Starting phenix.real_space_refine on Sun Mar 10 21:32:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/03_2024/7n0l_24108_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/03_2024/7n0l_24108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/03_2024/7n0l_24108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/03_2024/7n0l_24108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/03_2024/7n0l_24108_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/03_2024/7n0l_24108_updated.pdb" } resolution = 2.8 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 34 5.16 5 C 3460 2.51 5 N 868 2.21 5 O 902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 11": "OD1" <-> "OD2" Residue "A GLU 17": "OE1" <-> "OE2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 131": "OD1" <-> "OD2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "B ASP 11": "OD1" <-> "OD2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 38": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 131": "OD1" <-> "OD2" Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 327": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5270 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2587 Classifications: {'peptide': 313} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2587 Classifications: {'peptide': 313} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.34, per 1000 atoms: 0.63 Number of scatterers: 5270 At special positions: 0 Unit cell: (101.97, 89.61, 88.58, 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 34 16.00 P 6 15.00 O 902 8.00 N 868 7.00 C 3460 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: 1.87 Conformation dependent library (CDL) restraints added in 819.6 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 0 sheets defined 79.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 removed outlier: 3.728A pdb=" N TRP A 16 " --> pdb=" O CYS A 12 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 20 " --> pdb=" O TRP A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 69 removed outlier: 3.724A pdb=" N LYS A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 60 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N CYS A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 97 removed outlier: 4.235A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.516A pdb=" N LEU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 153 removed outlier: 3.638A pdb=" N SER A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 184 removed outlier: 3.601A pdb=" N ASN A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.902A pdb=" N ALA A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 249 removed outlier: 4.952A pdb=" N ASN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 271 removed outlier: 3.603A pdb=" N TRP A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 295 Proline residue: A 277 - end of helix removed outlier: 3.691A pdb=" N GLY A 282 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 313 through 334 removed outlier: 3.911A pdb=" N ARG A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS A 334 " --> pdb=" O HIS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 20 removed outlier: 3.626A pdb=" N TRP B 16 " --> pdb=" O CYS B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 69 removed outlier: 3.765A pdb=" N LYS B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 51 " --> pdb=" O CYS B 47 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 removed outlier: 4.314A pdb=" N ASN B 85 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 86 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU B 89 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG B 90 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B 91 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 94 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.517A pdb=" N LEU B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 153 removed outlier: 3.657A pdb=" N SER B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 184 removed outlier: 3.601A pdb=" N ASN B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 205 removed outlier: 3.903A pdb=" N ALA B 197 " --> pdb=" O TRP B 193 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 248 removed outlier: 4.954A pdb=" N ASN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLN B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 234 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 271 removed outlier: 3.607A pdb=" N TRP B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 295 Proline residue: B 277 - end of helix removed outlier: 3.692A pdb=" N GLY B 282 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 