Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 14:24:00 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/12_2021/7n0l_24108_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/12_2021/7n0l_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_2021/7n0l_24108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/12_2021/7n0l_24108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/12_2021/7n0l_24108_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0l_24108/12_2021/7n0l_24108_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "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-1.20rc4-4434/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: 3.35, 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 Amimo 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: 2.27 Conformation dependent library (CDL) restraints added in 679.0 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: 0.39 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: 1.38 Time building geometry restraints manager: 2.45 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="AO5* COA A 401 " pdb="AP1 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="AO5* COA B 401 " pdb="AP1 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="AC4* COA A 401 " pdb="AC5* COA A 401 " pdb="AO5* COA A 401 " pdb="AP1 COA A 401 " ideal model delta sinusoidal sigma weight residual 248.32 103.65 144.67 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="AO5* COA A 401 " pdb="AP2 COA A 401 " model vdw 1.691 2.720 nonbonded pdb="AO5* COA B 401 " pdb="AP2 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 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. 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 Write .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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.110 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.050 Process input model: 18.010 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:11.460 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 34.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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= 5.064 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 : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 9.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 : 0.676 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 25 residues processed: 123 average time/residue: 0.9239 time to fit residues: 119.6217 Evaluate side-chains 96 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 71 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 25 residues processed: 0 time to fit residues: 0.8907 ------------------------------------------------------------------------------- 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: 0.5980 chunk 36 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7922 moved from start: 0.2074 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= 0.156 Angle : 0.605 7.018 7328 Z= 0.300 Chirality : 0.039 0.163 782 Planarity : 0.005 0.027 894 Dihedral : 18.472 173.200 728 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer Outliers : 10.33 % 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 : -1.20 (0.65), residues: 90 *********************** 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: 56 poor density : 77 time to evaluate : 0.716 Fit side-chains outliers start: 56 outliers final: 27 residues processed: 130 average time/residue: 1.0551 time to fit residues: 143.7018 Evaluate side-chains 97 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 70 time to evaluate : 0.624 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 27 residues processed: 0 time to fit residues: 0.8794 ------------------------------------------------------------------------------- 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: 0.0770 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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: 0.7914 moved from start: 0.2679 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= 0.141 Angle : 0.560 6.459 7328 Z= 0.275 Chirality : 0.039 0.160 782 Planarity : 0.003 0.028 894 Dihedral : 17.048 174.228 728 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer Outliers : 8.67 % 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: -0.89 (0.32), residues: 614 helix: -0.27 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -1.65 (0.57), residues: 88 *********************** 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: 47 poor density : 85 time to evaluate : 0.650 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 27 residues processed: 129 average time/residue: 1.1029 time to fit residues: 148.5480 Evaluate side-chains 101 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 74 time to evaluate : 0.649 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 26 residues processed: 1 average time/residue: 0.0980 time to fit residues: 0.9848 ------------------------------------------------------------------------------- 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: 2.9990 chunk 42 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 30.0000 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5412 Z= 0.179 Angle : 0.588 8.721 7328 Z= 0.282 Chirality : 0.040 0.176 782 Planarity : 0.003 0.027 894 Dihedral : 17.035 178.000 728 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer Outliers : 7.20 % 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: 0.39 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.58 (0.61), residues: 86 *********************** 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 113 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 74 time to evaluate : 0.666 Fit side-chains outliers start: 39 outliers final: 32 residues processed: 111 average time/residue: 1.0507 time to fit residues: 122.3835 Evaluate side-chains 103 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 71 time to evaluate : 0.643 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 2 average time/residue: 0.0937 time to fit residues: 1.1290 ------------------------------------------------------------------------------- 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: 2.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.7936 moved from start: 0.2981 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= 0.187 Angle : 0.596 8.185 7328 Z= 0.285 Chirality : 0.041 0.186 782 Planarity : 0.003 0.027 894 Dihedral : 16.689 177.944 728 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer Outliers : 8.67 % 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: 0.65 (0.34), residues: 614 helix: 0.81 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -1.41 (0.65), residues: 88 *********************** 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 124 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 77 time to evaluate : 0.651 Fit side-chains outliers start: 47 outliers final: 35 residues processed: 119 average time/residue: 0.9676 time to fit residues: 121.1872 Evaluate side-chains 106 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 71 time to evaluate : 0.663 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 32 residues processed: 3 average time/residue: 0.4119 time to fit residues: 2.2608 ------------------------------------------------------------------------------- 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: 0.