Starting phenix.real_space_refine on Mon Aug 5 21:18:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt6_37827/08_2024/8wt6_37827.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt6_37827/08_2024/8wt6_37827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt6_37827/08_2024/8wt6_37827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt6_37827/08_2024/8wt6_37827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt6_37827/08_2024/8wt6_37827.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt6_37827/08_2024/8wt6_37827.cif" } resolution = 2.5 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= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 234 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 8431 2.51 5 N 2726 2.21 5 O 3302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 18": "OD1" <-> "OD2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 18": "OD1" <-> "OD2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 320": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14743 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2420 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 1 Chain: "B" Number of atoms: 2514 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 2503 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 305} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 318, 2503 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 305} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2540 Chain: "C" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2411 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 1 Chain: "D" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2498 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 12, 'TRANS': 304} Chain: "E" Number of atoms: 1275 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 59, 1252 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 12, 'rna3p_pur': 23, 'rna3p_pyr': 20} Link IDs: {'rna2p': 16, 'rna3p': 42} Conformer: "B" Number of residues, atoms: 59, 1252 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 12, 'rna3p_pur': 23, 'rna3p_pyr': 20} Link IDs: {'rna2p': 16, 'rna3p': 42} bond proxies already assigned to first conformer: 1369 Chain: "F" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1443 Classifications: {'RNA': 68} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 27, 'rna3p_pyr': 28} Link IDs: {'rna2p': 13, 'rna3p': 54} Chain: "G" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 2 Chain: "H" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 558 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "I" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 507 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 2 Chain: "J" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 602 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG B 221 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 221 " occ=0.50 residue: pdb=" P A G E 75 " occ=0.50 ... (44 atoms not shown) pdb=" C4 B G E 75 " occ=0.50 Time building chain proxies: 9.86, per 1000 atoms: 0.67 Number of scatterers: 14743 At special positions: 0 Unit cell: (119.52, 123.314, 115.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 234 15.00 Mg 2 11.99 O 3302 8.00 N 2726 7.00 C 8431 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: 7.22 Conformation dependent library (CDL) restraints added in 2.3 seconds 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2334 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 8 sheets defined 68.4% alpha, 9.3% beta 87 base pairs and 138 stacking pairs defined. Time for finding SS restraints: 6.16 Creating SS restraints... Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.827A pdb=" N GLY A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 117 Processing helix chain 'A' and resid 125 through 155 removed outlier: 4.112A pdb=" N GLU A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 187 Processing helix chain 'A' and resid 188 through 200 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.539A pdb=" N ALA A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.566A pdb=" N PHE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.591A pdb=" N ALA A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.715A pdb=" N ASN A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 313 Processing helix chain 'A' and resid 317 through 321 Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 66 through 77 Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.714A pdb=" N GLY B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 