Starting phenix.real_space_refine on Mon Aug 5 22:51:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt9_37830/08_2024/8wt9_37830.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt9_37830/08_2024/8wt9_37830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt9_37830/08_2024/8wt9_37830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt9_37830/08_2024/8wt9_37830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt9_37830/08_2024/8wt9_37830.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt9_37830/08_2024/8wt9_37830.cif" } resolution = 2.7 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= -0.001 sd= 0.028 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 241 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 8557 2.51 5 N 2771 2.21 5 O 3363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 300": "NH1" <-> "NH2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "D ASP 105": "OD1" <-> "OD2" Residue "D TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14982 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2530 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 319, 2515 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 12, 'TRANS': 306} Conformer: "B" Number of residues, atoms: 319, 2515 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 12, 'TRANS': 306} bond proxies already assigned to first conformer: 2547 Chain: "B" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2449 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2517 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 2506 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} Conformer: "B" Number of residues, atoms: 318, 2506 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} bond proxies already assigned to first conformer: 2543 Chain: "D" Number of atoms: 2456 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 310, 2447 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 310, 2447 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2485 Chain: "E" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1249 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 11, 'rna3p_pur': 22, 'rna3p_pyr': 22} Link IDs: {'rna2p': 14, 'rna3p': 44} Chain: "F" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1442 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: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 580 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "H" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 557 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "I" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "J" Number of atoms: 643 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 602 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Conformer: "B" Number of residues, atoms: 29, 602 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain breaks: 1 bond proxies already assigned to first conformer: 630 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AGLN A 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 139 " occ=0.50 residue: pdb=" N ASER A 241 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 241 " occ=0.50 residue: pdb=" N AARG C 237 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 237 " occ=0.50 residue: pdb=" N AGLN D 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN D 139 " occ=0.50 residue: pdb=" P A DT J 28 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B DT J 28 " occ=0.50 residue: pdb=" P A DA J 29 " occ=0.50 ... (40 atoms not shown) pdb=" C4 B DA J 29 " occ=0.50 Time building chain proxies: 12.06, per 1000 atoms: 0.80 Number of scatterers: 14982 At special positions: 0 Unit cell: (122.84, 123.947, 116.2, 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 241 15.00 Mg 2 11.99 O 3363 8.00 N 2771 7.00 C 8557 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: 7.20 Conformation dependent library (CDL) restraints added in 2.9 seconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 67.2% alpha, 10.7% beta 87 base pairs and 148 stacking pairs defined. Time for finding SS restraints: 6.34 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: 3.627A pdb=" N GLY A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 125 through 155 removed outlier: 4.162A pdb=" N GLU A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 188 removed outlier: 3.656A pdb=" N ASP A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 205 through 217 Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.671A pdb=" N PHE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 263 removed outlier: 3.756A pdb=" N LEU A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.532A 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 removed outlier: 3.588A pdb=" N ARG A 320 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 66 through 77 Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.532A pdb=" N GLY B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 125 through 154 removed outlier: 3.810A pdb=" N GLU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 188 removed outlier: 3.624A 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 Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.729A pdb=" N PHE B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 263 Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 274 through 287 removed outlier: 3.714A pdb=" N ASN B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) 