Starting phenix.real_space_refine on Tue Feb 13 20:41:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c99_30309/02_2024/7c99_30309_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c99_30309/02_2024/7c99_30309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c99_30309/02_2024/7c99_30309.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c99_30309/02_2024/7c99_30309.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c99_30309/02_2024/7c99_30309_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c99_30309/02_2024/7c99_30309_updated.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 27 5.49 5 S 33 5.16 5 C 4755 2.51 5 N 1341 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 90": "OE1" <-> "OE2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 201": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7656 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2397 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.64, per 1000 atoms: 0.61 Number of scatterers: 7656 At special positions: 0 Unit cell: (107.52, 78.12, 115.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 33 16.00 P 27 15.00 O 1497 8.00 N 1341 7.00 C 4755 6.00 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 Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.4 seconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 6 sheets defined 32.7% alpha, 9.7% beta 8 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 37 through 40 No H-bonds generated for 'chain 'A' and resid 37 through 40' Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.631A pdb=" N GLN A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 78 removed outlier: 3.643A pdb=" N ALA A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 94 removed outlier: 3.697A pdb=" N GLU A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.814A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 removed outlier: 3.500A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 170 through 173 No H-bonds generated for 'chain 'A' and resid 170 through 173' Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 226 through 229 No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 239 through 259 removed outlier: 4.056A pdb=" N GLN A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 37 through 40 No H-bonds generated for 'chain 'B' and resid 37 through 40' Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.631A pdb=" N GLN B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 removed outlier: 3.644A pdb=" N ALA B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 removed outlier: 3.697A pdb=" N GLU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.814A pdb=" N LEU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 142 removed outlier: 3.500A pdb=" N LEU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 170 through 173 No H-bonds generated for 'chain 'B' and resid 170 through 173' Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 226 through 229 No H-bonds generated for 'chain 'B' and resid 226 through 229' Processing helix chain 'B' and resid 239 through 259 removed outlier: 4.056A pdb=" N GLN B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 252 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 37 through 40 No H-bonds generated for 'chain 'C' and resid 37 through 40' Processing helix chain 'C' and resid 48 through 53 removed outlier: 3.632A pdb=" N GLN C 52 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 removed outlier: 3.643A pdb=" N ALA C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 94 removed outlier: 3.698A pdb=" N GLU C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 112 removed outlier: 3.814A pdb=" N LEU C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 removed outlier: 3.501A pdb=" N LEU C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 170 through 173 No H-bonds generated for 'chain 'C' and resid 170 through 173' Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 226 through 229 No H-bonds generated for 'chain 'C' and resid 226 through 229' Processing helix chain 'C' and resid 239 through 259 removed outlier: 4.056A pdb=" N GLN C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 296 Processing sheet with id= A, first strand: chain 'A' and resid 299 through 302 removed outlier: 6.816A pdb=" N VAL A 264 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ALA A 124 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 266 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 267 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LYS A 155 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A 220 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A 157 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE A 222 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 159 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 303 through 305 Processing sheet with id= C, first strand: chain 'B' and resid 299 