Starting phenix.real_space_refine on Sat Mar 16 20:23:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/03_2024/8amx_15528.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/03_2024/8amx_15528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/03_2024/8amx_15528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/03_2024/8amx_15528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/03_2024/8amx_15528.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/03_2024/8amx_15528.pdb" } resolution = 2.55 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= 0.045 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: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 10336 2.51 5 N 2536 2.21 5 O 2657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15633 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "B" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "C" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "D" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "E" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "F" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "G" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "H" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 8.42, per 1000 atoms: 0.54 Number of scatterers: 15633 At special positions: 0 Unit cell: (93.104, 92.2576, 120.189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 2657 8.00 N 2536 7.00 C 10336 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: 5.85 Conformation dependent library (CDL) restraints added in 2.7 seconds 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 31 through 61 Processing helix chain 'A' and resid 66 through 86 Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 167 through 190 Processing helix chain 'A' and resid 201 through 218 removed outlier: 3.817A pdb=" N VAL A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 244 through 253 removed outlier: 3.631A pdb=" N SER A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLY A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 276 Proline residue: A 261 - end of helix Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 61 Processing helix chain 'B' and resid 66 through 86 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 167 through 190 Processing helix chain 'B' and resid 201 through 218 removed outlier: 3.818A pdb=" N VAL B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 241 Proline residue: B 232 - end of helix Processing helix chain 'B' and resid 244 through 253 removed outlier: 3.636A pdb=" N SER B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 Proline residue: B 261 - end of helix Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 31 through 61 Processing helix chain 'C' and resid 66 through 86 Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 134 through 143 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 167 through 190 Processing helix chain 'C' and resid 201 through 218 removed outlier: 3.820A pdb=" N VAL C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 241 Proline residue: C 232 - end of helix Processing helix chain 'C' and resid 244 through 253 removed outlier: 3.631A pdb=" N SER C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLY C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 276 Proline residue: C 261 - end of helix Processing helix chain 'D' and resid 26 through 30 Processing helix chain 'D' and resid 31 through 61 Processing helix chain 'D' and resid 66 through 86 Processing helix chain 'D' and resid 94 through 104 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 134 Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 167 through 190 Processing helix chain 'D' and resid 201 through 218 removed outlier: 3.820A pdb=" N VAL D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 218 " --> pdb=" O GLY D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 241 Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 244 through 253 removed outlier: 3.635A pdb=" N SER D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLY D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU D 251 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 276 Proline residue: D 261 - end of helix Processing