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 77 Processing helix chain 'C' and resid 84 through 96 removed outlier: 3.544A pdb=" N GLY C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 Processing helix chain 'C' and resid 125 through 153 removed outlier: 3.912A pdb=" N GLU C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 188 removed outlier: 3.626A 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: 3.649A pdb=" N PHE C 228 " --> pdb=" O HIS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.596A 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 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 49 Processing helix chain 'D' and resid 66 through 77 Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 101 through 117 removed outlier: 3.511A pdb=" N ALA D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 152 Processing helix chain 'D' and resid 159 through 188 removed outlier: 3.653A pdb=" N ASP D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.831A pdb=" N PHE D 228 " --> pdb=" O HIS D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 262 removed outlier: 3.519A pdb=" N ALA D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 274 Processing helix chain 'D' and resid 274 through 286 Processing helix chain 'D' and resid 290 through 313 Processing helix chain 'D' and resid 317 through 322 removed outlier: 3.633A pdb=" N ASN D 322 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34 removed outlier: 6.540A pdb=" N HIS A 6 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N CYS A 58 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE A 8 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLU A 60 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ILE A 10 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 241 removed outlier: 3.685A pdb=" N ARG A 250 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR A 239 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ALA A 248 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASER A 241 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG A 246 " --> pdb=" O ASER A 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 34 removed outlier: 4.434A pdb=" N GLU B 60 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B 12 " --> pdb=" O GLU B 60 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 236 through 237 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 34 removed outlier: 6.782A pdb=" N HIS C 6 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N CYS C 58 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C 8 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N GLU C 60 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ILE C 10 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 236 through 241 removed outlier: 3.915A pdb=" N ARG C 250 " --> pdb=" O AARG C 237 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR C 239 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ALA C 248 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER C 241 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ARG C 246 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 34 removed outlier: 6.664A pdb=" N HIS D 6 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N CYS D 58 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE D 8 " --> pdb=" O CYS D 58 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLU D 60 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ILE D 10 " --> pdb=" O GLU D 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 236 through 237 680 hydrogen bonds defined for protein. 2003 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 222 hydrogen bonds 438 hydrogen bond angles 0 basepair planarities 87 basepair parallelities 150 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 7.46 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: 3485 1.34 - 1.46: 5386 1.46 - 1.58: 6336 1.58 - 1.69: 475 1.69 - 1.81: 84 Bond restraints: 15766 Sorted by residual: bond pdb=" P A F 110 " pdb=" OP2 A F 110 " ideal model delta sigma weight residual 1.485 1.560 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" P A F 110 " pdb=" OP1 A F 110 " ideal model delta sigma weight residual 1.485 1.559 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" P A F 110 " pdb=" O5' A F 110 " ideal model delta sigma weight residual 1.593 1.633 -0.040 1.50e-02 4.44e+03 7.07e+00 bond pdb=" C THR D 235 " pdb=" N PRO D 236 " ideal model delta sigma weight residual 1.329 1.358 -0.029 1.20e-02 6.94e+03 5.98e+00 bond pdb=" C ILE A 201 " pdb=" N PRO A 202 " ideal model delta sigma weight residual 1.333 1.357 -0.024 1.01e-02 9.80e+03 5.58e+00 ... (remaining 15761 not shown) Histogram of bond angle deviations from ideal: 94.68 - 102.64: 545 102.64 - 110.59: 5665 110.59 - 118.54: 7975 118.54 - 126.49: 7379 126.49 - 134.44: 805 Bond angle restraints: 22369 Sorted by residual: angle pdb=" O3' DC G 15 " pdb=" P DC G 16 " pdb=" O5' DC G 16 " ideal model delta sigma weight residual 104.00 94.68 9.32 1.50e+00 4.44e-01 3.86e+01 angle pdb=" O3' U F 159 " pdb=" P U F 160 " pdb=" O5' U F 160 " ideal model delta sigma weight residual 104.00 95.77 8.23 1.50e+00 4.44e-01 3.01e+01 angle pdb=" O3' DC G 23 " pdb=" P DC G 24 " pdb=" O5' DC G 24 " ideal model delta sigma weight residual 104.00 96.79 7.21 1.50e+00 4.44e-01 2.31e+01 angle pdb=" CG MET D 108 " pdb=" SD MET D 108 " pdb=" CE MET D 108 " ideal model delta sigma weight residual 