through 302 removed outlier: 6.816A pdb=" N VAL B 264 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ALA B 124 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B 266 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 267 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LYS B 155 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 220 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE B 157 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE B 222 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 159 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 303 through 305 Processing sheet with id= E, first strand: chain 'C' and resid 299 through 302 removed outlier: 6.815A pdb=" N VAL C 264 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ALA C 124 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C 266 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 267 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LYS C 155 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU C 220 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE C 157 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ILE C 222 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE C 159 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 303 through 305 153 hydrogen bonds defined for protein. 441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2021 1.33 - 1.45: 1371 1.45 - 1.57: 4313 1.57 - 1.69: 51 1.69 - 1.81: 57 Bond restraints: 7813 Sorted by residual: bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.680 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 1.795 1.684 0.111 2.00e-02 2.50e+03 3.09e+01 ... (remaining 7808 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.14: 247 106.14 - 112.74: 4072 112.74 - 119.34: 2410 119.34 - 125.94: 3742 125.94 - 132.54: 129 Bond angle restraints: 10600 Sorted by residual: angle pdb=" PB ANP A 402 " pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 126.95 104.40 22.55 3.00e+00 1.11e-01 5.65e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 104.41 22.54 3.00e+00 1.11e-01 5.65e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 105.31 21.64 3.00e+00 1.11e-01 5.20e+01 angle pdb=" N VAL A 184 " pdb=" CA VAL A 184 " pdb=" C VAL A 184 " ideal model delta sigma weight residual 113.71 107.64 6.07 9.50e-01 1.11e+00 4.09e+01 angle pdb=" N VAL B 184 " pdb=" CA VAL B 184 " pdb=" C VAL B 184 " ideal model delta sigma weight residual 113.71 107.66 6.05 9.50e-01 1.11e+00 4.06e+01 ... (remaining 10595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 4363 25.94 - 51.89: 301 51.89 - 77.83: 64 77.83 - 103.78: 18 103.78 - 129.72: 3 Dihedral angle restraints: 4749 sinusoidal: 2115 harmonic: 2634 Sorted by residual: dihedral pdb=" CA ASN A 163 " pdb=" C ASN A 163 " pdb=" N THR A 164 " pdb=" CA THR A 164 " ideal model delta harmonic sigma weight residual -180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ASN B 163 " pdb=" C ASN B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA ASN C 163 " pdb=" C ASN C 163 " pdb=" N THR C 164 " pdb=" CA THR C 164 " ideal model delta harmonic sigma weight residual -180.00 -151.62 -28.38 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 4746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 928 0.060 - 0.120: 231 0.120 - 0.180: 31 0.180 - 0.241: 1 0.241 - 0.301: 3 Chirality restraints: 1194 Sorted by residual: chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C3' ANP A 402 " pdb=" C2' ANP A 402 " pdb=" C4' ANP A 402 " pdb=" O3' ANP A 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 1191 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 317 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ASP B 317 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP B 317 " -0.017 2.00e-02 2.50e+03 pdb=" N SER B 318 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 317 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C ASP C 317 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP C 317 " -0.016 2.00e-02 2.50e+03 pdb=" N SER C 318 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 317 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C ASP A 317 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP A 317 " -0.016 2.00e-02 2.50e+03 pdb=" N SER A 318 " -0.014 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 29 2.40 - 3.03: 3880 3.03 - 3.65: 10361 3.65 - 4.28: 16535 4.28 - 4.90: 27941 Nonbonded interactions: 58746 Sorted by model distance: nonbonded pdb=" OD1 ASP A 168 " pdb=" NH2 ARG A 171 " model vdw 1.776 2.520 nonbonded pdb=" OD1 ASP B 168 " pdb=" NH2 ARG B 171 " model vdw 1.777 2.520 nonbonded pdb="CA CA B 401 " pdb=" O2G ANP B 402 " model vdw 2.084 2.510 nonbonded pdb="CA CA A 401 " pdb=" O2G ANP A 402 " model vdw 2.084 2.510 nonbonded pdb=" O2G ANP C 401 " pdb="CA CA C 402 " model vdw 2.099 2.510 ... (remaining 58741 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 'A' and resid 22 