Starting phenix.real_space_refine on Fri May 16 16:13:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wt9_37830/05_2025/8wt9_37830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wt9_37830/05_2025/8wt9_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/cci-nas-00/data/ceres_data/8wt9_37830/05_2025/8wt9_37830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wt9_37830/05_2025/8wt9_37830.map" model { file = "/net/cci-nas-00/data/ceres_data/8wt9_37830/05_2025/8wt9_37830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wt9_37830/05_2025/8wt9_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. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 12.02, 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 - 3.00 Amino acid : True - 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: 3.58 Conformation dependent library (CDL) restraints added in 2.1 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: 6.37 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: 5.71 Time building geometry restraints manager: 4.13 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: 0.00 - 2.10: 19710 2.10 - 4.19: 2427 4.19 - 6.29: 216 6.29 - 8.38: 14 8.38 - 10.48: 2 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: 0.760 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: 0.140 Process input model: 43.400 Find NCS groups from input model: 0.580 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:10.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.320 ------------------------------------------------------------------------------- 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= 0.477 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 Details of bonding type rmsd hydrogen bonds : bond 0.20347 ( 902) hydrogen bonds : angle 6.71794 ( 2441) covalent geometry : bond 0.00793 (15766) covalent geometry : angle 1.36173 (22369) *********************** 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 to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.227 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: 1.8236 time to fit residues: 218.9550 Evaluate side-chains 77 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.055353 restraints weight = 80134.335| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 3.17 r_work: 0.2375 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2433 r_free = 0.2433 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2433 r_free = 0.2433 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 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= 0.247 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 Details of bonding type rmsd hydrogen bonds : bond 0.06176 ( 902) hydrogen bonds : angle 4.12143 ( 2441) covalent geometry : bond 0.00558 (15766) covalent geometry : angle 0.63542 (22369) *********************** 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 to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.337 Fit side-chains REVERT: B 273 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8824 (mtpt) REVERT: C 139 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: D 191 MET cc_start: 0.9029 (mmm) cc_final: 0.8730 (mtp) REVERT: D 287 ASN cc_start: 0.8999 (t0) cc_final: 0.8728 (m110) outliers start: 6 outliers final: 2 residues processed: 77 average time/residue: 1.5472 time to fit residues: 129.9740 Evaluate side-chains 67 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 20 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 85 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.092338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.059288 restraints weight = 83797.541| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 3.31 r_work: 0.2470 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15766 Z= 0.128 Angle : 0.525 6.601 22369 Z= 0.295 Chirality : 0.036 0.187 2591 Planarity : 0.004 0.044 2007 Dihedral : 22.151 165.022 4645 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.98 % Allowed : 6.26 % 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: 2.11 (0.24), residues: 1258 helix: 2.50 (0.18), residues: 805 sheet: -0.50 (0.38), residues: 161 loop : -0.64 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 276 HIS 0.005 0.001 HIS B 256 PHE 0.009 0.001 PHE A 280 TYR 0.020 0.002 TYR A 74 ARG 0.010 0.001 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 902) hydrogen bonds : angle 3.66822 ( 2441) covalent geometry : bond 0.00265 (15766) covalent geometry : angle 0.52532 (22369) *********************** 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 90 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 1.196 Fit side-chains REVERT: D 54 HIS cc_start: 0.8672 (m90) cc_final: 0.8444 (m90) REVERT: D 191 MET cc_start: 0.8956 (mmm) cc_final: 0.8627 (mtp) REVERT: D 275 GLU cc_start: 0.8277 (pm20) cc_final: 0.8039 (pm20) REVERT: D 287 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8779 (m110) outliers start: 9 outliers final: 0 residues processed: 83 average time/residue: 1.4426 time to fit residues: 131.4220 Evaluate side-chains 69 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 287 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 140 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN D 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.089332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.056563 restraints weight = 92393.126| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 3.30 r_work: 0.2404 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2456 r_free = 0.2456 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2456 r_free = 0.2456 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15766 Z= 0.195 Angle : 0.537 6.081 22369 Z= 0.298 Chirality : 0.038 0.197 2591 Planarity : 0.004 0.045 2007 Dihedral : 22.162 164.788 4641 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.59 % Allowed : 7.04 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.24), residues: 1258 helix: 2.64 (0.18), residues: 803 sheet: -0.54 (0.39), residues: 151 loop : -0.66 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 46 HIS 0.005 0.001 HIS D 256 PHE 0.013 0.002 PHE C 112 TYR 0.013 0.001 TYR C 307 ARG 0.006 0.001 