100.90 111.38 -10.48 2.20e+00 2.07e-01 2.27e+01 angle pdb=" O3' U F 168 " pdb=" P G F 169 " pdb=" O5' G F 169 " ideal model delta sigma weight residual 104.00 111.04 -7.04 1.50e+00 4.44e-01 2.20e+01 ... (remaining 22364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.07: 8729 34.07 - 68.13: 676 68.13 - 102.20: 52 102.20 - 136.26: 0 136.26 - 170.33: 1 Dihedral angle restraints: 9458 sinusoidal: 5803 harmonic: 3655 Sorted by residual: dihedral pdb=" C5' C E 95 " pdb=" C4' C E 95 " pdb=" C3' C E 95 " pdb=" O3' C E 95 " ideal model delta sinusoidal sigma weight residual 147.00 86.35 60.65 1 8.00e+00 1.56e-02 7.65e+01 dihedral pdb=" O4' C E 95 " pdb=" C4' C E 95 " pdb=" C3' C E 95 " pdb=" C2' C E 95 " ideal model delta sinusoidal sigma weight residual 24.00 -32.53 56.53 1 8.00e+00 1.56e-02 6.73e+01 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 232.00 61.67 170.33 1 1.70e+01 3.46e-03 6.60e+01 ... (remaining 9455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 2386 0.148 - 0.297: 199 0.297 - 0.445: 0 0.445 - 0.594: 1 0.594 - 0.742: 5 Chirality restraints: 2591 Sorted by residual: chirality pdb=" P A F 110 " pdb=" OP1 A F 110 " pdb=" OP2 A F 110 " pdb=" O5' A F 110 " both_signs ideal model delta sigma weight residual True 2.41 -3.15 -0.74 2.00e-01 2.50e+01 1.38e+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 -0.65 2.00e-01 2.50e+01 1.05e+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 -2.96 -0.62 2.00e-01 2.50e+01 9.57e+00 ... (remaining 2588 not shown) Planarity restraints: 2007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A F 157 " -0.037 2.00e-02 2.50e+03 1.49e-02 6.10e+00 pdb=" N9 A F 157 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A F 157 " 0.008 2.00e-02 2.50e+03 pdb=" N7 A F 157 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A F 157 " 0.005 2.00e-02 2.50e+03 pdb=" C6 A F 157 " -0.010 2.00e-02 2.50e+03 pdb=" N6 A F 157 " -0.014 2.00e-02 2.50e+03 pdb=" N1 A F 157 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A F 157 " 0.007 2.00e-02 2.50e+03 pdb=" N3 A F 157 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A F 157 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 35 " -0.031 2.00e-02 2.50e+03 1.31e-02 4.72e+00 pdb=" N9 DA J 35 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA J 35 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA J 35 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA J 35 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA J 35 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA J 35 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA J 35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA J 35 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA J 35 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA J 35 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U F 168 " -0.024 2.00e-02 2.50e+03 1.35e-02 4.11e+00 pdb=" N1 U F 168 " 0.031 2.00e-02 2.50e+03 pdb=" C2 U F 168 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U F 168 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U F 168 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U F 168 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U F 168 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U F 168 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U F 168 " 0.004 2.00e-02 2.50e+03 ... (remaining 2004 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 9 2.27 - 2.92: 5260 2.92 - 3.58: 22496 3.58 - 4.24: 40738 4.24 - 4.90: 62012 Nonbonded interactions: 130515 Sorted by model distance: nonbonded pdb=" OG SER C 241 " pdb=" P DC H 18 " model vdw 1.607 3.400 nonbonded pdb=" OG BSER A 241 " pdb=" P B DA J 29 " model vdw 1.608 3.400 nonbonded pdb="MG MG B 401 " pdb=" O HOH B 502 " model vdw 2.065 2.170 nonbonded pdb="MG MG B 401 " pdb=" O HOH B 501 " model vdw 2.072 2.170 nonbonded pdb=" OE1 GLU B 60 " pdb="MG MG B 401 " model vdw 2.086 2.170 ... (remaining 130510 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 138 or resid 140 through 236 or (resid 238 throu \ gh 239 and (name N or name CA or name C or name O or name CB )) or resid 248 thr \ ough 322)) selection = (chain 'B' and (resid 5 through 138 or resid 140 through 236 or resid 238 throug \ h 322)) selection = (chain 'C' and (resid 5 through 138 or resid 140 through 236 or (resid 238 throu \ gh 239 and (name N or name CA or name C or name O or name CB )) or resid 248 thr \ ough 322)) selection = (chain 'D' and (resid 5 through 138 or resid 140 through 236 or (resid 238 throu \ gh 248 and (name N or name CA or name C or name O or name CB )) or resid 249 thr \ ough 322)) } 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 51.880 Find NCS groups from input model: 0.530 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: 0.000 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 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 0.075 15766 Z= 0.492 Angle : 1.362 10.479 22369 Z= 0.878 Chirality : 0.080 0.742 2591 Planarity : 0.003 0.029 2007 Dihedral : 20.155 170.329 7094 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.98 % Allowed : 2.44 % Favored : 96.58 % 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: -1.58 (0.19), residues: 1258 helix: -0.66 (0.15), residues: 794 sheet: -1.40 (0.34), residues: 153 loop : -1.36 (0.29), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.006 TRP B 169 HIS 0.006 0.002 HIS D 256 PHE 0.017 0.003 PHE D 231 TYR 0.017 