through 337) selection = (chain 'B' and resid 22 through 337) selection = (chain 'C' and resid 22 through 337) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 0.010 Extract box with map and model: 12.150 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.260 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.008 0.149 7813 Z= 0.478 Angle : 1.051 22.547 10600 Z= 0.544 Chirality : 0.053 0.301 1194 Planarity : 0.004 0.028 1290 Dihedral : 18.459 129.722 3057 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.91 (0.18), residues: 915 helix: -4.79 (0.09), residues: 384 sheet: -1.97 (0.34), residues: 162 loop : -3.63 (0.23), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 30 PHE 0.028 0.003 PHE C 128 TYR 0.008 0.002 TYR B 260 ARG 0.010 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.8734 (m) cc_final: 0.8488 (t) REVERT: A 244 GLN cc_start: 0.8190 (mt0) cc_final: 0.7940 (mt0) REVERT: A 273 ASP cc_start: 0.7985 (t0) cc_final: 0.7750 (t70) REVERT: A 331 THR cc_start: 0.9030 (p) cc_final: 0.8781 (t) REVERT: B 94 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7989 (mmtp) REVERT: B 119 MET cc_start: 0.8617 (mtt) cc_final: 0.8339 (mtm) REVERT: B 202 LEU cc_start: 0.9131 (tp) cc_final: 0.8626 (tt) REVERT: B 314 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8579 (tttt) REVERT: C 123 GLU cc_start: 0.7564 (tt0) cc_final: 0.7353 (tt0) REVERT: C 155 LYS cc_start: 0.8567 (mttt) cc_final: 0.8237 (mtpt) REVERT: C 335 ILE cc_start: 0.8921 (mm) cc_final: 0.8559 (mm) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2541 time to fit residues: 79.5382 Evaluate side-chains 154 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.0470 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 30 HIS A 261 ASN B 22 GLN B 30 HIS B 199 GLN B 243 GLN C 22 GLN C 30 HIS C 199 GLN C 243 GLN C 244 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7813 Z= 0.159 Angle : 0.532 6.096 10600 Z= 0.287 Chirality : 0.043 0.138 1194 Planarity : 0.003 0.024 1290 Dihedral : 17.613 157.383 1299 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.19 % Allowed : 10.80 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.21), residues: 915 helix: -3.55 (0.17), residues: 387 sheet: -1.46 (0.36), residues: 162 loop : -3.20 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 30 PHE 0.016 0.001 PHE B 128 TYR 0.007 0.001 TYR B 194 ARG 0.005 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 THR cc_start: 0.8750 (m) cc_final: 0.8540 (m) REVERT: A 93 GLU cc_start: 0.7852 (mp0) cc_final: 0.7368 (mm-30) REVERT: A 194 TYR cc_start: 0.8917 (m-80) cc_final: 0.8693 (m-80) REVERT: A 268 ASN cc_start: 0.8836 (p0) cc_final: 0.8613 (p0) REVERT: A 331 THR cc_start: 0.8947 (p) cc_final: 0.8724 (t) REVERT: B 119 MET cc_start: 0.8433 (mtt) cc_final: 0.8179 (mtm) REVERT: B 261 ASN cc_start: 0.9073 (t0) cc_final: 0.8805 (t0) REVERT: C 155 LYS cc_start: 0.8579 (mttt) cc_final: 0.8271 (mtpt) REVERT: C 335 ILE cc_start: 0.8843 (mm) cc_final: 0.8503 (mm) outliers start: 9 outliers final: 5 residues processed: 166 average time/residue: 0.2230 time to fit residues: 48.3566 Evaluate side-chains 147 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 142 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 88 optimal weight: 0.0970 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 261 ASN C 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7813 Z= 0.219 Angle : 0.523 5.572 10600 Z= 0.280 Chirality : 0.043 0.157 1194 Planarity : 0.003 0.024 1290 Dihedral : 16.509 148.169 1299 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.98 % Allowed : 14.10 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.23), residues: 915 helix: -2.86 (0.21), residues: 396 sheet: -1.06 (0.38), residues: 156 loop : -3.11 (0.25), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS A 211 PHE 0.018 0.002 PHE C 128 TYR 0.010 0.001 TYR A 194 ARG 0.004 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7518 (mm-30) REVERT: A 192 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.6797 (ttt180) REVERT: A 194 TYR cc_start: 0.9009 (m-80) cc_final: 0.8772 (m-80) REVERT: A 324 ASN cc_start: 0.8702 (m-40) cc_final: 0.8417 (m-40) REVERT: A 331 THR cc_start: 0.9006 (p) cc_final: 0.8786 (t) REVERT: C 117 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6854 (mt-10) REVERT: C 119 MET cc_start: 0.8130 (mtt) cc_final: 0.7794 (mtt) REVERT: C 155 LYS cc_start: 0.8465 (mttt) cc_final: 0.8174 (mtpt) REVERT: C 238 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 335 ILE cc_start: 0.8961 (mm) cc_final: 0.8600 (mm) outliers start: 15 outliers final: 9 residues processed: 137 average time/residue: 0.2097 time to fit residues: 38.5350 Evaluate side-chains 134 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 GLN B 261 ASN C 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7813 Z= 0.170 Angle : 0.466 5.545 10600 Z= 0.253 Chirality : 0.042 0.150 1194 Planarity : 0.003 0.018 