293 " --> pdb=" O ASN B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 313 through 334 removed outlier: 3.930A pdb=" N ARG B 327 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS B 334 " --> pdb=" O HIS B 330 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 981 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: 1.26 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.77: 5358 1.77 - 2.38: 50 2.38 - 2.98: 0 2.98 - 3.59: 0 3.59 - 4.19: 4 Bond restraints: 5412 Sorted by residual: bond pdb=" AO6 COA B 401 " pdb=" AP2 COA B 401 " ideal model delta sigma weight residual 1.610 4.190 -2.580 2.00e-02 2.50e+03 1.66e+04 bond pdb=" AO6 COA A 401 " pdb=" AP2 COA A 401 " ideal model delta sigma weight residual 1.610 4.187 -2.577 2.00e-02 2.50e+03 1.66e+04 bond pdb=" AP1 COA A 401 " pdb="AO5* COA A 401 " ideal model delta sigma weight residual 1.610 3.725 -2.115 2.00e-02 2.50e+03 1.12e+04 bond pdb=" AP1 COA B 401 " pdb="AO5* COA B 401 " ideal model delta sigma weight residual 1.610 3.721 -2.111 2.00e-02 2.50e+03 1.11e+04 bond pdb=" PC9 COA A 401 " pdb=" PO9 COA A 401 " ideal model delta sigma weight residual 1.410 1.178 0.232 2.00e-02 2.50e+03 1.34e+02 ... (remaining 5407 not shown) Histogram of bond angle deviations from ideal: 19.50 - 42.69: 4 42.69 - 65.87: 0 65.87 - 89.06: 4 89.06 - 112.24: 2645 112.24 - 135.42: 4675 Bond angle restraints: 7328 Sorted by residual: angle pdb=" AO3 COA B 401 " pdb=" AP2 COA B 401 " pdb=" AO6 COA B 401 " ideal model delta sigma weight residual 102.60 19.50 83.10 3.00e+00 1.11e-01 7.67e+02 angle pdb=" AO3 COA A 401 " pdb=" AP2 COA A 401 " pdb=" AO6 COA A 401 " ideal model delta sigma weight residual 102.60 19.62 82.98 3.00e+00 1.11e-01 7.65e+02 angle pdb=" AO3 COA A 401 " pdb=" AP1 COA A 401 " pdb="AO5* COA A 401 " ideal model delta sigma weight residual 102.60 41.28 61.32 3.00e+00 1.11e-01 4.18e+02 angle pdb=" AO3 COA B 401 " pdb=" AP1 COA B 401 " pdb="AO5* COA B 401 " ideal model delta sigma weight residual 102.60 41.45 61.15 3.00e+00 1.11e-01 4.16e+02 angle pdb=" AO2 COA B 401 " pdb=" AP1 COA B 401 " pdb="AO5* COA B 401 " ideal model delta sigma weight residual 109.50 84.70 24.80 3.00e+00 1.11e-01 6.84e+01 ... (remaining 7323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 2949 35.20 - 70.40: 143 70.40 - 105.60: 20 105.60 - 140.80: 2 140.80 - 176.00: 4 Dihedral angle restraints: 3118 sinusoidal: 1280 harmonic: 1838 Sorted by residual: dihedral pdb=" AO6 COA B 401 " pdb="PC11 COA B 401 " pdb="PC12 COA B 401 " pdb="PC10 COA B 401 " ideal model delta sinusoidal sigma weight residual -68.50 107.50 -176.00 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" AO6 COA A 401 " pdb="PC11 COA A 401 " pdb="PC12 COA A 401 " pdb="PC10 COA A 401 " ideal model delta sinusoidal sigma weight residual -68.50 107.30 -175.79 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" AP1 COA A 401 " pdb="AC5* COA A 401 " pdb="AO5* COA A 401 " pdb="AC4* COA A 401 " ideal model delta sinusoidal sigma weight residual 111.68 -103.65 -144.67 1 2.00e+01 2.50e-03 4.36e+01 ... (remaining 3115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 639 0.049 - 0.098: 138 0.098 - 0.147: 3 0.147 - 0.196: 0 0.196 - 0.245: 2 Chirality restraints: 782 Sorted by residual: chirality pdb="AC3* COA A 401 " pdb="AC2* COA A 401 " pdb="AC4* COA A 401 " pdb="AO3* COA A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.72 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb="AC3* COA B 401 " pdb="AC2* COA B 401 " pdb="AC4* COA B 401 " pdb="AO3* COA B 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.71 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA PRO B 300 " pdb=" N PRO B 300 " pdb=" C PRO B 300 " pdb=" CB PRO B 300 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.56e-01 ... (remaining 779 not shown) Planarity restraints: 894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 69 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 70 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 69 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO B 70 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 70 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 70 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 312 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO B 313 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " 0.016 5.00e-02 4.00e+02 ... (remaining 891 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 18 2.32 - 2.97: 2397 2.97 - 3.61: 7804 3.61 - 4.26: 13210 4.26 - 4.90: 21097 Nonbonded interactions: 44526 Sorted by model distance: nonbonded pdb=" AO6 COA A 401 " pdb=" AP1 COA A 401 " model vdw 1.675 2.720 