0.002 TYR B 78 ARG 0.015 0.002 ARG C 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.350 Fit side-chains REVERT: A 66 MET cc_start: 0.8236 (ppp) cc_final: 0.7997 (pp-130) REVERT: B 273 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8471 (mttm) REVERT: C 298 MET cc_start: 0.8201 (tpt) cc_final: 0.7879 (tpt) REVERT: D 287 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8324 (t0) outliers start: 10 outliers final: 0 residues processed: 112 average time/residue: 1.9149 time to fit residues: 229.7776 Evaluate side-chains 77 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain D residue 287 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN C 93 GLN C 287 ASN D 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15766 Z= 0.353 Angle : 0.635 7.175 22369 Z= 0.354 Chirality : 0.042 0.219 2591 Planarity : 0.005 0.049 2007 Dihedral : 22.140 162.271 4647 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.68 % Allowed : 6.06 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.23), residues: 1258 helix: 1.86 (0.17), residues: 799 sheet: -0.94 (0.35), residues: 165 loop : -0.84 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 276 HIS 0.005 0.001 HIS B 50 PHE 0.014 0.002 PHE C 231 TYR 0.019 0.002 TYR A 74 ARG 0.009 0.001 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.205 Fit side-chains REVERT: A 66 MET cc_start: 0.8006 (ppp) cc_final: 0.7740 (pp-130) REVERT: B 273 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8718 (mtpt) REVERT: C 139 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: D 191 MET cc_start: 0.8426 (mmm) cc_final: 0.8172 (mtp) outliers start: 6 outliers final: 2 residues processed: 77 average time/residue: 1.6975 time to fit residues: 142.6852 Evaluate side-chains 67 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain D residue 38 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15766 Z= 0.292 Angle : 0.559 6.346 22369 Z= 0.312 Chirality : 0.039 0.200 2591 Planarity : 0.004 0.047 2007 Dihedral : 22.232 163.149 4645 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.17 % Allowed : 6.06 % Favored : 92.77 % 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: 1.94 (0.24), residues: 1258 helix: 2.42 (0.18), residues: 801 sheet: -0.72 (0.37), residues: 165 loop : -0.70 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 46 HIS 0.005 0.001 HIS D 256 PHE 0.011 0.002 PHE C 112 TYR 0.020 0.002 TYR A 74 ARG 0.007 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 1.353 Fit side-chains REVERT: A 66 MET cc_start: 0.7923 (ppp) cc_final: 0.7679 (pp-130) outliers start: 11 outliers final: 2 residues processed: 76 average time/residue: 1.5243 time to fit residues: 126.9352 Evaluate side-chains 65 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 258 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15766 Z= 0.322 Angle : 0.555 6.154 22369 Z= 0.307 Chirality : 0.039 0.199 2591 Planarity : 0.004 0.048 2007 Dihedral : 22.260 163.319 4641 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.68 % Allowed : 7.33 % Favored : 91.98 % 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: 2.10 (0.24), residues: 1258 helix: 2.55 (0.18), residues: 801 sheet: -0.74 (0.37), residues: 165 loop : -0.60 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 46 HIS 0.004 0.001 HIS D 256 PHE 0.013 0.002 PHE C 231 TYR 0.019 0.002 TYR A 74 ARG 0.005 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 1.559 Fit side-chains REVERT: A 66 MET cc_start: 0.7830 (ppp) cc_final: 0.7602 (pp-130) outliers start: 6 outliers final: 2 residues processed: 69 average time/residue: 1.4113 time to fit residues: 107.5939 Evaluate side-chains 65 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 258 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8541 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15766 Z= 0.222 Angle : 0.514 6.034 22369 Z= 0.285 Chirality : 0.036 0.191 2591 Planarity : 0.004 0.048 2007 Dihedral : 22.198 164.338 4641 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.49 % Allowed : 8.02 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.24), residues: 1258 helix: 2.71 (0.18), residues: 803 sheet: -0.51 (0.39), residues: 161 loop : -0.47 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 46 HIS 0.004 0.001 HIS D 256 PHE 0.010 0.002 PHE C 231 TYR 0.017 0.001 TYR A 74 ARG 0.007 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 1.304 Fit side-chains REVERT: A 66 MET cc_start: 0.7880 (ppp) cc_final: 0.7665 (pp-130) outliers start: 4 outliers final: 1 residues processed: 73 average time/residue: 1.5206 time to fit residues: 123.0483 Evaluate side-chains 68 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.0030 chunk 124 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 11 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15766 Z= 0.156 Angle : 0.483 5.877 22369 Z= 0.268 Chirality : 0.034 0.205 2591 Planarity : 0.004 0.049 2007 Dihedral : 22.126 168.557 4641 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.68 % Allowed : 8.11 % Favored : 91.20 % 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: 2.65 (0.24), residues: 1258 helix: 2.89 (0.18), residues: 804 sheet: -0.28 (0.40), residues: 149 loop : -0.32 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 46 HIS 0.003 0.000 HIS B 256 PHE 0.009 0.001 PHE D 112 TYR 0.012 0.001 TYR B 307 ARG 0.008 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 1.287 Fit side-chains REVERT: A 66 