125 through 155 removed outlier: 3.769A pdb=" N GLU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 159 through 188 removed outlier: 3.623A pdb=" N ASP B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 200 Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.508A pdb=" N ALA B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.704A pdb=" N PHE B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 263 removed outlier: 3.567A pdb=" N ARG B 260 " --> pdb=" O HIS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 290 through 313 Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 84 through 95 removed outlier: 3.739A pdb=" N GLY C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 117 Processing helix chain 'C' and resid 125 through 153 removed outlier: 3.790A pdb=" N GLU C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 188 removed outlier: 3.558A pdb=" N ASP C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 200 Processing helix chain 'C' and resid 205 through 217 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.723A pdb=" N PHE C 228 " --> pdb=" O HIS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.576A pdb=" N ALA C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.600A pdb=" N ASN C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 313 Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'D' and resid 36 through 50 Processing helix chain 'D' and resid 66 through 77 Processing helix chain 'D' and resid 84 through 95 removed outlier: 3.670A pdb=" N GLY D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 125 through 155 removed outlier: 3.956A pdb=" N GLU D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'D' and resid 159 through 187 Processing helix chain 'D' and resid 188 through 199 Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.570A pdb=" N ALA D 210 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.537A pdb=" N PHE D 228 " --> pdb=" O HIS D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.584A pdb=" N LEU D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 274 removed outlier: 3.549A pdb=" N SER D 272 " --> pdb=" O MET D 268 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 287 Processing helix chain 'D' and resid 290 through 313 Processing helix chain 'D' and resid 317 through 321 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34 removed outlier: 6.480A pdb=" N HIS A 6 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N CYS A 58 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 8 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N GLU A 60 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE A 10 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 34 removed outlier: 6.775A pdb=" N HIS B 6 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N CYS B 58 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 8 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N GLU B 60 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ILE B 10 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 236 through 237 removed outlier: 3.796A pdb=" N ARG B 250 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 240 through 241 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 34 removed outlier: 6.520A pdb=" N HIS C 6 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N CYS C 58 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE C 8 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLU C 60 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ILE C 10 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 28 through 34 removed outlier: 6.673A pdb=" N HIS D 6 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N CYS D 58 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE D 8 " --> pdb=" O CYS D 58 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N GLU D 60 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ILE D 10 " --> pdb=" O GLU D 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 236 through 237 removed outlier: 3.776A pdb=" N ARG D 250 " --> pdb=" O ARG D 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 240 through 241 672 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 220 hydrogen bonds 424 hydrogen bond angles 0 basepair planarities 87 basepair parallelities 140 stacking parallelities Total time for adding SS restraints: 5.52 Time building geometry restraints manager: 7.