nonbonded pdb=" AO6 COA B 401 " pdb=" AP1 COA B 401 " model vdw 1.676 2.720 nonbonded pdb=" AP2 COA A 401 " pdb="AO5* COA A 401 " model vdw 1.691 2.720 nonbonded pdb=" AP2 COA B 401 " pdb="AO5* COA B 401 " model vdw 1.691 2.720 nonbonded pdb=" O GLN A 44 " pdb=" OG1 THR A 48 " model vdw 2.185 2.440 ... (remaining 44521 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' selection = chain 'B' } 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: 0.740 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: 0.000 Extract box with map and model: 3.880 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.300 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.065 2.580 5412 Z= 4.150 Angle : 1.950 83.097 7328 Z= 0.691 Chirality : 0.038 0.245 782 Planarity : 0.003 0.045 894 Dihedral : 21.578 175.996 1930 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 9.23 % Allowed : 20.30 % Favored : 70.48 % 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: -6.10 (0.22), residues: 614 helix: -3.82 (0.14), residues: 530 sheet: None (None), residues: 0 loop : -3.06 (0.55), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 192 HIS 0.002 0.001 HIS B 283 PHE 0.007 0.001 PHE A 235 TYR 0.007 0.001 TYR A 239 ARG 0.002 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 123 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 73 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7926 (pp20) cc_final: 0.7366 (pp20) REVERT: A 77 MET cc_start: 0.5173 (mpt) cc_final: 0.4909 (mpt) REVERT: A 87 MET cc_start: 0.6170 (ppp) cc_final: 0.5926 (ppp) REVERT: A 327 ARG cc_start: 0.7613 (ttm170) cc_final: 0.7369 (mtt180) REVERT: B 20 GLN cc_start: 0.6717 (pp30) cc_final: 0.6515 (tt0) REVERT: B 39 GLU cc_start: 0.7932 (pp20) cc_final: 0.7376 (pp20) REVERT: B 84 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6914 (tp30) REVERT: B 87 MET cc_start: 0.5988 (ppp) cc_final: 0.5775 (ppp) REVERT: B 327 ARG cc_start: 0.7611 (ttm170) cc_final: 0.7239 (mtt180) outliers start: 50 outliers final: 25 residues processed: 123 average time/residue: 1.0363 time to fit residues: 133.7645 Evaluate side-chains 101 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 304 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 156 ASN A 165 ASN A 230 GLN A 334 HIS ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN B 156 ASN B 165 ASN B 230 GLN B 334 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5412 Z= 0.165 Angle : 0.604 7.373 7328 Z= 0.298 Chirality : 0.039 0.153 782 Planarity : 0.005 0.027 894 Dihedral : 19.930 168.676 773 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 8.49 % Allowed : 20.85 % Favored : 70.66 % 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 (0.30), residues: 614 helix: -1.61 (0.19), residues: 524 sheet: None (None), residues: 0 loop : -1.23 (0.65), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 192 HIS 0.003 0.001 HIS B 283 PHE 0.019 0.001 PHE A 333 TYR 0.010 0.001 TYR B 240 ARG 0.007 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 125 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 79 time to evaluate : 0.636 Fit side-chains REVERT: A 39 GLU cc_start: 0.7549 (pp20) cc_final: 0.7049 (pp20) REVERT: A 82 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6639 (tm-30) REVERT: A 84 GLU cc_start: 0.7176 (tp30) cc_final: 0.6658 (tp30) REVERT: A 327 ARG cc_start: 0.7554 (ttm170) cc_final: 0.7176 (mtt180) REVERT: B 39 GLU cc_start: 0.7553 (pp20) cc_final: 0.7055 (pp20) REVERT: B 84 GLU cc_start: 0.7330 (tm-30) cc_final: 0.6865 (tp30) REVERT: B 327 ARG cc_start: 0.7610 (ttm170) cc_final: 0.7228 (mtt180) outliers start: 46 outliers final: 21 residues processed: 122 average time/residue: 1.2246 time to fit residues: 155.5015 Evaluate side-chains 96 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 74 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 304 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5412 Z= 0.196 Angle : 0.597 7.346 7328 Z= 0.292 Chirality : 0.041 0.203 782 Planarity : 0.004 0.028 894 Dihedral : 18.499 165.551 754 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 8.67 % Allowed : 23.99 % Favored : 67.34 % 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: -1.08 (0.32), residues: 614 helix: -0.40 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -1.76 (0.58), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 192 HIS 0.002 0.001 HIS B 283 PHE 0.022 0.001 PHE B 333 TYR 0.009 0.001 TYR B 133 ARG 0.004 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 133 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 86 time to evaluate : 0.592 Fit side-chains REVERT: A 39 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6993 (pp20) REVERT: A 66 LYS cc_start: 0.7677 (ptmm) cc_final: 0.7339 (tppp) REVERT: A 84 GLU cc_start: 0.7091 (tp30) cc_final: 0.6553 (tp30) REVERT: A 121 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8640 (mt) REVERT: A 135 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7586 (mttm) REVERT: A 241 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7594 (tp-100) REVERT: A 327 ARG cc_start: 0.7659 (ttm170) cc_final: 0.7254 (mtt180) REVERT: B 31 ARG cc_start: 0.7506 (mtm110) cc_final: 0.6437 (mmm160) REVERT: B 39 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6990 (pp20) REVERT: B 66 LYS cc_start: 0.7609 (ptmm) cc_final: 0.7223 (tppp) REVERT: B 84 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7053 (tp30) REVERT: B 121 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8630 (mt) REVERT: B 135 LYS cc_start: 0.7901 (mtpt) cc_final: 0.7603 (mttm) REVERT: B 327 ARG cc_start: 0.7626 (ttm170) cc_final: 0.7256 (mtt180) outliers start: 47 outliers final: 22 residues processed: 124 average time/residue: 1.1926 time to fit residues: 154.0502 Evaluate side-chains 107 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 80 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 304 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.0370 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5412 Z= 0.140 Angle : 0.545 6.814 7328 Z= 0.263 Chirality : 0.039 0.177 782 Planarity : 0.003 0.028 894 Dihedral : 17.543 157.994 747 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 6.27 % Allowed : 26.38 % Favored : 67.34 % 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: 0.05 (0.33), residues: 614 helix: 0.41 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.68 (0.57), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 192 HIS 0.002 0.001 HIS B 283 PHE 0.008 0.001 PHE A 226 TYR 0.010 0.001 TYR B 133 ARG 0.003 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 114 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 80 time to evaluate : 0.612 Fit side-chains REVERT: A 39 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7039 (pp20) REVERT: A 66 LYS cc_start: 0.7750 (ptmm) cc_final: 0.7415 (tppp) REVERT: A 84 GLU cc_start: 0.7164 (tp30) cc_final: 0.6658 (tp30) REVERT: A 135 LYS cc_start: 0.7829 (mtpt) cc_final: 0.7536 (mttm) REVERT: A 241 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7583 (tp-100) REVERT: A 327 ARG cc_start: 0.7591 (ttm170) cc_final: 0.7222 (mtt180) REVERT: B 31 ARG cc_start: 0.7500 (mtm110) cc_final: 0.6436 (mmm160) REVERT: B 39 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7009 (pp20) REVERT: B 66 LYS cc_start: 0.7588 (ptmm) cc_final: 0.7366 (tmmm) REVERT: B 84 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6859 (tp30) REVERT: B 135 LYS cc_start: 0.7858 (mtpt) cc_final: 0.7572 (mttm) REVERT: B 327 ARG cc_start: 0.7618 (ttm170) cc_final: 0.7245 (mtt180) outliers start: 34 outliers final: 18 residues processed: 111 average time/residue: 1.1798 time to fit residues: 136.5471 Evaluate side-chains 98 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 299 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5412 Z= 0.244 Angle : 0.616 7.279 7328 Z= 0.296 Chirality : 0.043 0.210 782 Planarity : 0.003 0.027 894 Dihedral : 16.672 158.303 737 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 7.01 % Allowed : 26.57 % Favored : 66.42 % 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: 0.29 (0.33), residues: 614 helix: 0.59 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.72 (0.58), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 192 HIS 0.002 0.001 HIS A 283 PHE 0.009 0.001 PHE A 284 TYR 0.009 0.001 TYR B 240 ARG 0.004 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 120 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 82 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6989 (pp20) REVERT: A 84 GLU cc_start: 0.7163 (tp30) cc_final: 0.6706 (tp30) REVERT: A 135 LYS cc_start: 0.7927 (mtpt) cc_final: 0.7613 (mttm) REVERT: A 241 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7611 (tp-100) REVERT: A 327 ARG cc_start: 0.7636 (ttm170) cc_final: 0.7243 (mtt180) REVERT: B 31 ARG cc_start: 0.7556 (mtm110) cc_final: 0.6591 (mmm160) REVERT: B 39 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6981 (pp20) REVERT: B 66 LYS cc_start: 0.7684 (ptmm) cc_final: 0.7472 (tppp) REVERT: B 84 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7002 (tp30) REVERT: B 135 LYS cc_start: 0.7915 (mtpt) cc_final: 0.7604 (mttm) REVERT: B 327 ARG cc_start: 0.7642 (ttm170) cc_final: 0.7258 (mtt180) outliers start: 38 outliers final: 27 residues processed: 113 average time/residue: 1.2158 