MET cc_start: 0.7782 (ppp) cc_final: 0.7510 (pp-130) REVERT: D 299 MET cc_start: 0.8053 (mtp) cc_final: 0.7678 (mtp) outliers start: 6 outliers final: 1 residues processed: 79 average time/residue: 1.3499 time to fit residues: 117.7295 Evaluate side-chains 70 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15766 Z= 0.176 Angle : 0.482 6.058 22369 Z= 0.266 Chirality : 0.034 0.201 2591 Planarity : 0.004 0.048 2007 Dihedral : 22.110 167.898 4641 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.39 % Allowed : 8.02 % Favored : 91.59 % 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: 2.80 (0.24), residues: 1258 helix: 2.99 (0.18), residues: 804 sheet: -0.19 (0.40), residues: 149 loop : -0.25 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 46 HIS 0.003 0.001 HIS D 256 PHE 0.011 0.001 PHE D 112 TYR 0.020 0.001 TYR A 74 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 1.218 Fit side-chains REVERT: A 66 MET cc_start: 0.7779 (ppp) cc_final: 0.7516 (pp-130) outliers start: 3 outliers final: 2 residues processed: 72 average time/residue: 1.2864 time to fit residues: 102.8555 Evaluate side-chains 68 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain D residue 191 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN C 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15766 Z= 0.211 Angle : 0.492 5.932 22369 Z= 0.271 Chirality : 0.035 0.196 2591 Planarity : 0.004 0.049 2007 Dihedral : 22.135 166.156 4641 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.49 % Allowed : 8.41 % Favored : 91.10 % 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: 2.81 (0.24), residues: 1258 helix: 3.00 (0.18), residues: 802 sheet: -0.17 (0.40), residues: 149 loop : -0.24 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 46 HIS 0.003 0.001 HIS D 256 PHE 0.012 0.002 PHE D 112 TYR 0.019 0.001 TYR A 74 ARG 0.005 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.481 Fit side-chains REVERT: A 66 MET cc_start: 0.7799 (ppp) cc_final: 0.7576 (pp-130) outliers start: 4 outliers final: 2 residues processed: 67 average time/residue: 1.4306 time to fit residues: 106.0919 Evaluate side-chains 68 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain D residue 191 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 0.0770 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- 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: 0.8497 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15766 Z= 0.168 Angle : 0.479 6.038 22369 Z= 0.264 Chirality : 0.034 0.202 2591 Planarity : 0.004 0.049 2007 Dihedral : 22.120 166.736 4641 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.59 % Allowed : 8.31 % Favored : 91.10 % 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: 2.89 (0.24), residues: 1258 helix: 3.05 (0.18), residues: 803 sheet: -0.11 (0.40), residues: 149 loop : -0.19 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 46 HIS 0.003 0.000 HIS D 256 PHE 0.011 0.001 PHE D 112 TYR 0.019 0.001 TYR A 74 ARG 0.005 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 1.344 Fit side-chains REVERT: A 66 MET cc_start: 0.7783 (ppp) cc_final: 0.7545 (pp-130) outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 1.4647 time to fit residues: 113.3985 Evaluate side-chains 69 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 191 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 6.9990 chunk 82 optimal weight: 0.0670 chunk 64 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN C 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15766 Z= 0.331 Angle : 0.536 9.246 22369 Z= 0.293 Chirality : 0.038 0.196 2591 Planarity : 0.004 0.048 2007 Dihedral : 22.213 163.598 4641 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.39 % Allowed : 8.80 % 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: 2.64 (0.24), residues: 1258 helix: 2.85 (0.18), residues: 805 sheet: -0.45 (0.38), residues: 165 loop : -0.13 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 46 HIS 0.004 0.001 HIS B 145 PHE 0.014 0.002 PHE C 112 TYR 0.023 0.002 TYR A 74 ARG 0.005 0.000 ARG D 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 1.412 Fit side-chains REVERT: A 66 MET cc_start: 0.7808 (ppp) cc_final: 0.7584 (pp-130) outliers start: 3 outliers final: 2 residues processed: 65 average time/residue: 1.4919 time to fit residues: 107.0284 Evaluate side-chains 65 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain D residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.091298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.058625 restraints weight = 76845.623| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.11 r_work: 0.2467 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2476 r_free = 0.2476 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15766 Z= 0.169 Angle : 0.493 8.638 22369 Z= 0.271 Chirality : 0.034 0.197 2591 Planarity : 0.004 0.048 2007 Dihedral : 22.183 164.560 4641 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.39 % Allowed : 8.80 % 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: 2.78 (0.24), residues: 1258 helix: 2.95 (0.18), residues: 805 sheet: -0.11 (0.41), residues: 149 loop : -0.21 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 46 HIS 0.004 0.001 HIS D 256 PHE 0.010 0.001 PHE D 112 TYR 0.018 0.001 TYR A 74 ARG 0.005 0.000 ARG D 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.20 seconds wall clock time: 68 minutes 5.52 seconds (4085.52 seconds total)