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3123 1.34 - 1.46: 5359 1.46 - 1.57: 6479 1.57 - 1.69: 459 1.69 - 1.81: 84 Bond restraints: 15504 Sorted by residual: bond pdb=" C ILE C 201 " pdb=" N PRO C 202 " ideal model delta sigma weight residual 1.333 1.359 -0.026 1.01e-02 9.80e+03 6.41e+00 bond pdb=" O5' C F 176 " pdb=" C5' C F 176 " ideal model delta sigma weight residual 1.420 1.458 -0.038 1.50e-02 4.44e+03 6.31e+00 bond pdb=" O5' G E 53 " pdb=" C5' G E 53 " ideal model delta sigma weight residual 1.420 1.457 -0.037 1.50e-02 4.44e+03 6.16e+00 bond pdb=" O5' G E 41 " pdb=" C5' G E 41 " ideal model delta sigma weight residual 1.420 1.456 -0.036 1.50e-02 4.44e+03 5.84e+00 bond pdb=" C ILE D 201 " pdb=" N PRO D 202 " ideal model delta sigma weight residual 1.333 1.358 -0.024 1.01e-02 9.80e+03 5.70e+00 ... (remaining 15499 not shown) Histogram of bond angle deviations from ideal: 95.56 - 103.33: 699 103.33 - 111.11: 6293 111.11 - 118.88: 7180 118.88 - 126.65: 7046 126.65 - 134.43: 762 Bond angle restraints: 21980 Sorted by residual: angle pdb=" O3' U F 132 " pdb=" P G F 133 " pdb=" O5' G F 133 " ideal model delta sigma weight residual 104.00 114.05 -10.05 1.50e+00 4.44e-01 4.49e+01 angle pdb=" O3' DG J 32 " pdb=" P DT J 33 " pdb=" O5' DT J 33 " ideal model delta sigma weight residual 104.00 95.56 8.44 1.50e+00 4.44e-01 3.17e+01 angle pdb=" O3' DA H 21 " pdb=" P DT H 22 " pdb=" O5' DT H 22 " ideal model delta sigma weight residual 104.00 95.72 8.28 1.50e+00 4.44e-01 3.04e+01 angle pdb=" O3' DA I 24 " pdb=" P DT I 25 " pdb=" O5' DT I 25 " ideal model delta sigma weight residual 104.00 95.81 8.19 1.50e+00 4.44e-01 2.98e+01 angle pdb=" O3' DA G 26 " pdb=" P DC G 27 " pdb=" O5' DC G 27 " ideal model delta sigma weight residual 104.00 96.69 7.31 1.50e+00 4.44e-01 2.37e+01 ... (remaining 21975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 8658 34.82 - 69.63: 606 69.63 - 104.45: 53 104.45 - 139.27: 0 139.27 - 174.09: 1 Dihedral angle restraints: 9318 sinusoidal: 5712 harmonic: 3606 Sorted by residual: dihedral pdb=" O4' U F 159 " pdb=" C1' U F 159 " pdb=" N1 U F 159 " pdb=" C2 U F 159 " ideal model delta sinusoidal sigma weight residual -128.00 46.09 -174.09 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C E 42 " pdb=" C2' C E 42 " pdb=" C1' C E 42 " pdb=" C3' C E 42 " ideal model delta sinusoidal sigma weight residual 25.00 -9.61 34.61 1 8.00e+00 1.56e-02 2.65e+01 dihedral pdb=" C4' C E 42 " pdb=" O4' C E 42 " pdb=" C1' C E 42 " pdb=" C2' C E 42 " ideal model delta sinusoidal sigma weight residual 3.00 -29.14 32.14 1 8.00e+00 1.56e-02 2.30e+01 ... (remaining 9315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 2253 0.130 - 0.261: 288 0.261 - 0.391: 0 0.391 - 0.521: 0 0.521 - 0.652: 8 Chirality restraints: 2549 Sorted by residual: chirality pdb=" P DA I 18 " pdb=" OP1 DA I 18 " pdb=" OP2 DA I 18 " pdb=" O5' DA I 18 " both_signs ideal model delta sigma weight residual True 2.35 -3.00 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DG I 5 " pdb=" OP1 DG I 5 " pdb=" OP2 DG I 5 " pdb=" O5' DG I 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DG J 12 " pdb=" OP1 DG J 12 " pdb=" OP2 DG J 12 " pdb=" O5' DG J 12 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 2546 not shown) Planarity restraints: 1975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A F 157 " -0.071 2.00e-02 2.50e+03 2.87e-02 2.27e+01 pdb=" N9 A F 157 " 0.046 2.00e-02 2.50e+03 pdb=" C8 A F 157 " 0.016 2.00e-02 2.50e+03 pdb=" N7 A F 157 " 0.007 2.00e-02 2.50e+03 pdb=" C5 A F 157 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A F 157 " -0.016 2.00e-02 2.50e+03 pdb=" N6 A F 157 " -0.028 2.00e-02 2.50e+03 pdb=" N1 A F 157 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A F 157 " 0.006 2.00e-02 2.50e+03 pdb=" N3 A F 157 " 0.015 2.00e-02 2.50e+03 pdb=" C4 A F 157 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 132 " 0.040 2.00e-02 2.50e+03 2.08e-02 9.72e+00 pdb=" N1 U F 132 " -0.043 2.00e-02 2.50e+03 pdb=" C2 U F 132 " -0.012 2.00e-02 2.50e+03 pdb=" O2 U F 132 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U F 132 " 0.007 2.00e-02 2.50e+03 pdb=" C4 U F 132 " 0.010 2.00e-02 2.50e+03 pdb=" O4 U F 132 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U F 132 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U F 132 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 26 " 0.040 2.00e-02 2.50e+03 1.96e-02 9.64e+00 pdb=" N1 DT I 26 " -0.042 2.00e-02 2.50e+03 pdb=" C2 DT I 26 " -0.009 2.00e-02 2.50e+03 pdb=" O2 DT I 26 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 26 " 0.008 2.00e-02 2.50e+03 pdb=" O4 DT I 26 " 0.015 2.00e-02 2.50e+03 pdb=" C5 DT