Starting phenix.real_space_refine (version: dev) on Tue Dec 13 04:54:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/12_2022/7z0l_14427_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/12_2022/7z0l_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_14427/12_2022/7z0l_14427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/12_2022/7z0l_14427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/12_2022/7z0l_14427_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0l_14427/12_2022/7z0l_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 Convert atoms to be neutral 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-4807/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: 6.32, per 1000 atoms: 0.46 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: 11.20 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: 0.44 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: 4.69 Time building geometry restraints manager: 11.46 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: 0.640 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: 0.210 Extract box with map and model: 3.230 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.130 Process input model: 43.650 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.260 ------------------------------------------------------------------------------- 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 : 1.153 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: 0.4689 time to fit residues: 127.0776 Evaluate side-chains 158 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2590 time to fit residues: 1.8528 ------------------------------------------------------------------------------- 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: 0.4980 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: 1.4386 ------------------------------------------------------------------------------- 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 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5007 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 7232 Z= 0.247 Angle : 0.687 6.769 9859 Z= 0.368 Chirality : 0.047 0.529 1113 Planarity : 0.007 0.065 1245 Dihedral : 10.271 107.356 999 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 2.20 % 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: 0.01 (0.38), residues: 140 sheet: 0.34 (0.28), residues: 290 loop : 0.13 (0.32), residues: 410 *********************** 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 176 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 1.114 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: 17 outliers final: 15 residues processed: 167 average time/residue: 0.4766 time to fit residues: 102.1379 Evaluate side-chains 169 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.2127 time to fit residues: 6.8373 ------------------------------------------------------------------------------- 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: 2.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5029 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 7232 Z= 0.206 Angle : 0.615 6.469 9859 Z= 0.322 Chirality : 0.045 0.515 1113 Planarity : 0.005 0.047 1245 Dihedral : 9.934 104.575 999 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 2.07 % 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: 0.55 (0.28), residues: 840 helix: 1.41 (0.40), residues: 140 sheet: 0.28 (0.29), residues: 277 loop : 0.20 (0.32), residues: 423 *********************** 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: 16 poor density : 154 time to evaluate : 1.208 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 outliers start: 16 outliers final: 10 residues processed: 162 average time/residue: 0.4769 time to fit residues: 98.3473 Evaluate side-chains 145 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.049 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 10 average time/residue: 0.1464 time to fit residues: 3.9597 ------------------------------------------------------------------------------- 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: 5.9990 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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: 0.5085 moved from start: 0.3685 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= 0.224 Angle : 0.619 6.930 9859 Z= 0.321 Chirality : 0.045 0.501 1113 Planarity : 0.005 0.046 1245 Dihedral : 9.821 104.959 999 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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: 0.47 (0.29), residues: 840 helix: 1.44 (0.41), residues: 140 sheet: 0.10 (0.29), residues: 277 loop : 0.22 (0.32), residues: 423 *********************** 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 153 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 146 average time/residue: 0.4873 time to fit residues: 90.2843 Evaluate side-chains 148 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.1608 time to fit residues: 5.1238 ------------------------------------------------------------------------------- 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: 4.9990 chunk 61 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 0.0670 chunk 73 optimal weight: 5.9990 chunk 20 optimal weight: 40.0000 chunk 27 optimal weight: 9.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5199 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 7232 Z= 0.296 Angle : 0.670 7.730 9859 Z= 0.356 Chirality : 0.045 0.474 1113 Planarity : 0.006 0.045 1245 Dihedral : 9.912 105.538 999 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.29), residues: 840 helix: 1.14 (0.41), residues: 138 sheet: -0.19 (0.31), residues: 270 loop : -0.03 (0.32), residues: 432 *********************** 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 141 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 1.011 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 outliers start: 8 outliers final: 7 residues processed: 136 average time/residue: 0.4868 time to fit residues: 84.7931 Evaluate side-chains 133 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1514 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: 0.8980 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 0.0870 chunk 20 optimal weight: 40.0000 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 0.0470 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.5056 ------------------------------------------------------------------------------- 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: 0.5103 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7232 Z= 0.168 Angle : 0.581 6.270 9859 Z= 0.298 Chirality : 0.045 0.476 1113 Planarity : 0.005 0.052 1245 Dihedral : 9.664 105.195 999 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: 0.43 (0.29), residues: 840 helix: 1.61 (0.40), residues: 138 sheet: -0.11 (0.30), residues: 277 loop : 0.28 (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 139 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 1.040 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: 2 residues processed: 137 average time/residue: 0.5038 time to fit residues: 89.6002 Evaluate side-chains 133 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1918 time to fit residues: 2.2577 ------------------------------------------------------------------------------- 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: 1.