helix chain 'E' and resid 26 through 30 removed outlier: 3.571A pdb=" N GLN E 30 " --> pdb=" O GLN E 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 26 through 30' Processing helix chain 'E' and resid 31 through 61 Processing helix chain 'E' and resid 66 through 86 Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 111 through 134 Processing helix chain 'E' and resid 134 through 143 Processing helix chain 'E' and resid 154 through 158 Processing helix chain 'E' and resid 167 through 190 Processing helix chain 'E' and resid 201 through 218 removed outlier: 3.820A pdb=" N VAL E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY E 218 " --> pdb=" O GLY E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 241 Proline residue: E 232 - end of helix Processing helix chain 'E' and resid 244 through 253 removed outlier: 3.634A pdb=" N SER E 248 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY E 250 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU E 251 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 276 Proline residue: E 261 - end of helix Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 61 Processing helix chain 'F' and resid 66 through 86 Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 111 through 134 Processing helix chain 'F' and resid 134 through 143 Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 167 through 190 Processing helix chain 'F' and resid 201 through 218 removed outlier: 3.820A pdb=" N VAL F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY F 218 " --> pdb=" O GLY F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 241 Proline residue: F 232 - end of helix Processing helix chain 'F' and resid 244 through 253 removed outlier: 3.634A pdb=" N SER F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY F 250 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU F 251 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN F 252 " --> pdb=" O SER F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 276 Proline residue: F 261 - end of helix Processing helix chain 'G' and resid 26 through 30 removed outlier: 3.507A pdb=" N GLN G 30 " --> pdb=" O GLN G 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 26 through 30' Processing helix chain 'G' and resid 31 through 61 Processing helix chain 'G' and resid 66 through 86 Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 111 through 134 Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'G' and resid 154 through 158 Processing helix chain 'G' and resid 167 through 190 Processing helix chain 'G' and resid 201 through 218 removed outlier: 3.820A pdb=" N VAL G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 241 Proline residue: G 232 - end of helix Processing helix chain 'G' and resid 244 through 253 removed outlier: 3.630A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY G 250 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU G 251 " --> pdb=" O PHE G 247 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN G 252 " --> pdb=" O SER G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 276 Proline residue: G 261 - end of helix Processing helix chain 'H' and resid 26 through 30 Processing helix chain 'H' and resid 31 through 61 Processing helix chain 'H' and resid 66 through 86 Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'H' and resid 111 through 134 Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 154 through 158 Processing helix chain 'H' and resid 167 through 190 Processing helix chain 'H' and resid 201 through 218 removed outlier: 3.820A pdb=" N VAL H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY H 218 " --> pdb=" O GLY H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 241 Proline residue: H 232 - end of helix Processing helix chain 'H' and resid 244 through 253 removed outlier: 3.627A pdb=" N SER H 248 " --> pdb=" O LYS H 244 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY H 250 " --> pdb=" O VAL H 246 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU H 251 " --> pdb=" O PHE H 247 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN H 252 " --> pdb=" O SER H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 276 Proline residue: H 261 - end of helix 1100 hydrogen bonds defined for protein. 