I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 26 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DT I 26 " -0.002 2.00e-02 2.50e+03 ... (remaining 1972 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 15 2.27 - 2.92: 5204 2.92 - 3.58: 21840 3.58 - 4.24: 39791 4.24 - 4.90: 60500 Nonbonded interactions: 127350 Sorted by model distance: nonbonded pdb=" OG SER B 241 " pdb=" P DT I 21 " model vdw 1.607 3.400 nonbonded pdb=" OG SER D 241 " pdb=" P DA G 26 " model vdw 1.609 3.400 nonbonded pdb=" OE2 GLU C 60 " pdb="MG MG C 401 " model vdw 1.856 2.170 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 502 " model vdw 1.908 2.170 nonbonded pdb="MG MG A 401 " pdb=" O HOH G 101 " model vdw 1.965 2.170 ... (remaining 127345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 220 or resid 222 through 321)) selection = (chain 'B' and (resid 5 through 220 or resid 222 through 238 or resid 251 throug \ h 321)) selection = (chain 'C' and (resid 5 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 220 or resid 222 through 321)) selection = (chain 'D' and (resid 5 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 220 or resid 222 through 238 or r \ esid 251 through 321)) } 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=0.50 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 48.600 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 15504 Z= 0.496 Angle : 1.365 10.051 21980 Z= 0.875 Chirality : 0.083 0.652 2549 Planarity : 0.005 0.044 1975 Dihedral : 19.929 174.086 6984 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.40 % Allowed : 2.47 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.20), residues: 1237 helix: -0.78 (0.15), residues: 786 sheet: -0.88 (0.37), residues: 160 loop : -1.21 (0.30), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.009 TRP D 169 HIS 0.012 0.002 HIS D 256 PHE 0.024 0.004 PHE A 231 TYR 0.024 0.003 TYR B 264 ARG 0.021 0.003 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 LYS cc_start: 0.9418 (mttm) cc_final: 0.9211 (mtmm) REVERT: B 71 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8372 (mt-10) REVERT: C 265 MET cc_start: 0.9357 (mmm) cc_final: 0.9029 (mmt) REVERT: D 105 ASP cc_start: 0.8265 (t70) cc_final: 0.8041 (p0) REVERT: D 287 ASN cc_start: 0.9065 (t0) cc_final: 0.8504 (t0) REVERT: D 307 TYR cc_start: 0.9076 (t80) cc_final: 0.8660 (t80) outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 1.9883 time to fit residues: 224.8081 Evaluate side-chains 77 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain C residue 60 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN B 93 GLN B 99 ASN B 139 GLN D 99 ASN D 256 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15504 Z= 0.186 Angle : 0.578 7.338 21980 Z= 0.326 Chirality : 0.039 0.229 2549 Planarity : 0.004 0.039 1975 Dihedral : 22.020 174.412 4558 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.69 % Allowed : 7.11 % Favored : 92.19 % 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: 1.71 (0.23), residues: 1237 helix: 2.01 (0.17), residues: 794 sheet: -0.27 (0.39), residues: 164 loop : -0.46 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 46 HIS 0.004 0.001 HIS D 256 PHE 0.015 0.001 PHE C 280 TYR 0.016 0.002 TYR B 215 ARG 0.005 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: A 221 ARG cc_start: 0.8701 (ttp80) cc_final: 0.8467 (ttm-80) REVERT: A 258 SER cc_start: 0.9355 (m) cc_final: 0.9120 (t) REVERT: B 290 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8184 (mttt) REVERT: D 105 ASP cc_start: 0.7995 (t70) cc_final: 0.7604 (p0) REVERT: D 187 ASP cc_start: 0.8497 (m-30) cc_final: 0.8243 (t0) REVERT: D 287 ASN cc_start: 0.9044 (t0) cc_final: 0.8748 (t160) outliers start: 7 outliers final: 0 residues processed: 87 average time/residue: 1.6351 time to fit residues: 154.1476 Evaluate side-chains 75 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN B 139 GLN C 150 ASN D 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 15504 Z= 0.504 Angle : 0.622 7.384 21980 Z= 0.345 Chirality : 0.045 0.265 2549 Planarity : 0.005 0.045 1975 Dihedral : 22.040 172.291 4554 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.69 % Allowed : 8.50 % Favored : 90.81 % 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: 2.07 (0.24), residues: 1237 helix: 2.32 (0.18), residues: 793 sheet: -0.37 (0.37), residues: 176 loop : -0.23 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 46 HIS 0.006 0.001 HIS D 256 PHE 0.018 0.002 PHE B 231 TYR 0.014 0.002 TYR B 307 ARG 0.006 0.001 