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.7926 moved from start: 0.3093 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= 0.171 Angle : 0.593 9.445 7328 Z= 0.283 Chirality : 0.040 0.190 782 Planarity : 0.003 0.027 894 Dihedral : 16.324 176.525 728 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer Outliers : 7.75 % 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 (0.34), residues: 614 helix: 1.09 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.30 (0.65), residues: 86 *********************** 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 115 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 73 time to evaluate : 0.665 Fit side-chains outliers start: 42 outliers final: 35 residues processed: 112 average time/residue: 0.9363 time to fit residues: 110.6481 Evaluate side-chains 105 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 70 time to evaluate : 0.691 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 32 residues processed: 3 average time/residue: 0.1044 time to fit residues: 1.3727 ------------------------------------------------------------------------------- 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: 2.9990 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 37 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2944 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= 0.311 Angle : 0.667 7.440 7328 Z= 0.321 Chirality : 0.045 0.217 782 Planarity : 0.004 0.038 894 Dihedral : 16.284 176.244 728 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 8.86 % 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: 0.65 (0.33), residues: 614 helix: 0.85 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.89 (0.58), residues: 84 *********************** 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 123 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 75 time to evaluate : 0.663 Fit side-chains outliers start: 48 outliers final: 34 residues processed: 116 average time/residue: 1.0209 time to fit residues: 124.3741 Evaluate side-chains 110 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 76 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 31 residues processed: 3 average time/residue: 0.0933 time to fit residues: 1.2037 ------------------------------------------------------------------------------- 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: 0.8980 chunk 37 optimal weight: 0.0010 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- 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: 0.7905 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 5412 Z= 0.137 Angle : 0.570 9.030 7328 Z= 0.268 Chirality : 0.040 0.201 782 Planarity : 0.003 0.028 894 Dihedral : 16.249 179.963 728 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer Outliers : 7.38 % 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: 1.28 (0.34), residues: 614 helix: 1.29 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.75 (0.61), residues: 84 *********************** 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: 40 poor density : 78 time to evaluate : 0.677 Fit side-chains outliers start: 40 outliers final: 30 residues processed: 113 average time/residue: 1.0130 time to fit residues: 120.1424 Evaluate side-chains 102 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 72 time to evaluate : 0.630 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 1 average time/residue: 0.1011 time to fit residues: 0.9963 ------------------------------------------------------------------------------- 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: 0.5980 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.0030 chunk 40 optimal weight: 5.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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: 0.7899 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 5412 Z= 0.133 Angle : 0.562 6.339 7328 Z= 0.265 Chirality : 0.039 0.202 782 Planarity : 0.003 0.027 894 Dihedral : 15.939 177.557 728 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer Outliers : 5.72 % 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: 1.65 (0.34), residues: 614 helix: 1.54 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.64 (0.61), residues: 84 *********************** 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 112 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 81 time to evaluate : 0.696 Fit side-chains outliers start: 31 outliers final: 25 residues processed: 112 average time/residue: 1.1051 time to fit residues: 129.4458 Evaluate side-chains 95 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 70 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 25 residues processed: 0 time to fit residues: 0.9226 ------------------------------------------------------------------------------- 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: 0.0970 chunk 56 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.0020 chunk 15 optimal weight: 0.7980 chunk 45 optimal weight: 0.0770 chunk 7 optimal weight: 6.9990 overall best weight: 0.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN B 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3806 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= 0.128 Angle : 0.575 11.121 7328 Z= 0.264 Chirality : 0.039 0.195 782 Planarity : 0.003 0.027 894 Dihedral : 15.639 176.182 728 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer Outliers : 4.98 % 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: 1.96 (0.34), residues: 614 helix: 1.78 (0.23), residues: 528 sheet: None (None), residues: 0 loop : -1.69 (0.63), residues: 86 ********************** 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 105 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 78 time to evaluate : 0.660 Fit side-chains outliers start: 27 outliers final: 21 residues processed: 104 average time/residue: 1.0959 time to fit residues: 119.2954 Evaluate side-chains 92 residues out of total 568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 0.645 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 0.8630 ------------------------------------------------------------------------------- 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: 1.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN B 54 GLN B 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.151910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116795 restraints weight = 6918.589| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.59 r_work: 0.3475 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.3449 rms_B_bonded: 1.49 restraints_weight: 0.1250 r_work: 0.3435 rms_B_bonded: 1.63 restraints_weight: 0.0625 r_work: 0.3419 rms_B_bonded: 1.81 restraints_weight: 0.0312 r_work: 0.3402 rms_B_bonded: 2.04 restraints_weight: 0.0156 r_work: 0.3383 rms_B_bonded: 2.33 restraints_weight: 0.0078 r_work: 0.3362 rms_B_bonded: 2.67 restraints_weight: 0.0039 r_work: 0.3338 rms_B_bonded: 3.09 restraints_weight: 0.0020 r_work: 0.3312 rms_B_bonded: 3.58 restraints_weight: 0.0010 r_work: 0.3282 rms_B_bonded: 4.16 restraints_weight: 0.0005 r_work: 0.3249 rms_B_bonded: 4.85 restraints_weight: 0.0002 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 5412 Z= 0.155 Angle : 0.611 10.104 7328 Z= 0.280 Chirality : 0.040 0.186 782 Planarity : 0.003 0.039 894 Dihedral : 15.396 173.900 728 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer Outliers : 4.06 % 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: 2.11 (0.34), residues: 614 helix: 1.85 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.51 (0.66), residues: 84 =============================================================================== Job complete usr+sys time: 2307.45 seconds wall clock time: 41 minutes 34.22 seconds (2494.22 seconds total)