1290 Dihedral : 16.255 149.372 1299 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.11 % Allowed : 15.28 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.24), residues: 915 helix: -2.22 (0.23), residues: 396 sheet: -0.88 (0.39), residues: 156 loop : -2.97 (0.26), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 295 PHE 0.018 0.001 PHE C 128 TYR 0.008 0.001 TYR A 194 ARG 0.004 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: A 324 ASN cc_start: 0.8689 (m-40) cc_final: 0.8453 (m-40) REVERT: A 331 THR cc_start: 0.8981 (p) cc_final: 0.8775 (t) REVERT: B 93 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: C 117 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6903 (mt-10) REVERT: C 119 MET cc_start: 0.8144 (mtt) cc_final: 0.7854 (mtt) REVERT: C 155 LYS cc_start: 0.8421 (mttt) cc_final: 0.8205 (mtpt) REVERT: C 192 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.6764 (ttt180) REVERT: C 238 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7725 (mt-10) REVERT: C 335 ILE cc_start: 0.8989 (mm) cc_final: 0.8617 (mm) outliers start: 16 outliers final: 11 residues processed: 139 average time/residue: 0.2182 time to fit residues: 40.2556 Evaluate side-chains 141 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 261 ASN C 100 HIS C 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.084 7813 Z= 0.694 Angle : 0.807 7.798 10600 Z= 0.423 Chirality : 0.055 0.249 1194 Planarity : 0.006 0.069 1290 Dihedral : 16.705 148.902 1299 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 3.29 % Allowed : 17.26 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.89 (0.24), residues: 915 helix: -2.54 (0.22), residues: 396 sheet: -1.23 (0.39), residues: 159 loop : -3.12 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 30 PHE 0.028 0.004 PHE C 128 TYR 0.014 0.003 TYR B 316 ARG 0.006 0.001 ARG C 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.6854 (ttt90) REVERT: B 93 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: B 107 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7542 (mp0) REVERT: C 72 LYS cc_start: 0.8494 (mttt) cc_final: 0.8207 (tttt) REVERT: C 155 LYS cc_start: 0.8481 (mttt) cc_final: 0.8246 (mtpt) REVERT: C 335 ILE cc_start: 0.9127 (mm) cc_final: 0.8778 (mm) outliers start: 25 outliers final: 14 residues processed: 139 average time/residue: 0.2250 time to fit residues: 41.0105 Evaluate side-chains 132 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN C 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7813 Z= 0.185 Angle : 0.506 6.485 10600 Z= 0.272 Chirality : 0.043 0.168 1194 Planarity : 0.003 0.022 1290 Dihedral : 16.383 152.746 1299 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.71 % Allowed : 19.10 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.25), residues: 915 helix: -1.93 (0.24), residues: 399 sheet: -0.88 (0.40), residues: 153 loop : -3.03 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.020 0.002 PHE C 128 TYR 0.009 0.001 TYR A 260 ARG 0.003 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.6907 (ttt90) REVERT: B 93 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: C 117 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6990 (mt-10) REVERT: C 192 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6888 (ttt180) REVERT: C 335 ILE cc_start: 0.9047 (mm) cc_final: 0.8669 (mm) outliers start: 13 outliers final: 9 residues processed: 136 average time/residue: 0.2395 time to fit residues: 42.8209 Evaluate side-chains 143 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 5.9990 chunk 49 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN C 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7813 Z= 0.213 Angle : 0.504 5.990 10600 Z= 0.271 Chirality : 0.044 0.179 1194 Planarity : 0.003 0.024 1290 Dihedral : 16.231 152.384 1299 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.77 % Allowed : 19.10 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.26), residues: 915 helix: -1.63 (0.25), residues: 399 sheet: -0.77 (0.40), residues: 153 loop : -2.93 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 211 PHE 0.022 0.002 PHE C 128 TYR 0.007 0.001 TYR B 205 ARG 0.003 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 192 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.6767 (ttt180) REVERT: B 93 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: C 72 LYS cc_start: 0.8448 (mttt) cc_final: 0.8240 (tttt) REVERT: C 117 GLU cc_start: 0.7244 (mt-10) cc_final: 0.7031 (mt-10) REVERT: C 192 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.6904 (ttt180) REVERT: C 238 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7773 (mt-10) REVERT: C 335 ILE cc_start: 0.9050 (mm) cc_final: 0.8714 (mm) outliers start: 21 outliers final: 13 residues processed: 144 average time/residue: 0.2158 time to fit residues: 41.1253 Evaluate side-chains 150 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN B 261 ASN C 