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 1.419 Fit side-chains REVERT: A 221 ARG cc_start: 0.8756 (ttp80) cc_final: 0.8436 (ttm-80) REVERT: A 258 SER cc_start: 0.9354 (m) cc_final: 0.9121 (t) REVERT: D 105 ASP cc_start: 0.8147 (t0) cc_final: 0.7696 (p0) REVERT: D 187 ASP cc_start: 0.8530 (m-30) cc_final: 0.8257 (t0) REVERT: D 287 ASN cc_start: 0.9125 (t0) cc_final: 0.8766 (t160) outliers start: 7 outliers final: 0 residues processed: 78 average time/residue: 1.7862 time to fit residues: 150.2646 Evaluate side-chains 68 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN B 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15504 Z= 0.167 Angle : 0.504 7.192 21980 Z= 0.286 Chirality : 0.036 0.223 2549 Planarity : 0.004 0.046 1975 Dihedral : 21.939 172.841 4554 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.89 % Allowed : 9.19 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.24), residues: 1237 helix: 2.63 (0.18), residues: 794 sheet: -0.11 (0.39), residues: 162 loop : -0.21 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 46 HIS 0.005 0.001 HIS D 256 PHE 0.012 0.001 PHE C 280 TYR 0.015 0.001 TYR B 74 ARG 0.009 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.400 Fit side-chains REVERT: A 221 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8464 (ttm-80) REVERT: A 258 SER cc_start: 0.9294 (m) cc_final: 0.9086 (t) REVERT: B 27 ARG cc_start: 0.8520 (mtm-85) cc_final: 0.8267 (mtp-110) outliers start: 9 outliers final: 1 residues processed: 83 average time/residue: 1.6777 time to fit residues: 150.9457 Evaluate side-chains 74 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN B 139 GLN C 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15504 Z= 0.238 Angle : 0.509 6.663 21980 Z= 0.288 Chirality : 0.037 0.233 2549 Planarity : 0.004 0.045 1975 Dihedral : 21.881 173.011 4554 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.59 % Allowed : 9.58 % Favored : 89.82 % 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: 2.59 (0.24), residues: 1237 helix: 2.73 (0.18), residues: 794 sheet: -0.10 (0.38), residues: 162 loop : -0.15 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 46 HIS 0.005 0.001 HIS D 256 PHE 0.013 0.002 PHE B 112 TYR 0.014 0.001 TYR D 307 ARG 0.008 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.343 Fit side-chains REVERT: A 221 ARG cc_start: 0.8789 (ttp80) cc_final: 0.8481 (ttm-80) REVERT: B 27 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.7857 (mtm110) outliers start: 6 outliers final: 1 residues processed: 78 average time/residue: 1.5340 time to fit residues: 130.4907 Evaluate side-chains 71 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 93 GLN B 139 GLN C 287 ASN D 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 15504 Z= 0.405 Angle : 0.562 6.336 21980 Z= 0.314 Chirality : 0.042 0.251 2549 Planarity : 0.005 0.047 1975 Dihedral : 21.933 173.174 4554 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.59 % Allowed : 10.38 % Favored : 89.03 % 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: 2.49 (0.24), residues: 1237 helix: 2.65 (0.18), residues: 794 sheet: -0.08 (0.38), residues: 162 loop : -0.22 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 46 HIS 0.007 0.001 HIS D 256 PHE 0.016 0.002 PHE B 112 TYR 0.016 0.002 TYR B 74 ARG 0.007 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 1.358 Fit side-chains REVERT: A 221 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8497 (ttm-80) REVERT: B 27 ARG cc_start: 0.8522 (mtm-85) cc_final: 0.7845 (mtm110) outliers start: 6 outliers final: 1 residues processed: 74 average time/residue: 1.7103 time to fit residues: 137.5232 Evaluate side-chains 71 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN B 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15504 Z= 0.209 Angle : 0.526 6.329 21980 Z= 0.297 Chirality : 0.038 0.236 2549 Planarity : 0.004 0.046 1975 Dihedral : 21.969 173.402 4554 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.40 % Allowed : 10.97 % Favored : 88.64 % 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: 2.58 (0.24), residues: 1237 helix: 2.71 (0.18), residues: 794 sheet: -0.02 (0.38), residues: 162 loop : -0.16 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 46 HIS 0.005 0.001 HIS D 256 PHE 0.012 0.002 PHE B 112 TYR 0.015 0.002 TYR C 307 ARG 0.007 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 1.429 Fit side-chains REVERT: A 221 ARG cc_start: 0.8809 (ttp80) cc_final: 0.8522 (ttm-80) REVERT: B 27 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.7838 (mtm110) outliers