Starting phenix.real_space_refine (version: dev) on Tue Feb 21 04:46:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/02_2023/7z0l_14427_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/02_2023/7z0l_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_14427/02_2023/7z0l_14427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/02_2023/7z0l_14427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/02_2023/7z0l_14427_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/02_2023/7z0l_14427_trim.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 7.04, per 1000 atoms: 0.51 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: 11.36 Conformation dependent library (CDL) restraints added in 1.2 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: 0.48 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: 4.96 Time building geometry restraints manager: 11.77 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=" N PHE B 251 " pdb=" CA PHE B 251 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.46e+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=" C2 NAG H 1 " pdb=" N2 NAG H 1 " pdb=" C7 NAG H 1 " ideal model delta sigma weight residual 123.12 127.95 -4.83 1.28e+00 6.08e-01 1.42e+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=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 123.12 127.53 -4.41 1.28e+00 6.08e-01 1.18e+01 ... (remaining 25108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.28: 5260 20.28 - 40.55: 236 40.55 - 60.83: 100 60.83 - 81.11: 53 81.11 - 101.38: 9 Dihedral angle restraints: 5658 sinusoidal: 2651 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 5655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1074 0.124 - 0.247: 37 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 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. 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: 0.400 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: 0.220 Extract box with map and model: 3.260 Check model and map are aligned: 0.210 Process input model: 46.610 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4948 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= 0.291 Angle : 0.926 8.123 9859 Z= 0.539 Chirality : 0.062 0.617 1113 Planarity : 0.013 0.191 1245 Dihedral : 14.096 101.384 2672 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 % 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 *********************** 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 : 1.200 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 outliers start: 5 outliers final: 1 residues processed: 213 average time/residue: 0.5320 time to fit residues: 141.5890 Evaluate side-chains 158 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2632 time to fit residues: 1.9179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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: 0.5016 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 7232 Z= 0.252 Angle : 0.686 6.594 9859 Z= 0.364 Chirality : 0.046 0.533 1113 Planarity : 0.006 0.054 1245 Dihedral : 10.221 108.147 999 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 2.71 % 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: 0.17 (0.28), residues: 840 helix: 0.10 (0.38), residues: 139 sheet: 0.29 (0.28), residues: 290 loop : 0.15 (0.32), residues: 411 *********************** 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 182 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 1.250 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 outliers start: 21 outliers final: 16 residues processed: 172 average time/residue: 0.5159 time to fit residues: 111.7030 Evaluate side-chains 170 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.1759 time to fit residues: 5.9870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN C 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5168 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 7232 Z= 0.321 Angle : 0.702 8.192 9859 Z= 0.375 Chirality : 0.046 0.502 1113 Planarity : 0.006 0.057 1245 Dihedral : 10.134 104.547 999 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.64 % Favored : 95.24 % Rotamer Outliers : 2.71 % 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: -0.16 (0.28), residues: 840 helix: 0.63 (0.40), residues: 140 sheet: -0.16 (0.29), residues: 273 loop : -0.20 (0.31), residues: 427 *********************** 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 170 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.256 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 outliers start: 21 outliers final: 14 residues processed: 161 average time/residue: 0.5231 time to fit residues: 105.7378 Evaluate side-chains 145 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.212 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.1561 time to fit residues: 5.4474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 35 HIS B 372 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5147 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 7232 Z= 0.234 Angle : 0.637 7.885 9859 Z= 0.335 Chirality : 0.045 0.492 1113 Planarity : 0.005 0.045 1245 Dihedral : 9.967 105.023 999 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 1.94 % 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: 0.10 (0.29), residues: 840 helix: 1.06 (0.40), residues: 140 sheet: -0.06 (0.30), residues: 278 loop : -0.05 (0.32), residues: 422 *********************** 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 152 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 1.178 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 outliers start: 15 outliers final: 10 residues processed: 145 average time/residue: 0.5587 time to fit residues: 101.8330 Evaluate side-chains 136 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2025 time to fit residues: 4.8864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 61 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 20 optimal weight: 40.0000 chunk 27 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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: 0.5182 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7232 Z= 0.245 Angle : 0.639 7.607 9859 Z= 0.334 Chirality : 0.045 0.476 1113 Planarity : 0.005 0.041 1245 Dihedral : 9.889 105.271 999 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.42 % 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: 1.07 (0.40), residues: 138 sheet: -0.24 (0.30), residues: 278 loop : -0.07 (0.32), residues: 424 *********************** 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 143 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 1.175 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 outliers start: 11 outliers final: 7 residues processed: 139 average time/residue: 0.5332 time to fit residues: 92.8418 Evaluate side-chains 133 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1546 time to fit residues: 3.4773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 40.0000 chunk 82 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 43 optimal weight: 0.0870 chunk 79 optimal weight: 0.