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 902) hydrogen bonds : angle 3.64341 ( 2441) covalent geometry : bond 0.00438 (15766) covalent geometry : angle 0.53659 (22369) *********************** 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 75 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 1.327 Fit side-chains REVERT: C 322 ASN cc_start: 0.7560 (m-40) cc_final: 0.7356 (m-40) REVERT: D 191 MET cc_start: 0.8922 (mmm) cc_final: 0.8702 (mtp) REVERT: D 287 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8797 (m110) outliers start: 5 outliers final: 2 residues processed: 72 average time/residue: 1.3115 time to fit residues: 104.3935 Evaluate side-chains 69 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain D residue 287 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 109 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.089397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.056193 restraints weight = 96872.684| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 3.43 r_work: 0.2398 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2453 r_free = 0.2453 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2453 r_free = 0.2453 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15766 Z= 0.190 Angle : 0.526 6.001 22369 Z= 0.292 Chirality : 0.038 0.193 2591 Planarity : 0.004 0.049 2007 Dihedral : 22.186 163.799 4641 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.59 % Allowed : 7.72 % Favored : 91.69 % 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: 2.32 (0.24), residues: 1258 helix: 2.70 (0.18), residues: 803 sheet: -0.62 (0.38), residues: 165 loop : -0.49 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 46 HIS 0.005 0.001 HIS D 256 PHE 0.012 0.002 PHE C 112 TYR 0.022 0.002 TYR A 74 ARG 0.007 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 902) hydrogen bonds : angle 3.60212 ( 2441) covalent geometry : bond 0.00430 (15766) covalent geometry : angle 0.52626 (22369) *********************** 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 73 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 1.394 Fit side-chains REVERT: C 322 ASN cc_start: 0.7736 (m-40) cc_final: 0.7517 (m-40) REVERT: D 54 HIS cc_start: 0.8708 (m90) cc_final: 0.8475 (m90) REVERT: D 191 MET cc_start: 0.8908 (mmm) cc_final: 0.8699 (mtp) REVERT: D 275 GLU cc_start: 0.8211 (pm20) cc_final: 0.7975 (pm20) REVERT: D 287 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8798 (m110) outliers start: 5 outliers final: 1 residues processed: 69 average time/residue: 1.3824 time to fit residues: 105.5867 Evaluate side-chains 67 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain D residue 287 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 0 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 35 optimal weight: 0.0670 chunk 43 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.091468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.058865 restraints weight = 91154.420| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.32 r_work: 0.2459 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2469 r_free = 0.2469 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2543 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= 0.127 Angle : 0.498 6.386 22369 Z= 0.276 Chirality : 0.035 0.191 2591 Planarity : 0.004 0.048 2007 Dihedral : 22.147 165.513 4641 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.88 % Allowed : 7.62 % 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: 2.51 (0.24), residues: 1258 helix: 2.78 (0.18), residues: 805 sheet: -0.24 (0.40), residues: 147 loop : -0.45 (0.35), residues: 306 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 0.010 0.001 PHE D 112 TYR 0.018 0.001 TYR A 74 ARG 0.005 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 902) hydrogen bonds : angle 3.48236 ( 2441) covalent geometry : bond 0.00274 (15766) covalent geometry : angle 0.49779 (22369) *********************** 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 to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 1.213 Fit side-chains REVERT: A 299 MET cc_start: 0.9208 (mtp) cc_final: 0.8974 (mtp) REVERT: B 251 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8844 (ttp) REVERT: C 265 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.9030 (mmp) REVERT: C 322 ASN cc_start: 0.7745 (m-40) cc_final: 0.7532 (m-40) REVERT: D 54 HIS cc_start: 0.8684 (m90) cc_final: 0.8464 (m90) REVERT: D 191 MET cc_start: 0.8920 (mmm) cc_final: 0.8667 (mtp) REVERT: D 275 GLU cc_start: 0.8257 (pm20) cc_final: 0.8047 (pm20) REVERT: D 287 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8875 (m110) outliers start: 8 outliers final: 2 residues processed: 76 average time/residue: 1.3526 time to fit residues: 113.3919 Evaluate side-chains 74 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 287 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 27 optimal weight: 0.0970 chunk 137 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.088217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.055880 restraints weight = 80771.572| |-----------------------------------------------------------------------------| r_work (start): 0.2603 rms_B_bonded: 3.17 r_work: 0.2370 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 15766 Z= 0.321 Angle : 0.587 5.955 22369 Z= 0.320 Chirality : 0.042 0.204 2591 Planarity : 0.004 0.049 2007 Dihedral : 22.272 162.554 4641 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.08 % Allowed : 7.43 % 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: 2.28 (0.24), residues: 1258 helix: 2.62 (0.18), residues: 804 sheet: -0.65 (0.37), residues: 165 loop : -0.34 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 46 HIS 0.005 0.001 HIS B 145 PHE 0.018 0.002 PHE C 112 TYR 0.016 0.002 TYR A 307 ARG 0.004 0.001 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.05288 ( 902) hydrogen bonds : angle 3.67123 ( 2441) covalent geometry : bond 0.00731 (15766) covalent geometry : angle 0.58704 (22369) *********************** 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 74 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 1.387 Fit side-chains REVERT: C 265 MET cc_start: 0.9378 (mmt) cc_final: 0.9166 (mmp) REVERT: D 144 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8913 (mtp) outliers start: 10 outliers final: 2 residues processed: 68 average time/residue: 1.3855 time to fit residues: 104.3051 Evaluate side-chains 66 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain D residue 144 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 18 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 ASN C 322 ASN D 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.090794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.058209 restraints weight = 85865.644| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.22 r_work: 0.2454 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2462 r_free = 0.2462 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2462 r_free = 0.2462 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2619 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= 0.136 Angle : 0.498 6.066 22369 Z= 0.276 Chirality : 0.035 0.192 2591 Planarity : 0.004 0.047 2007 Dihedral : 22.185 164.611 4641 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.59 % Allowed : 7.82 % 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: 2.54 (0.24), residues: 1258 helix: 2.78 (0.18), residues: 806 sheet: -0.27 (0.40), residues: 149 loop : -0.36 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 46 HIS 0.003 0.001 HIS B 256 PHE 0.009 0.001 PHE D 112 TYR 0.012 0.001 TYR A 307 ARG 0.005 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 902) hydrogen bonds : angle 3.50708 ( 2441) covalent geometry : bond 0.00299 (15766) covalent geometry : angle 0.49812 (22369) *********************** 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 71 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 1.382 Fit side-chains REVERT: C 265 MET cc_start: 0.9330 (OUTLIER) cc_final: 0.8999 (mmp) outliers start: 5 outliers final: 1 residues processed: 67 average time/residue: 1.3431 time to fit residues: 99.4332 Evaluate side-chains 67 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 73 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 114 optimal weight: 0.0170 chunk 118 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.092260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.059715 restraints weight = 89408.570| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.28 r_work: 0.2482 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15766 Z= 0.122 Angle : 0.477 5.692 22369 Z= 0.265 Chirality : 0.034 0.203 2591 Planarity : 0.004 0.048 2007 Dihedral : 22.119 168.145 4641 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.59 % Allowed : 8.11 % Favored : 91.30 % 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: 2.98 (0.18), residues: 805 sheet: -0.16 (0.41), residues: 149 loop : -0.24 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 46 HIS 0.003 0.001 HIS B 256 PHE 0.010 0.001 PHE D 112 TYR 0.022 0.001 TYR A 74 ARG 0.005 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 902) hydrogen bonds : angle 3.40779 ( 2441) covalent geometry : bond 0.00263 (15766) covalent geometry : angle 0.47745 (22369) *********************** 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 to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 1.294 Fit side-chains REVERT: C 265 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.9017 (mmp) outliers start: 5 outliers final: 1 residues processed: 70 average time/residue: 1.6218 time to fit residues: 124.9076 Evaluate side-chains 67 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 99 optimal weight: 0.0980 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.091435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.058984 restraints weight = 83901.696| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.20 r_work: 0.2468 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15766 Z= 0.149 Angle : 0.486 6.230 22369 Z= 0.269 Chirality : 0.035 0.198 2591 Planarity : 0.004 0.048 2007 Dihedral : 22.122 166.640 4641 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.29 % Allowed : 8.41 % Favored : 91.30 % 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: 2.79 (0.24), residues: 1258 helix: 2.97 (0.18), residues: 805 sheet: -0.15 (0.40), residues: 149 loop : -0.26 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 46 HIS 0.004 0.001 HIS D 256 PHE 0.011 0.002 PHE D 112 TYR 0.019 0.002 TYR A 74 ARG 0.005 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 902) hydrogen bonds : angle 3.43896 ( 2441) covalent geometry : bond 0.00332 (15766) covalent geometry : angle 0.48643 (22369) ********************** 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 to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 1.381 Fit side-chains REVERT: C 265 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9077 (mmp) outliers start: 2 outliers final: 1 residues processed: 65 average time/residue: 1.3618 time to fit residues: 97.9287 Evaluate side-chains 67 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 265 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 123 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 48 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.091179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.058490 restraints weight = 82642.224| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 3.19 r_work: 0.2460 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15766 Z= 0.149 Angle : 0.488 6.074 22369 Z= 0.269 Chirality : 0.035 0.196 2591 Planarity : 0.004 0.048 2007 Dihedral : 22.130 165.598 4641 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.29 % Allowed : 8.31 % Favored : 91.40 % 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: 2.79 (0.24), residues: 1258 helix: 2.96 (0.18), residues: 805 sheet: -0.13 (0.40), residues: 149 loop : -0.23 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.005 0.000 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 902) hydrogen bonds : angle 3.44442 ( 2441) covalent geometry : bond 0.00331 (15766) covalent geometry : angle 0.48783 (22369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8787.44 seconds wall clock time: 152 minutes 12.59 seconds (9132.59 seconds total)