start: 4 outliers final: 1 residues processed: 75 average time/residue: 1.7718 time to fit residues: 143.9567 Evaluate side-chains 72 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN B 139 GLN C 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15504 Z= 0.222 Angle : 0.508 6.720 21980 Z= 0.287 Chirality : 0.037 0.230 2549 Planarity : 0.004 0.048 1975 Dihedral : 21.895 173.421 4554 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.30 % Allowed : 11.36 % Favored : 88.34 % 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: 2.69 (0.24), residues: 1237 helix: 2.80 (0.18), residues: 794 sheet: 0.02 (0.38), residues: 162 loop : -0.15 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 46 HIS 0.006 0.001 HIS D 256 PHE 0.012 0.001 PHE B 112 TYR 0.013 0.001 TYR B 307 ARG 0.007 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 1.363 Fit side-chains REVERT: A 221 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8558 (ttm-80) REVERT: B 27 ARG cc_start: 0.8491 (mtm-85) cc_final: 0.7844 (mtm110) outliers start: 3 outliers final: 2 residues processed: 76 average time/residue: 1.5569 time to fit residues: 128.8790 Evaluate side-chains 75 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN B 139 GLN D 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15504 Z= 0.347 Angle : 0.542 6.085 21980 Z= 0.303 Chirality : 0.040 0.244 2549 Planarity : 0.004 0.047 1975 Dihedral : 21.904 173.371 4554 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.40 % Allowed : 11.86 % Favored : 87.75 % 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: 2.62 (0.24), residues: 1237 helix: 2.75 (0.18), residues: 795 sheet: 0.03 (0.38), residues: 162 loop : -0.21 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 46 HIS 0.006 0.001 HIS D 256 PHE 0.015 0.002 PHE B 112 TYR 0.017 0.001 TYR B 74 ARG 0.007 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 1.369 Fit side-chains REVERT: A 221 ARG cc_start: 0.8856 (ttp80) cc_final: 0.8520 (ttm-80) REVERT: B 27 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.7837 (mtm110) outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 1.6319 time to fit residues: 131.3685 Evaluate side-chains 75 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 0.2980 chunk 119 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15504 Z= 0.187 Angle : 0.512 7.388 21980 Z= 0.289 Chirality : 0.037 0.230 2549 Planarity : 0.004 0.048 1975 Dihedral : 21.934 173.624 4554 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.30 % Allowed : 11.96 % Favored : 87.75 % 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: 2.68 (0.24), residues: 1237 helix: 2.80 (0.18), residues: 794 sheet: 0.03 (0.38), residues: 162 loop : -0.17 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 46 HIS 0.006 0.001 HIS D 256 PHE 0.010 0.002 PHE B 112 TYR 0.014 0.001 TYR C 307 ARG 0.007 0.000 ARG B 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 1.429 Fit side-chains REVERT: A 221 ARG cc_start: 0.8853 (ttp80) cc_final: 0.8537 (ttm-80) REVERT: B 27 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.7822 (mtm110) outliers start: 3 outliers final: 2 residues processed: 75 average time/residue: 1.6809 time to fit residues: 137.1743 Evaluate side-chains 74 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain D residue 158 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN B 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.083302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.056215 restraints weight = 43244.534| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 2.31 r_work: 0.2472 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2338 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2346 r_free = 0.2346 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2346 r_free = 0.2346 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15504 Z= 0.174 Angle : 0.490 6.477 21980 Z= 0.276 Chirality : 0.035 0.224 2549 Planarity : 0.004 0.047 1975 Dihedral : 21.848 173.283 4554 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.40 % Allowed : 11.76 % Favored : 87.85 % 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: 2.82 (0.24), residues: 1237 helix: 2.89 (0.18), residues: 795 sheet: 0.13 (0.38), residues: 160 loop : -0.10 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 46 HIS 0.006 0.001 HIS D 256 PHE 0.011 0.001 PHE B 112 TYR 0.013 0.001 TYR C 307 ARG 0.007 0.000 ARG B 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3935.21 seconds wall clock time: 70 minutes 44.65 seconds (4244.65 seconds total)