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- 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: 0.5201 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 7232 Z= 0.240 Angle : 0.626 7.551 9859 Z= 0.329 Chirality : 0.045 0.465 1113 Planarity : 0.005 0.056 1245 Dihedral : 9.835 105.776 999 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 1.42 % 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: -0.05 (0.29), residues: 840 helix: 1.14 (0.40), residues: 137 sheet: -0.37 (0.30), residues: 278 loop : -0.05 (0.33), residues: 425 *********************** 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 140 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.289 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 outliers start: 11 outliers final: 8 residues processed: 135 average time/residue: 0.5525 time to fit residues: 94.9369 Evaluate side-chains 135 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1786 time to fit residues: 4.0662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN B 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5220 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 7232 Z= 0.232 Angle : 0.618 7.621 9859 Z= 0.324 Chirality : 0.044 0.451 1113 Planarity : 0.005 0.057 1245 Dihedral : 9.775 106.098 999 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.78 % 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: -0.07 (0.30), residues: 840 helix: 1.31 (0.41), residues: 137 sheet: -0.48 (0.29), residues: 294 loop : -0.02 (0.34), residues: 409 *********************** 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 137 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 1.188 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 outliers start: 6 outliers final: 5 residues processed: 132 average time/residue: 0.5278 time to fit residues: 87.5804 Evaluate side-chains 129 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1511 time to fit residues: 2.8759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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: 0.5216 moved from start: 0.4923 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= 0.208 Angle : 0.601 7.052 9859 Z= 0.314 Chirality : 0.044 0.448 1113 Planarity : 0.005 0.056 1245 Dihedral : 9.704 106.111 999 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 1.42 % 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: 0.02 (0.30), residues: 840 helix: 1.50 (0.40), residues: 137 sheet: -0.51 (0.29), residues: 294 loop : 0.07 (0.34), residues: 409 *********************** 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 140 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.146 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 outliers start: 11 outliers final: 10 residues processed: 133 average time/residue: 0.5609 time to fit residues: 93.1783 Evaluate side-chains 136 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.1827 time to fit residues: 4.7792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 45 optimal weight: 0.0870 chunk 33 optimal weight: 0.0010 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 overall best weight: 0.3964 ------------------------------------------------------------------------------- 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: 0.5130 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7232 Z= 0.165 Angle : 0.576 5.868 9859 Z= 0.293 Chirality : 0.044 0.436 1113 Planarity : 0.004 0.047 1245 Dihedral : 9.480 105.848 999 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.52 % 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: 0.39 (0.30), residues: 840 helix: 1.79 (0.40), residues: 137 sheet: -0.30 (0.29), residues: 287 loop : 0.32 (0.34), residues: 416 *********************** 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 141 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 1.187 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 outliers start: 4 outliers final: 3 residues processed: 139 average time/residue: 0.5514 time to fit residues: 95.6640 Evaluate side-chains 135 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.070 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.1964 time to fit residues: 2.3340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5148 moved from start: 0.5060 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= 0.170 Angle : 0.576 9.773 9859 Z= 0.292 Chirality : 0.043 0.422 1113 Planarity : 0.004 0.047 1245 Dihedral : 9.434 106.227 999 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 0.39 % 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: 0.43 (0.30), residues: 840 helix: 1.81 (0.39), residues: 137 sheet: -0.25 (0.29), residues: 287 loop : 0.33 (0.34), residues: 416 ********************** 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 136 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 1.278 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 outliers start: 3 outliers final: 3 residues processed: 134 average time/residue: 0.5917 time to fit residues: 98.3777 Evaluate side-chains 134 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.174 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.2334 time to fit residues: 2.5859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 30.0000 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 28 optimal weight: 30.0000 chunk 69 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.5023 r_free = 0.5023 target = 0.224689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.176215 restraints weight = 39337.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.186994 restraints weight = 16352.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.193872 restraints weight = 9075.983| |-----------------------------------------------------------------------------| r_work (final): 0.4695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5179 moved from start: 0.5213 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= 0.178 Angle : 0.574 8.118 9859 Z= 0.292 Chirality : 0.043 0.414 1113 Planarity : 0.004 0.044 1245 Dihedral : 9.418 106.328 999 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.39 % 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: 0.41 (0.30), residues: 840 helix: 1.88 (0.39), residues: 138 sheet: -0.30 (0.29), residues: 287 loop : 0.31 (0.34), residues: 415 =============================================================================== Job complete usr+sys time: 3691.55 seconds wall clock time: 65 minutes 49.14 seconds (3949.14 seconds total)