time to fit residues: 143.1854 Evaluate side-chains 109 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 79 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 299 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5412 Z= 0.149 Angle : 0.552 6.226 7328 Z= 0.265 Chirality : 0.040 0.179 782 Planarity : 0.003 0.028 894 Dihedral : 15.779 178.633 736 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 5.54 % Allowed : 28.23 % Favored : 66.24 % 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: 0.96 (0.34), residues: 614 helix: 1.04 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.52 (0.62), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 192 HIS 0.002 0.001 HIS B 30 PHE 0.007 0.001 PHE A 226 TYR 0.010 0.001 TYR A 133 ARG 0.003 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 112 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 82 time to evaluate : 0.623 Fit side-chains REVERT: A 39 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7049 (pp20) REVERT: A 135 LYS cc_start: 0.7842 (mtpt) cc_final: 0.7542 (mttm) REVERT: A 327 ARG cc_start: 0.7648 (ttm170) cc_final: 0.7263 (mtt180) REVERT: B 31 ARG cc_start: 0.7445 (mtm110) cc_final: 0.6547 (mmm160) REVERT: B 39 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7012 (pp20) REVERT: B 84 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6870 (tp30) REVERT: B 87 MET cc_start: 0.6646 (ppp) cc_final: 0.6124 (ppp) REVERT: B 135 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7576 (mttm) REVERT: B 327 ARG cc_start: 0.7631 (ttm170) cc_final: 0.7258 (mtt180) outliers start: 30 outliers final: 14 residues processed: 109 average time/residue: 1.2873 time to fit residues: 146.2180 Evaluate side-chains 91 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 0.0070 chunk 37 optimal weight: 40.0000 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5412 Z= 0.164 Angle : 0.568 6.572 7328 Z= 0.273 Chirality : 0.041 0.201 782 Planarity : 0.003 0.027 894 Dihedral : 12.602 126.189 735 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 3.69 % Allowed : 29.89 % Favored : 66.42 % 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: 1.27 (0.34), residues: 614 helix: 1.27 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.64 (0.61), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 192 HIS 0.002 0.001 HIS B 30 PHE 0.008 0.001 PHE A 226 TYR 0.009 0.001 TYR A 133 ARG 0.004 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 97 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 0.585 Fit side-chains REVERT: A 39 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7044 (pp20) REVERT: A 135 LYS cc_start: 0.7848 (mtpt) cc_final: 0.7548 (mttm) REVERT: A 327 ARG cc_start: 0.7650 (ttm170) cc_final: 0.7267 (mtt180) REVERT: B 39 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7030 (pp20) REVERT: B 59 GLN cc_start: 0.7630 (mt0) cc_final: 0.7374 (mm110) REVERT: B 84 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6879 (tp30) REVERT: B 87 MET cc_start: 0.6648 (ppp) cc_final: 0.6126 (ppp) REVERT: B 135 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7560 (mttm) REVERT: B 188 ARG cc_start: 0.7717 (mmt90) cc_final: 0.7329 (mtp180) REVERT: B 327 ARG cc_start: 0.7634 (ttm170) cc_final: 0.7258 (mtt180) outliers start: 20 outliers final: 16 residues processed: 97 average time/residue: 1.2018 time to fit residues: 121.5803 Evaluate side-chains 93 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 30.0000 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.0670 chunk 33 optimal weight: 1.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5412 Z= 0.148 Angle : 0.556 6.430 7328 Z= 0.265 Chirality : 0.040 0.192 782 Planarity : 0.003 0.027 894 Dihedral : 10.803 103.560 735 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 4.24 % Allowed : 29.70 % Favored : 66.05 % 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: 1.54 (0.34), residues: 614 helix: 1.46 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.64 (0.62), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 192 HIS 0.002 0.001 HIS A 283 PHE 0.009 0.001 PHE A 94 TYR 0.010 0.001 TYR B 133 ARG 0.004 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 103 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.606 Fit side-chains REVERT: A 39 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7030 (pp20) REVERT: A 135 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7560 (mttm) REVERT: A 327 ARG cc_start: 0.7628 (ttm170) cc_final: 0.7231 (mtt180) REVERT: B 39 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7063 (pp20) REVERT: B 84 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6869 (tp30) REVERT: B 87 