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7813 Z= 0.138 Angle : 0.454 5.714 10600 Z= 0.246 Chirality : 0.042 0.159 1194 Planarity : 0.002 0.020 1290 Dihedral : 16.033 151.347 1299 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.98 % Allowed : 19.89 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.26), residues: 915 helix: -1.20 (0.26), residues: 393 sheet: -0.66 (0.40), residues: 156 loop : -2.85 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 211 PHE 0.020 0.001 PHE C 128 TYR 0.007 0.001 TYR C 190 ARG 0.004 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 324 ASN cc_start: 0.8691 (m-40) cc_final: 0.8489 (m-40) REVERT: B 93 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: C 117 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6981 (mt-10) REVERT: C 192 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7651 (tpt-90) REVERT: C 335 ILE cc_start: 0.9042 (mm) cc_final: 0.8664 (mm) outliers start: 15 outliers final: 10 residues processed: 143 average time/residue: 0.2237 time to fit residues: 41.9922 Evaluate side-chains 149 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 0.0370 chunk 63 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS B 261 ASN C 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7813 Z= 0.163 Angle : 0.471 5.652 10600 Z= 0.254 Chirality : 0.043 0.167 1194 Planarity : 0.002 0.021 1290 Dihedral : 15.985 150.444 1299 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.11 % Allowed : 20.42 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.27), residues: 915 helix: -1.08 (0.26), residues: 396 sheet: -0.58 (0.40), residues: 156 loop : -2.70 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 211 PHE 0.021 0.001 PHE C 128 TYR 0.011 0.001 TYR B 194 ARG 0.006 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: B 93 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: C 72 LYS cc_start: 0.7661 (tttt) cc_final: 0.7148 (tptt) REVERT: C 117 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6958 (mt-10) REVERT: C 192 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.6793 (ttt180) REVERT: C 238 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7838 (pm20) REVERT: C 335 ILE cc_start: 0.9044 (mm) cc_final: 0.8669 (mm) outliers start: 16 outliers final: 13 residues processed: 144 average time/residue: 0.2120 time to fit residues: 40.3951 Evaluate side-chains 158 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 89 optimal weight: 0.0030 chunk 82 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS B 244 GLN B 261 ASN C 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7813 Z= 0.175 Angle : 0.478 5.738 10600 Z= 0.257 Chirality : 0.043 0.168 1194 Planarity : 0.003 0.024 1290 Dihedral : 15.970 149.933 1299 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.37 % Allowed : 20.16 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.27), residues: 915 helix: -1.00 (0.26), residues: 396 sheet: -0.54 (0.40), residues: 156 loop : -2.64 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 211 PHE 0.021 0.001 PHE C 128 TYR 0.006 0.001 TYR C 190 ARG 0.006 0.000 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: B 93 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: C 38 LYS cc_start: 0.7629 (pttm) cc_final: 0.6515 (ptmm) REVERT: C 72 LYS cc_start: 0.7670 (tttt) cc_final: 0.7129 (tptt) REVERT: C 117 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6956 (mt-10) REVERT: C 192 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.6779 (ttt180) REVERT: C 238 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7733 (pm20) REVERT: C 335 ILE cc_start: 0.9050 (mm) cc_final: 0.8680 (mm) outliers start: 18 outliers final: 14 residues processed: 143 average time/residue: 0.2145 time to fit residues: 40.7942 Evaluate side-chains 156 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 320 GLU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 323 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 0.0370 chunk 4 optimal weight: 0.0170 chunk 51 optimal weight: 0.6980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.152386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121231 restraints weight = 10526.813| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.07 r_work: 0.3135 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7813 Z= 0.163 Angle : 0.474 5.700 10600 Z= 0.255 Chirality : 0.043 0.165 1194 Planarity : 0.003 0.025 1290 Dihedral : 15.938 149.436 1299 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.24 % Allowed : 20.29 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.27), residues: 915 helix: -0.90 (0.27), residues: 396 sheet: -0.53 (0.40), residues: 156 loop : -2.60 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 211 PHE 0.021 0.001 PHE C 128 TYR 0.006 0.001 TYR C 190 ARG 0.006 0.000 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2101.52 seconds wall clock time: 38 minutes 27.25 seconds (2307.25 seconds total)