Starting phenix.real_space_refine on Thu Sep 26 20:15:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/09_2024/7z0l_14427_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/09_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_14427/09_2024/7z0l_14427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/09_2024/7z0l_14427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/09_2024/7z0l_14427_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/09_2024/7z0l_14427_trim.cif" } 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. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.65, 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 - 3.00 Amino acid : True - 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: 3.41 Conformation dependent library (CDL) restraints added in 1.1 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: 1.14 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: 4.59 Time building geometry restraints manager: 4.08 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: 0.00 - 1.62: 23706 1.62 - 3.25: 1271 3.25 - 4.87: 111 4.87 - 6.50: 20 6.50 - 8.12: 5 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 2.450 nonbonded pdb=" O ALA B 203 " pdb=" H SER B 213 " model vdw 1.480 2.450 nonbonded pdb=" O PHE B 326 " pdb=" HG1 THR B 330 " model vdw 1.537 2.450 nonbonded pdb="HE22 GLN B 204 " pdb=" OD1 ASP B 208 " model vdw 1.556 2.450 nonbonded pdb=" O VAL B 201 " pdb=" H SER B 216 " model vdw 1.585 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 2.450 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: 0.880 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 30.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.750 ------------------------------------------------------------------------------- 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 : 1.021 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: 0.5112 time to fit residues: 136.4438 Evaluate side-chains 163 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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: 1.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.0570 chunk 22 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 66 optimal weight: 7.9990 chunk 25 optimal weight: 40.0000 chunk 40 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- 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 C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5140 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7232 Z= 0.220 Angle : 0.722 12.033 9859 Z= 0.368 Chirality : 0.046 0.233 1113 Planarity : 0.007 0.068 1245 Dihedral : 12.514 85.965 1181 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.42 % Allowed : 11.11 % Favored : 87.47 % 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 (0.28), residues: 840 helix: 0.26 (0.39), residues: 138 sheet: 0.32 (0.28), residues: 290 loop : 0.33 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 356 HIS 0.006 0.002 HIS C 63 PHE 0.017 0.002 PHE B 61 TYR 0.015 0.002 TYR A 116 ARG 0.005 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 180 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 1.154 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: symmetry clash REVERT: A 144 CYS cc_start: 0.9274 (m) cc_final: 0.8756 (m) REVERT: B 31 ARG cc_start: 0.7339 (tpm-80) cc_final: 0.6024 (mmm160) REVERT: B 35 HIS cc_start: 0.3063 (p-80) cc_final: 0.2584 (p90) REVERT: B 264 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7652 (mm-30) REVERT: B 440 ASP cc_start: 0.8718 (m-30) cc_final: 0.7956 (m-30) REVERT: C 60 VAL cc_start: 0.7406 (t) cc_final: 0.7159 (p) outliers start: 11 outliers final: 8 residues processed: 176 average time/residue: 0.5427 time to fit residues: 121.3959 Evaluate side-chains 164 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 289 SER 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: 9.9990 chunk 64 optimal weight: 0.0060 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 366 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5250 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 7232 Z= 0.254 Angle : 0.711 11.773 9859 Z= 0.354 Chirality : 0.043 0.222 1113 Planarity : 0.006 0.051 1245 Dihedral : 10.099 68.262 1181 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.97 % Allowed : 11.50 % Favored : 85.53 % 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: 0.29 (0.29), residues: 840 helix: 1.08 (0.39), residues: 139 sheet: 0.03 (0.30), residues: 279 loop : 0.16 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 356 HIS 0.009 0.002 HIS C 63 PHE 0.012 0.002 PHE B 159 TYR 0.017 0.002 TYR C 209 ARG 0.003 0.000 ARG B 81 *********************** 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 183 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 1.115 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: B 31 ARG cc_start: 0.7391 (tpm-80) cc_final: 0.6044 (mmm160) REVERT: B 35 HIS cc_start: 0.3337 (p-80) cc_final: 0.2877 (p90) REVERT: B 102 MET cc_start: 0.4097 (mmm) cc_final: 0.3500 (mmm) REVERT: B 205 ASP cc_start: -0.4115 (OUTLIER) cc_final: -0.4512 (t70) REVERT: B 260 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7936 (tm-30) REVERT: B 264 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7643 (mm-30) REVERT: B 387 LYS cc_start: 0.4518 (tppt) cc_final: 0.3916 (mppt) REVERT: B 440 ASP cc_start: 0.8731 (m-30) cc_final: 0.7983 (m-30) REVERT: C 55 LEU cc_start: 0.7119 (mt) cc_final: 0.6768 (tp) REVERT: C 60 VAL cc_start: 0.7392 (t) cc_final: 0.7182 (p) outliers start: 23 outliers final: 18 residues processed: 171 average time/residue: 0.5080 time to fit residues: 109.8602 Evaluate side-chains 168 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 A residue 274 ASP 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 205 ASP Chi-restraints excluded: chain B residue 289 SER 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: 9.9990 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 0.0050 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- 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: 0.5302 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7232 Z= 0.245 Angle : 0.676 7.860 9859 Z= 0.340 Chirality : 0.043 0.193 1113 Planarity : 0.005 0.048 1245 Dihedral : 8.603 63.970 1181 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.49 % Allowed : 12.66 % Favored : 83.85 % 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: 0.01 (0.29), residues: 840 helix: 0.99 (0.40), residues: 139 sheet: -0.25 (0.30), residues: 273 loop : -0.01 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 356 HIS 0.007 0.002 HIS C 63 PHE 0.012 0.002 PHE A 212 TYR 0.019 0.002 TYR C 209 ARG 0.003 0.000 ARG B 439 *********************** 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 176 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 0.985 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 216 ASP cc_start: 0.8496 (t0) cc_final: 0.7927 (m-30) REVERT: B 35 HIS cc_start: 0.3246 (p-80) cc_final: 0.2843 (p90) REVERT: B 204 GLN cc_start: 0.1047 (OUTLIER) cc_final: -0.0255 (tt0) REVERT: B 260 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7985 (tm-30) REVERT: B 264 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7629 (mm-30) REVERT: B 337 MET cc_start: 0.7584 (mtm) cc_final: 0.7132 (ptp) REVERT: B 359 ARG cc_start: 0.8236 (mtp180) cc_final: 0.7662 (mtp180) REVERT: B 387 LYS cc_start: 0.4423 (tppt) cc_final: 0.3845 (mppt) REVERT: C 55 LEU cc_start: 0.7165 (mt) cc_final: 0.6785 (tp) REVERT: C 60 VAL cc_start: 0.7411 (t) cc_final: 0.7187 (p) REVERT: C 96 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7648 (m-30) outliers start: 27 outliers final: 21 residues processed: 161 average time/residue: 0.4341 time to fit residues: 88.6852 Evaluate side-chains 163 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 201 VAL Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 ASP 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 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: 2.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 20 optimal weight: 40.0000 chunk 27 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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: 0.5369 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7232 Z= 0.275 Angle : 0.679 7.871 9859 Z= 0.347 Chirality : 0.043 0.168 1113 Planarity : 0.006 0.053 1245 Dihedral : 8.756 66.376 1181 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.52 % Allowed : 12.79 % Favored : 82.69 % 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: -0.22 (0.29), residues: 840 helix: 1.04 (0.41), residues: 138 sheet: -0.52 (0.29), residues: 297 loop : -0.11 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 214 HIS 0.008 0.002 HIS C 63 PHE 0.014 0.002 PHE C 92 TYR 0.021 0.002 TYR A 30 ARG 0.005 0.000 ARG B 439 *********************** 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 175 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 1.380 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 129 PRO cc_start: 0.4958 (Cg_exo) cc_final: 0.4556 (Cg_endo) REVERT: A 144 CYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8415 (m) REVERT: A 216 ASP cc_start: 0.8659 (t0) cc_final: 0.8060 (m-30) REVERT: B 204 GLN cc_start: 0.1445 (OUTLIER) cc_final: -0.0279 (tt0) REVERT: B 208 ASP cc_start: 0.1824 (OUTLIER) cc_final: 0.0753 (t70) REVERT: B 260 GLU cc_start: 0.8210 (tm-30) cc_final: 0.8002 (tm-30) REVERT: B 264 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7587 (mm-30) REVERT: B 359 ARG cc_start: 0.8271 (mtp180) cc_final: 0.7713 (mtp180) REVERT: B 387 LYS cc_start: 0.4459 (tppt) cc_final: 0.3925 (mppt) REVERT: B 440 ASP cc_start: 0.8743 (m-30) cc_final: 0.8015 (m-30) REVERT: C 60 VAL cc_start: 0.7420 (t) cc_final: 0.7195 (p) REVERT: C 96 ASP cc_start: 0.8459 (m-30) cc_final: 0.7728 (m-30) outliers start: 35 outliers final: 27 residues processed: 159 average time/residue: 0.5216 time to fit residues: 106.1493 Evaluate side-chains 164 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 144 CYS 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 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 201 VAL 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 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 118 GLU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 187 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 20 optimal weight: 40.0000 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 B 372 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5338 moved from start: 0.4573 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= 0.204 Angle : 0.643 7.575 9859 Z= 0.323 Chirality : 0.042 0.175 1113 Planarity : 0.005 0.045 1245 Dihedral : 8.461 65.824 1181 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.75 % Allowed : 15.25 % Favored : 81.01 % 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: -0.04 (0.29), residues: 840 helix: 1.31 (0.40), residues: 138 sheet: -0.38 (0.30), residues: 290 loop : -0.08 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 215 HIS 0.008 0.002 HIS B 368 PHE 0.020 0.002 PHE B 96 TYR 0.018 0.002 TYR C 209 ARG 0.003 0.000 ARG B 439 *********************** 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: 29 poor density : 133 time to evaluate : 1.115 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: A 216 ASP cc_start: 0.8639 (t0) cc_final: 0.8021 (m-30) REVERT: B 204 GLN cc_start: 0.1251 (OUTLIER) cc_final: -0.0037 (tt0) REVERT: B 208 ASP cc_start: 0.1610 (OUTLIER) cc_final: 0.0909 (t70) REVERT: B 264 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7437 (mm-30) REVERT: B 337 MET cc_start: 0.7451 (mtm) cc_final: 0.7099 (ptp) REVERT: B 387 LYS cc_start: 0.4474 (tppt) cc_final: 0.4018 (mppt) REVERT: B 440 ASP cc_start: 0.8816 (m-30) cc_final: 0.8123 (m-30) REVERT: C 60 VAL cc_start: 0.7465 (t) cc_final: 0.7239 (p) REVERT: C 96 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7694 (m-30) REVERT: C 136 GLU cc_start: 0.9038 (pm20) cc_final: 0.8825 (pm20) outliers start: 29 outliers final: 23 residues processed: 147 average time/residue: 0.5421 time to fit residues: 100.1546 Evaluate side-chains 157 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 144 CYS 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 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 372 GLN Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 187 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.0010 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5333 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7232 Z= 0.203 Angle : 0.632 6.913 9859 Z= 0.316 Chirality : 0.042 0.173 1113 Planarity : 0.005 0.059 1245 Dihedral : 8.312 65.534 1181 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.23 % Allowed : 16.02 % Favored : 80.75 % 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 (0.30), residues: 840 helix: 1.53 (0.39), residues: 137 sheet: -0.34 (0.30), residues: 290 loop : -0.03 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 356 HIS 0.005 0.001 HIS A 71 PHE 0.012 0.002 PHE B 286 TYR 0.014 0.002 TYR A 30 ARG 0.005 0.000 ARG B 87 *********************** 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 159 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.129 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: A 144 CYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8521 (m) REVERT: A 216 ASP cc_start: 0.8624 (t0) cc_final: 0.8001 (m-30) REVERT: B 204 GLN cc_start: 0.1233 (OUTLIER) cc_final: 0.0467 (tt0) REVERT: B 264 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7519 (mm-30) REVERT: B 289 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.7874 (t) REVERT: B 337 MET cc_start: 0.7465 (mtm) cc_final: 0.7059 (ptp) REVERT: B 387 LYS cc_start: 0.4495 (tppt) cc_final: 0.4065 (mppt) REVERT: C 60 VAL cc_start: 0.7457 (t) cc_final: 0.7230 (p) REVERT: C 96 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: C 136 GLU cc_start: 0.9064 (pm20) cc_final: 0.8840 (pm20) outliers start: 25 outliers final: 21 residues processed: 147 average time/residue: 0.5117 time to fit residues: 94.7539 Evaluate side-chains 158 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 105 ILE Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 144 CYS 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 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 C residue 93 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 178 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 78 optimal weight: 0.0970 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 372 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5353 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7232 Z= 0.201 Angle : 0.626 7.026 9859 Z= 0.313 Chirality : 0.042 0.167 1113 Planarity : 0.005 0.043 1245 Dihedral : 8.182 64.704 1181 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.01 % Allowed : 15.50 % Favored : 80.49 % 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: 0.14 (0.30), residues: 840 helix: 1.84 (0.39), residues: 137 sheet: -0.45 (0.29), residues: 303 loop : 0.07 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 356 HIS 0.005 0.001 HIS C 63 PHE 0.014 0.002 PHE B 286 TYR 0.016 0.002 TYR C 209 ARG 0.005 0.000 ARG B 290 *********************** 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 169 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 1.126 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: A 216 ASP cc_start: 0.8593 (t0) cc_final: 0.8081 (m-30) REVERT: B 204 GLN cc_start: 0.1348 (OUTLIER) cc_final: 0.0137 (tt0) REVERT: B 208 ASP cc_start: 0.1776 (OUTLIER) cc_final: 0.1116 (t70) REVERT: B 264 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7538 (mm-30) REVERT: B 387 LYS cc_start: 0.4382 (tppt) cc_final: 0.4007 (mppt) REVERT: C 60 VAL cc_start: 0.7457 (t) cc_final: 0.7225 (p) REVERT: C 96 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: C 136 GLU cc_start: 0.9097 (pm20) cc_final: 0.8874 (pm20) outliers start: 31 outliers final: 25 residues processed: 154 average time/residue: 0.5164 time to fit residues: 100.3240 Evaluate side-chains 160 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 