Starting phenix.real_space_refine on Thu Dec 7 22:21:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/12_2023/7n0l_24108_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/12_2023/7n0l_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_24108/12_2023/7n0l_24108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/12_2023/7n0l_24108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/12_2023/7n0l_24108_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/12_2023/7n0l_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-1.21rc1-5172/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: 3.37, per 1000 atoms: 0.64 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: 1.89 Conformation dependent library (CDL) restraints added in 878.7 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: 0.88 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: 1.28 Time building geometry restraints manager: 2.08 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: 1.380 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: 3.960 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.100 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.220 ------------------------------------------------------------------------------- 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 : 0.612 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 25 residues processed: 123 average time/residue: 1.0633 time to fit residues: 136.9859 Evaluate side-chains 96 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 71 time to evaluate : 0.544 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 25 residues processed: 0 time to fit residues: 0.7619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 36 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7667 moved from start: 0.2078 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= 0.153 Angle : 0.602 6.990 7328 Z= 0.299 Chirality : 0.038 0.143 782 Planarity : 0.005 0.026 894 Dihedral : 18.530 169.932 728 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 10.52 % Allowed : 19.93 % Favored : 69.56 % 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: -2.57 (0.30), residues: 614 helix: -1.55 (0.20), residues: 524 sheet: None (None), residues: 0 loop : -1.15 (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 0.009 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 133 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 76 time to evaluate : 0.620 Fit side-chains outliers start: 57 outliers final: 29 residues processed: 130 average time/residue: 1.0807 time to fit residues: 146.8319 Evaluate side-chains 102 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 73 time to evaluate : 0.546 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 1 average time/residue: 0.0890 time to fit residues: 0.9366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 0.0050 chunk 45 optimal weight: 3.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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: 0.7661 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5412 Z= 0.146 Angle : 0.567 6.648 7328 Z= 0.277 Chirality : 0.039 0.173 782 Planarity : 0.003 0.027 894 Dihedral : 17.164 178.121 728 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 8.86 % Allowed : 24.35 % Favored : 66.79 % 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: -0.80 (0.32), residues: 614 helix: -0.21 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.65 (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 0.022 0.001 PHE B 333 TYR 0.009 0.001 TYR B 133 ARG 0.005 0.000 ARG A 31 *********************** 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 132 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 84 time to evaluate : 0.619 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 27 residues processed: 128 average time/residue: 1.2045 time to fit residues: 160.4368 Evaluate side-chains 100 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 73 time to evaluate : 0.574 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 27 residues processed: 0 time to fit residues: 0.7709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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: 0.7730 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5412 Z= 0.321 Angle : 0.673 7.619 7328 Z= 0.327 Chirality : 0.045 0.210 782 Planarity : 0.004 0.027 894 Dihedral : 17.149 170.008 728 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 8.49 % Allowed : 24.17 % 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: -0.42 (0.32), residues: 614 helix: 0.06 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.75 (0.60), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 192 HIS 0.002 0.001 HIS A 283 PHE 0.012 0.001 PHE A 284 TYR 0.010 0.002 TYR B 238 ARG 0.004 0.001 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 122 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 76 time to evaluate : 0.680 Fit side-chains outliers start: 46 outliers final: 34 residues processed: 118 average time/residue: 1.0977 time to fit residues: 135.5655 Evaluate side-chains 110 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 76 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 30 residues processed: 4 average time/residue: 0.1025 time to fit residues: 1.4559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7671 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 : 0.003 0.026 5412 Z= 0.163 Angle : 0.581 6.970 7328 Z= 0.279 Chirality : 0.040 0.187 782 Planarity : 0.003 0.026 894 Dihedral : 16.840 172.968 728 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 7.93 % Allowed : 24.54 % Favored : 67.53 % 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: 0.48 (0.34), residues: 614 helix: 0.67 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.36 (0.67), 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 0.008 0.001 PHE A 127 TYR 0.010 0.001 TYR A 133 ARG 0.003 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 122 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 79 time to evaluate : 0.621 Fit side-chains outliers start: 43 outliers final: 34 residues processed: 119 average time/residue: 1.1500 time to fit residues: 142.7310 Evaluate side-chains 107 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 73 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 32 residues processed: 3 average time/residue: 0.0911 time to fit residues: 1.1958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7665 moved from start: 0.3139 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= 0.160 Angle : 0.586 8.308 7328 Z= 0.281 Chirality : 0.040 0.190 782 Planarity : 0.003 0.029 894 Dihedral : 16.338 169.134 728 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 