3252 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 6.38 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: 4726 1.34 - 1.46: 2818 1.46 - 1.57: 8296 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 16032 Sorted by residual: bond pdb=" CA LEU B 231 " pdb=" C LEU B 231 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.26e-02 6.30e+03 8.09e-01 bond pdb=" CA LEU H 231 " pdb=" C LEU H 231 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.26e-02 6.30e+03 7.43e-01 bond pdb=" CB PRO C 233 " pdb=" CG PRO C 233 " ideal model delta sigma weight residual 1.492 1.449 0.043 5.00e-02 4.00e+02 7.23e-01 bond pdb=" CB PRO E 233 " pdb=" CG PRO E 233 " ideal model delta sigma weight residual 1.492 1.450 0.042 5.00e-02 4.00e+02 7.21e-01 bond pdb=" CB PRO G 233 " pdb=" CG PRO G 233 " ideal model delta sigma weight residual 1.492 1.450 0.042 5.00e-02 4.00e+02 7.19e-01 ... (remaining 16027 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.53: 527 106.53 - 113.41: 8416 113.41 - 120.30: 6264 120.30 - 127.18: 6394 127.18 - 134.07: 239 Bond angle restraints: 21840 Sorted by residual: angle pdb=" CA TYR G 223 " pdb=" CB TYR G 223 " pdb=" CG TYR G 223 " ideal model delta sigma weight residual 113.90 119.60 -5.70 1.80e+00 3.09e-01 1.00e+01 angle pdb=" CA TYR C 223 " pdb=" CB TYR C 223 " pdb=" CG TYR C 223 " ideal model delta sigma weight residual 113.90 119.52 -5.62 1.80e+00 3.09e-01 9.75e+00 angle pdb=" CA TYR D 223 " pdb=" CB TYR D 223 " pdb=" CG TYR D 223 " ideal model delta sigma weight residual 113.90 119.50 -5.60 1.80e+00 3.09e-01 9.68e+00 angle pdb=" CA TYR F 223 " pdb=" CB TYR F 223 " pdb=" CG TYR F 223 " ideal model delta sigma weight residual 113.90 119.37 -5.47 1.80e+00 3.09e-01 9.23e+00 angle pdb=" CA TYR B 223 " pdb=" CB TYR B 223 " pdb=" CG TYR B 223 " ideal model delta sigma weight residual 113.90 119.34 -5.44 1.80e+00 3.09e-01 9.14e+00 ... (remaining 21835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 8440 17.35 - 34.69: 412 34.69 - 52.04: 120 52.04 - 69.39: 12 69.39 - 86.73: 8 Dihedral angle restraints: 8992 sinusoidal: 3344 harmonic: 5648 Sorted by residual: dihedral pdb=" CA PHE B 76 " pdb=" C PHE B 76 " pdb=" N GLY B 77 " pdb=" CA GLY B 77 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA PHE C 76 " pdb=" C PHE C 76 " pdb=" N GLY C 77 " pdb=" CA GLY C 77 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA PHE H 76 " pdb=" C PHE H 76 " pdb=" N GLY H 77 " pdb=" CA GLY H 77 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 8989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1311 0.034 - 0.067: 855 0.067 - 0.101: 212 0.101 - 0.134: 52 0.134 - 0.168: 18 Chirality restraints: 2448 Sorted by residual: chirality pdb=" CA TYR G 223 " pdb=" N TYR G 223 " pdb=" C TYR G 223 " pdb=" CB TYR G 223 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA TYR C 223 " pdb=" N TYR C 223 " pdb=" C TYR C 223 " pdb=" CB TYR C 223 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA TYR A 223 " pdb=" N TYR A 223 " pdb=" C TYR A 223 " pdb=" CB TYR A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 2445 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO H 232 " -0.027 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO H 233 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 233 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 233 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 232 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO C 233 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 233 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 233 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 232 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO D 233 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 233 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 233 " 0.022 5.00e-02 4.00e+02 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 6160 2.91 - 3.41: 15448 3.41 - 3.91: 26498 3.91 - 4.40: 30277 4.40 - 4.90: 51861 Nonbonded interactions: 130244 Sorted by model distance: nonbonded pdb=" NH2 ARG G 229 " pdb=" O HOH G 401 " model vdw 2.414 2.520 nonbonded pdb=" OD2 ASP A 230 " pdb=" O HOH A 401 " model vdw 2.414 2.440 nonbonded pdb=" NH2 