105 ILE Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 35 HIS 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 C residue 93 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 187 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 0.0770 chunk 78 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 59 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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: 0.5294 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7232 Z= 0.163 Angle : 0.604 7.075 9859 Z= 0.296 Chirality : 0.042 0.182 1113 Planarity : 0.005 0.057 1245 Dihedral : 7.912 62.996 1181 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.10 % Allowed : 16.54 % Favored : 80.36 % 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: 0.31 (0.30), residues: 840 helix: 2.07 (0.38), residues: 137 sheet: -0.31 (0.29), residues: 297 loop : 0.11 (0.34), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 356 HIS 0.003 0.001 HIS A 71 PHE 0.013 0.001 PHE B 334 TYR 0.017 0.001 TYR A 30 ARG 0.003 0.000 ARG B 87 *********************** 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 170 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 1.057 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: A 216 ASP cc_start: 0.8639 (t0) cc_final: 0.8003 (m-30) REVERT: B 39 TYR cc_start: 0.1404 (t80) cc_final: 0.0700 (t80) REVERT: B 204 GLN cc_start: 0.1063 (OUTLIER) cc_final: 0.0733 (tt0) REVERT: B 264 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 273 ARG cc_start: 0.8350 (mtp180) cc_final: 0.7853 (ttp-170) REVERT: B 337 MET cc_start: 0.7454 (mtm) cc_final: 0.7073 (ptp) REVERT: B 370 ARG cc_start: 0.8827 (ttt-90) cc_final: 0.8457 (mtp180) REVERT: B 387 LYS cc_start: 0.4346 (tppt) cc_final: 0.3981 (mppt) REVERT: C 60 VAL cc_start: 0.7492 (t) cc_final: 0.7270 (p) REVERT: C 96 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7520 (m-30) outliers start: 24 outliers final: 20 residues processed: 157 average time/residue: 0.5235 time to fit residues: 102.8853 Evaluate side-chains 162 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 144 CYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 35 HIS 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 C residue 93 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 41 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.5277 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7232 Z= 0.165 Angle : 0.613 7.126 9859 Z= 0.303 Chirality : 0.042 0.184 1113 Planarity : 0.005 0.048 1245 Dihedral : 7.639 60.862 1181 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.33 % Allowed : 17.31 % Favored : 80.36 % 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: 0.48 (0.30), residues: 840 helix: 2.31 (0.38), residues: 137 sheet: -0.20 (0.29), residues: 297 loop : 0.18 (0.34), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 356 HIS 0.003 0.001 HIS A 71 PHE 0.013 0.001 PHE B 334 TYR 0.036 0.002 TYR A 30 ARG 0.004 0.000 ARG B 323 ********************** 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 160 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.157 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 216 ASP cc_start: 0.8609 (t0) cc_final: 0.8012 (m-30) REVERT: B 39 TYR cc_start: 0.1394 (t80) cc_final: 0.0691 (t80) REVERT: B 204 GLN cc_start: 0.0769 (OUTLIER) cc_final: 0.0458 (tt0) REVERT: B 264 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7509 (mm-30) REVERT: B 273 ARG cc_start: 0.8352 (mtp180) cc_final: 0.7859 (ttp-170) REVERT: B 387 LYS cc_start: 0.4393 (tppt) cc_final: 0.4057 (mppt) REVERT: C 60 VAL cc_start: 0.7459 (t) cc_final: 0.7241 (p) REVERT: C 96 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7631 (m-30) outliers start: 18 outliers final: 16 residues processed: 153 average time/residue: 0.5307 time to fit residues: 102.1947 Evaluate side-chains 158 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 131 ASN Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 251 LEU 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 C residue 93 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 40.0000 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.5014 r_free = 0.5014 target = 0.221494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.174003 restraints weight = 36666.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.184212 restraints weight = 15141.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.190890 restraints weight = 8390.517| |-----------------------------------------------------------------------------| r_work (final): 0.4689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5377 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7232 Z= 0.201 Angle : 0.619 7.124 9859 Z= 0.307 Chirality : 0.042 0.170 1113 Planarity : 0.005 0.052 1245 Dihedral : 7.721 59.506 1181 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.84 % Allowed : 16.93 % Favored : 80.23 % 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: 0.45 (0.30), residues: 840 helix: 2.33 (0.39), residues: 137 sheet: -0.22 (0.29), residues: 297 loop : 0.14 (0.34), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 356 HIS 0.005 0.001 HIS C 63 PHE 0.011 0.002 PHE B 159 TYR 0.014 0.002 TYR A 30 ARG 0.003 0.000 ARG B 323 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3770.64 seconds wall clock time: 68 minutes 19.52 seconds (4099.52 seconds total)