8.49 % Allowed : 25.09 % 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: 1.05 (0.34), residues: 614 helix: 1.06 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.21 (0.68), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 192 HIS 0.002 0.001 HIS A 283 PHE 0.006 0.001 PHE B 226 TYR 0.010 0.001 TYR B 133 ARG 0.004 0.000 ARG A 249 *********************** 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 119 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 73 time to evaluate : 0.638 Fit side-chains outliers start: 46 outliers final: 33 residues processed: 114 average time/residue: 1.0210 time to fit residues: 122.1500 Evaluate side-chains 103 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 70 time to evaluate : 0.566 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 31 residues processed: 2 average time/residue: 0.1053 time to fit residues: 1.1023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.7697 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5412 Z= 0.225 Angle : 0.615 7.352 7328 Z= 0.297 Chirality : 0.043 0.233 782 Planarity : 0.003 0.030 894 Dihedral : 15.396 155.050 728 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 7.56 % Allowed : 26.57 % 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: 0.93 (0.33), residues: 614 helix: 1.05 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.81 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 192 HIS 0.002 0.001 HIS A 283 PHE 0.010 0.001 PHE B 284 TYR 0.009 0.001 TYR B 240 ARG 0.004 0.000 ARG A 249 *********************** 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 114 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 73 time to evaluate : 0.607 Fit side-chains outliers start: 41 outliers final: 34 residues processed: 111 average time/residue: 1.0826 time to fit residues: 125.7445 Evaluate side-chains 103 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 69 time to evaluate : 0.599 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 31 residues processed: 3 average time/residue: 0.0955 time to fit residues: 1.2138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.0370 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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: 0.7637 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5412 Z= 0.135 Angle : 0.568 11.352 7328 Z= 0.267 Chirality : 0.039 0.200 782 Planarity : 0.003 0.027 894 Dihedral : 14.735 174.439 728 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 6.64 % Allowed : 28.04 % Favored : 65.31 % 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 : -1.66 (0.61), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 192 HIS 0.002 0.001 HIS B 283 PHE 0.007 0.001 PHE B 226 TYR 0.010 0.001 TYR A 133 ARG 0.003 0.000 ARG A 249 *********************** 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 118 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 82 time to evaluate : 0.628 Fit side-chains outliers start: 36 outliers final: 28 residues processed: 116 average time/residue: 1.1207 time to fit residues: 135.7517 Evaluate side-chains 96 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 68 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 26 residues processed: 2 average time/residue: 0.1052 time to fit residues: 1.1432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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: 0.7695 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5412 Z= 0.241 Angle : 0.644 10.349 7328 Z= 0.303 Chirality : 0.043 0.203 782 Planarity : 0.004 0.039 894 Dihedral : 14.208 177.628 728 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 6.09 % Allowed : 28.41 % 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: 1.24 (0.33), residues: 614 helix: 1.27 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.88 (0.60), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 192 HIS 0.002 0.001 HIS A 283 PHE 0.025 0.001 PHE A 333 TYR 0.009 0.001 TYR B 133 ARG 0.006 0.001 ARG B 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 105 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 72 time to evaluate : 0.611 Fit side-chains outliers start: 33 outliers final: 29 residues processed: 103 average time/residue: 1.1111 time to fit residues: 119.7010 Evaluate side-chains 99 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 70 time to evaluate : 0.553 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 28 residues processed: 2 average time/residue: 0.0908 time to fit residues: 1.0140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7651 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5412 Z= 0.155 Angle : 0.576 8.139 7328 Z= 0.270 Chirality : 0.040 0.209 782 Planarity : 0.003 0.027 894 Dihedral : 11.108 127.378 728 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 5.35 % Allowed : 29.34 % Favored : 65.31 % 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: 1.62 (0.34), residues: 614 helix: 1.53 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.73 (0.61), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 192 HIS 0.002 0.001 HIS A 283 PHE 0.006 0.001 PHE A 226 TYR 0.010 0.001 TYR B 133 ARG 0.003 0.000 ARG A 249 ********************** 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 101 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 0.510 Fit side-chains outliers start: 29 outliers final: 28 residues processed: 99 average time/residue: 1.1745 time to fit residues: 121.2654 Evaluate side-chains 96 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 68 time to evaluate : 0.610 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 1 average time/residue: 0.0971 time to fit residues: 0.9641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 20 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 0.0050 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119098 restraints weight = 7087.556| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.59 r_work: 0.3369 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5412 Z= 0.143 Angle : 0.576 7.958 7328 Z= 0.270 Chirality : 0.039 0.205 782 Planarity : 0.003 0.039 894 Dihedral : 9.109 114.767 728 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 5.72 % Allowed : 28.60 % Favored : 65.68 % 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: 1.88 (0.34), residues: 614 helix: 1.71 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.66 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 192 HIS 0.002 0.000 HIS A 283 PHE 0.007 0.001 PHE A 94 TYR 0.010 0.001 TYR B 133 ARG 0.007 0.000 ARG B 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2586.72 seconds wall clock time: 46 minutes 37.27 seconds (2797.27 seconds total)