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS ** B 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5229 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7232 Z= 0.280 Angle : 0.643 7.754 9859 Z= 0.339 Chirality : 0.044 0.436 1113 Planarity : 0.005 0.059 1245 Dihedral : 9.785 106.473 999 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 1.29 % 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: 0.06 (0.29), residues: 840 helix: 1.28 (0.41), residues: 138 sheet: -0.40 (0.29), residues: 292 loop : 0.11 (0.33), residues: 410 *********************** 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 142 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.109 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 outliers start: 10 outliers final: 8 residues processed: 137 average time/residue: 0.4985 time to fit residues: 86.6723 Evaluate side-chains 140 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1746 time to fit residues: 3.8586 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 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: 4.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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: 0.5224 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 7232 Z= 0.234 Angle : 0.616 7.125 9859 Z= 0.321 Chirality : 0.044 0.447 1113 Planarity : 0.005 0.059 1245 Dihedral : 9.735 106.248 999 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: 0.03 (0.29), residues: 840 helix: 1.41 (0.40), residues: 138 sheet: -0.50 (0.29), residues: 283 loop : 0.08 (0.33), residues: 419 *********************** 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: 6 poor density : 134 time to evaluate : 1.191 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: 6 outliers final: 3 residues processed: 137 average time/residue: 0.5146 time to fit residues: 90.7302 Evaluate side-chains 135 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1611 time to fit residues: 2.3168 ------------------------------------------------------------------------------- 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: 9.9990 chunk 78 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 33 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.0270 chunk 68 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 0.0060 overall best weight: 0.2370 ------------------------------------------------------------------------------- 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: 0.5124 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7232 Z= 0.171 Angle : 0.593 6.896 9859 Z= 0.297 Chirality : 0.045 0.430 1113 Planarity : 0.005 0.074 1245 Dihedral : 9.491 105.808 999 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: 0.51 (0.30), residues: 840 helix: 2.08 (0.39), residues: 136 sheet: -0.27 (0.29), residues: 281 loop : 0.34 (0.34), residues: 423 *********************** 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 143 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 1.110 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: 6 outliers final: 5 residues processed: 138 average time/residue: 0.5155 time to fit residues: 89.6653 Evaluate side-chains 140 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1685 time to fit residues: 2.7563 ------------------------------------------------------------------------------- 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: 0.2980 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: 0.8980 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5148 moved from start: 0.5090 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= 0.179 Angle : 0.584 6.766 9859 Z= 0.295 Chirality : 0.044 0.413 1113 Planarity : 0.004 0.048 1245 Dihedral : 9.441 106.324 999 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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: 0.57 (0.30), residues: 840 helix: 2.18 (0.38), residues: 137 sheet: -0.26 (0.29), residues: 281 loop : 0.39 (0.34), residues: 422 ********************** 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 137 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 1.059 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 outliers start: 3 outliers final: 2 residues processed: 135 average time/residue: 0.4821 time to fit residues: 83.0608 Evaluate side-chains 133 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.101 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.1938 time to fit residues: 2.1821 ------------------------------------------------------------------------------- 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: 0.0980 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 30.0000 chunk 69 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.5030 r_free = 0.5030 target = 0.225244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.177411 restraints weight = 39803.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.188499 restraints weight = 16762.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.195490 restraints weight = 9300.841| |-----------------------------------------------------------------------------| r_work (final): 0.4681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 moved from start: 0.5204 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= 0.184 Angle : 0.577 6.501 9859 Z= 0.293 Chirality : 0.043 0.408 1113 Planarity : 0.005 0.073 1245 Dihedral : 9.438 106.371 999 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % 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: 0.50 (0.30), residues: 840 helix: 2.15 (0.38), residues: 138 sheet: -0.31 (0.29), residues: 281 loop : 0.34 (0.34), residues: 421 =============================================================================== Job complete usr+sys time: 3605.99 seconds wall clock time: 64 minutes 25.83 seconds (3865.83 seconds total)