t80) REVERT: B 204 GLN cc_start: 0.1512 (OUTLIER) cc_final: 0.0007 (tt0) REVERT: B 208 ASP cc_start: 0.1873 (OUTLIER) cc_final: 0.1229 (t70) REVERT: B 264 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7730 (mm-30) REVERT: B 289 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.7910 (t) REVERT: B 387 LYS cc_start: 0.4841 (tppt) cc_final: 0.4468 (mppt) REVERT: B 440 ASP cc_start: 0.8741 (m-30) cc_final: 0.8350 (m-30) REVERT: C 55 LEU cc_start: 0.7351 (mt) cc_final: 0.6939 (tp) REVERT: C 60 VAL cc_start: 0.7366 (t) cc_final: 0.7106 (p) REVERT: C 96 ASP cc_start: 0.8427 (m-30) cc_final: 0.7929 (m-30) outliers start: 29 outliers final: 24 residues processed: 151 average time/residue: 0.4949 time to fit residues: 94.4027 Evaluate side-chains 163 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5313 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7232 Z= 0.166 Angle : 0.594 7.036 9859 Z= 0.293 Chirality : 0.042 0.183 1113 Planarity : 0.004 0.045 1245 Dihedral : 7.846 60.683 1181 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.71 % Allowed : 15.63 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.33 (0.30), residues: 840 helix: 1.75 (0.40), residues: 137 sheet: -0.29 (0.29), residues: 291 loop : 0.24 (0.34), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 356 HIS 0.006 0.001 HIS A 71 PHE 0.015 0.001 PHE B 334 TYR 0.014 0.001 TYR C 209 ARG 0.003 0.000 ARG C 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.8291 (t0) cc_final: 0.7718 (m-30) REVERT: B 204 GLN cc_start: 0.1593 (OUTLIER) cc_final: 0.0448 (tt0) REVERT: B 208 ASP cc_start: 0.1825 (OUTLIER) cc_final: 0.1291 (t70) REVERT: B 264 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7685 (mm-30) REVERT: B 273 ARG cc_start: 0.8324 (mtp180) cc_final: 0.7845 (ttp-170) REVERT: B 289 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.7907 (t) REVERT: B 387 LYS cc_start: 0.4815 (tppt) cc_final: 0.4458 (mppt) REVERT: B 440 ASP cc_start: 0.8759 (m-30) cc_final: 0.8355 (m-30) REVERT: C 55 LEU cc_start: 0.7194 (mt) cc_final: 0.6784 (tp) REVERT: C 60 VAL cc_start: 0.7437 (t) cc_final: 0.7199 (p) REVERT: C 96 ASP cc_start: 0.8407 (m-30) cc_final: 0.7912 (m-30) outliers start: 21 outliers final: 18 residues processed: 153 average time/residue: 0.5437 time to fit residues: 103.3564 Evaluate side-chains 161 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.222605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.175173 restraints weight = 39421.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.185799 restraints weight = 16373.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.192545 restraints weight = 9058.648| |-----------------------------------------------------------------------------| r_work (final): 0.4691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5362 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7232 Z= 0.183 Angle : 0.599 7.074 9859 Z= 0.295 Chirality : 0.042 0.166 1113 Planarity : 0.004 0.044 1245 Dihedral : 7.673 58.937 1181 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.58 % Allowed : 16.28 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.37 (0.30), residues: 840 helix: 1.85 (0.40), residues: 138 sheet: -0.31 (0.29), residues: 291 loop : 0.27 (0.34), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 356 HIS 0.006 0.001 HIS A 71 PHE 0.011 0.001 PHE B 334 TYR 0.014 0.001 TYR C 209 ARG 0.003 0.000 ARG B 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3848.36 seconds wall clock time: 70 minutes 6.23 seconds (4206.23 seconds total)