ARG D 229 " pdb=" O HOH D 401 " model vdw 2.417 2.520 nonbonded pdb=" NH2 ARG F 229 " pdb=" O HOH F 401 " model vdw 2.418 2.520 nonbonded pdb=" NH2 ARG B 229 " pdb=" O HOH B 401 " model vdw 2.419 2.520 ... (remaining 130239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.060 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: 14.080 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 40.600 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.004 0.043 16032 Z= 0.279 Angle : 0.627 5.699 21840 Z= 0.344 Chirality : 0.045 0.168 2448 Planarity : 0.006 0.040 2712 Dihedral : 11.934 86.732 5440 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.44 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % 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 (0.20), residues: 2008 helix: 2.09 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : -0.29 (0.29), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 169 HIS 0.005 0.001 HIS E 57 PHE 0.013 0.002 PHE C 236 TYR 0.022 0.003 TYR G 223 ARG 0.002 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.619 Fit side-chains REVERT: A 147 MET cc_start: 0.8306 (mmm) cc_final: 0.8087 (mmp) REVERT: A 244 LYS cc_start: 0.8411 (pttt) cc_final: 0.8049 (pttm) REVERT: B 147 MET cc_start: 0.8305 (mmm) cc_final: 0.8088 (mmp) REVERT: B 175 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7862 (mm-30) REVERT: B 244 LYS cc_start: 0.8445 (pttt) cc_final: 0.8074 (pttm) REVERT: C 147 MET cc_start: 0.8311 (mmm) cc_final: 0.8097 (mmp) REVERT: C 175 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7857 (mm-30) REVERT: C 244 LYS cc_start: 0.8445 (pttt) cc_final: 0.8062 (pttm) REVERT: D 147 MET cc_start: 0.8312 (mmm) cc_final: 0.8095 (mmp) REVERT: D 175 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7853 (mm-30) REVERT: D 244 LYS cc_start: 0.8445 (pttt) cc_final: 0.8064 (pttm) REVERT: E 147 MET cc_start: 0.8313 (mmm) cc_final: 0.8095 (mmp) REVERT: E 175 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7866 (mm-30) REVERT: E 244 LYS cc_start: 0.8448 (pttt) cc_final: 0.8064 (pttm) REVERT: F 147 MET cc_start: 0.8309 (mmm) cc_final: 0.8093 (mmp) REVERT: F 244 LYS cc_start: 0.8447 (pttt) cc_final: 0.8063 (pttm) REVERT: G 147 MET cc_start: 0.8304 (mmm) cc_final: 0.8086 (mmp) REVERT: G 175 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7843 (mm-30) REVERT: G 244 LYS cc_start: 0.8437 (pttt) cc_final: 0.8056 (pttm) REVERT: H 147 MET cc_start: 0.8305 (mmm) cc_final: 0.8087 (mmp) REVERT: H 175 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7862 (mm-30) REVERT: H 244 LYS cc_start: 0.8438 (pttt) cc_final: 0.8059 (pttm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 1.5562 time to fit residues: 350.1368 Evaluate side-chains 197 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 245 GLN B 245 GLN C 245 GLN D 245 GLN E 245 GLN F 165 HIS F 245 GLN G 165 HIS G 245 GLN H 245 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16032 Z= 0.259 Angle : 0.632 5.598 21840 Z= 0.351 Chirality : 0.044 0.159 2448 Planarity : 0.006 0.040 2712 Dihedral : 4.898 18.578 2160 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.54 % Favored : 96.12 % Rotamer: Outliers : 1.07 % Allowed : 8.23 % Favored : 90.70 % 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: 2.30 (0.19), residues: 2008 helix: 2.29 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : -0.36 (0.28), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 169 HIS 0.005 0.001 HIS B 57 PHE 0.014 0.002 PHE C 236 TYR 0.021 0.002 TYR G 223 ARG 0.002 0.000 ARG E 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 1.664 Fit side-chains REVERT: A 147 MET cc_start: 0.8288 (mmm) cc_final: 0.8084 (mmp) REVERT: A 244 LYS cc_start: 0.8421 (pttt) cc_final: 0.8068 (pttm) REVERT: B 33 MET cc_start: 0.7398 (mmm) cc_final: 0.7161 (tpt) REVERT: B 147 MET cc_start: 0.8287 (mmm) cc_final: 0.8082 (mmp) REVERT: B 244 LYS cc_start: 0.8464 (pttt) cc_final: 0.8085 (pttm) REVERT: C 36 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: C 147 MET cc_start: 0.8296 (mmm) cc_final: 0.8092 (mmp) REVERT: C 244 LYS cc_start: 0.8450 (pttt) cc_final: 0.8074 (pttm) REVERT: D 147 MET cc_start: 0.8299 (mmm) cc_final: 0.8092 (mmp) REVERT: D 244 LYS cc_start: 