MET cc_start: 0.6660 (ppp) cc_final: 0.6137 (ppp) REVERT: B 135 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7580 (mttm) REVERT: B 327 ARG cc_start: 0.7627 (ttm170) cc_final: 0.7238 (mtt180) outliers start: 23 outliers final: 13 residues processed: 102 average time/residue: 1.1715 time to fit residues: 124.6494 Evaluate side-chains 87 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5412 Z= 0.336 Angle : 0.698 6.594 7328 Z= 0.333 Chirality : 0.046 0.204 782 Planarity : 0.004 0.041 894 Dihedral : 11.626 108.436 734 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.43 % Allowed : 29.70 % Favored : 65.87 % 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: 0.96 (0.33), residues: 614 helix: 1.03 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.70 (0.63), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 192 HIS 0.002 0.001 HIS B 30 PHE 0.011 0.002 PHE B 284 TYR 0.011 0.002 TYR B 133 ARG 0.008 0.001 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 101 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 0.631 Fit side-chains REVERT: A 39 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7055 (pp20) REVERT: A 57 ARG cc_start: 0.7464 (mmm-85) cc_final: 0.6699 (ttt180) REVERT: A 93 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7270 (tt) REVERT: A 241 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7602 (tp-100) REVERT: A 327 ARG cc_start: 0.7675 (ttm170) cc_final: 0.7296 (mtt180) REVERT: B 39 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7045 (pp20) REVERT: B 57 ARG cc_start: 0.7423 (mmm-85) cc_final: 0.6738 (ttt180) REVERT: B 84 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6933 (tp30) REVERT: B 241 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7560 (tp-100) REVERT: B 327 ARG cc_start: 0.7687 (ttm170) cc_final: 0.7299 (mtt180) outliers start: 24 outliers final: 17 residues processed: 95 average time/residue: 1.1281 time to fit residues: 112.0425 Evaluate side-chains 97 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5412 Z= 0.169 Angle : 0.588 6.157 7328 Z= 0.281 Chirality : 0.041 0.197 782 Planarity : 0.003 0.032 894 Dihedral : 11.055 99.949 734 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.87 % Allowed : 30.63 % Favored : 65.50 % 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: 1.48 (0.34), residues: 614 helix: 1.42 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.69 (0.62), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 192 HIS 0.002 0.000 HIS B 283 PHE 0.006 0.001 PHE B 318 TYR 0.009 0.001 TYR B 133 ARG 0.008 0.001 ARG B 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 95 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.631 Fit side-chains REVERT: A 39 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7075 (pp20) REVERT: A 57 ARG cc_start: 0.7449 (mmm-85) cc_final: 0.6746 (ttt180) REVERT: A 135 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7552 (mttm) REVERT: A 327 ARG cc_start: 0.7628 (ttm170) cc_final: 0.7249 (mtt180) REVERT: B 39 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7066 (pp20) REVERT: B 57 ARG cc_start: 0.7420 (mmm-85) cc_final: 0.6705 (ttt180) REVERT: B 84 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6885 (tp30) REVERT: B 87 MET cc_start: 0.6673 (ppp) cc_final: 0.6151 (ppp) REVERT: B 135 LYS cc_start: 0.7866 (mtpt) cc_final: 0.7562 (mttm) REVERT: B 327 ARG cc_start: 0.7667 (ttm170) cc_final: 0.7285 (mtt180) outliers start: 21 outliers final: 16 residues processed: 92 average time/residue: 1.1581 time to fit residues: 111.3853 Evaluate side-chains 91 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 304 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.0870 chunk 33 optimal weight: 0.5980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.145247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112254 restraints weight = 6917.761| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.64 r_work: 0.3333 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5412 Z= 0.149 Angle : 0.566 6.302 7328 Z= 0.270 Chirality : 0.040 0.200 782 Planarity : 0.003 0.031 894 Dihedral : 10.411 93.609 734 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 3.69 % Allowed : 30.81 % Favored : 65.50 % 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: 1.82 (0.34), residues: 614 helix: 1.66 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.66 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 192 HIS 0.002 0.001 HIS B 283 PHE 0.030 0.001 PHE B 333 TYR 0.010 0.001 TYR B 133 ARG 0.007 0.001 ARG B 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2558.44 seconds wall clock time: 45 minutes 57.29 seconds (2757.29 seconds total)