0.8469 (pttt) cc_final: 0.8083 (pttm) REVERT: E 147 MET cc_start: 0.8297 (mmm) cc_final: 0.8094 (mmp) REVERT: E 175 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7870 (mm-30) REVERT: E 244 LYS cc_start: 0.8467 (pttt) cc_final: 0.8081 (pttm) REVERT: F 147 MET cc_start: 0.8293 (mmm) cc_final: 0.8090 (mmp) REVERT: F 244 LYS cc_start: 0.8470 (pttt) cc_final: 0.8080 (pttm) REVERT: G 147 MET cc_start: 0.8290 (mmm) cc_final: 0.8084 (mmp) REVERT: G 175 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7855 (mm-30) REVERT: G 244 LYS cc_start: 0.8438 (pttt) cc_final: 0.8068 (pttm) REVERT: H 147 MET cc_start: 0.8287 (mmm) cc_final: 0.8081 (mmp) REVERT: H 244 LYS cc_start: 0.8445 (pttt) cc_final: 0.8075 (pttm) outliers start: 17 outliers final: 8 residues processed: 191 average time/residue: 1.5166 time to fit residues: 315.0446 Evaluate side-chains 196 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 187 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain H residue 149 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16032 Z= 0.295 Angle : 0.654 5.821 21840 Z= 0.362 Chirality : 0.046 0.167 2448 Planarity : 0.006 0.041 2712 Dihedral : 4.984 18.811 2160 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.74 % Favored : 95.92 % Rotamer: Outliers : 1.88 % Allowed : 8.54 % Favored : 89.57 % 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: 2.21 (0.19), residues: 2008 helix: 2.24 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : -0.43 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 169 HIS 0.005 0.001 HIS B 57 PHE 0.015 0.002 PHE H 236 TYR 0.022 0.002 TYR G 223 ARG 0.002 0.000 ARG E 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 1.440 Fit side-chains REVERT: A 147 MET cc_start: 0.8260 (mmm) cc_final: 0.8049 (mmp) REVERT: A 244 LYS cc_start: 0.8451 (pttt) cc_final: 0.8102 (pttm) REVERT: B 29 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7438 (tp) REVERT: B 33 MET cc_start: 0.7498 (mmm) cc_final: 0.7230 (tpt) REVERT: B 147 MET cc_start: 0.8256 (mmm) cc_final: 0.8049 (mmp) REVERT: B 244 LYS cc_start: 0.8479 (pttt) cc_final: 0.8098 (pttm) REVERT: C 32 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6518 (tttt) REVERT: C 147 MET cc_start: 0.8265 (mmm) cc_final: 0.8060 (mmp) REVERT: C 244 LYS cc_start: 0.8456 (pttt) cc_final: 0.8088 (pttm) REVERT: D 147 MET cc_start: 0.8272 (mmm) cc_final: 0.8067 (mmp) REVERT: D 244 LYS cc_start: 0.8459 (pttt) cc_final: 0.8090 (pttm) REVERT: E 147 MET cc_start: 0.8275 (mmm) cc_final: 0.8066 (mmp) REVERT: E 175 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7881 (mm-30) REVERT: E 244 LYS cc_start: 0.8460 (pttt) cc_final: 0.8094 (pttm) REVERT: F 147 MET cc_start: 0.8270 (mmm) cc_final: 0.8065 (mmp) REVERT: F 244 LYS cc_start: 0.8460 (pttt) cc_final: 0.8091 (pttm) REVERT: G 147 MET cc_start: 0.8263 (mmm) cc_final: 0.8058 (mmp) REVERT: G 244 LYS cc_start: 0.8448 (pttt) cc_final: 0.8083 (pttm) REVERT: H 147 MET cc_start: 0.8256 (mmm) cc_final: 0.8048 (mmp) REVERT: H 244 LYS cc_start: 0.8448 (pttt) cc_final: 0.8085 (pttm) outliers start: 30 outliers final: 8 residues processed: 202 average time/residue: 1.4923 time to fit residues: 327.6421 Evaluate side-chains 200 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain H residue 149 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16032 Z= 0.203 Angle : 0.582 5.467 21840 Z= 0.322 Chirality : 0.042 0.153 2448 Planarity : 0.005 0.039 2712 Dihedral : 4.763 18.383 2160 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.64 % Favored : 96.02 % Rotamer: Outliers : 0.82 % Allowed : 10.30 % Favored : 88.88 % 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 (0.19), residues: 2008 helix: 2.41 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.20 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 169 HIS 0.004 0.001 HIS G 57 PHE 0.013 0.002 PHE D 236 TYR 0.020 0.002 TYR G 223 ARG 0.001 0.000 ARG E 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 190 time to evaluate : 1.690 Fit side-chains REVERT: A 244 LYS cc_start: 0.8439 (pttt) cc_final: 0.8087 (pttm) REVERT: B 244 LYS cc_start: 0.8483 (pttt) cc_final: 0.8111 (pttm) REVERT: C 244 LYS cc_start: 0.8431 (pttt) cc_final: 0.8067 (pttm) REVERT: D 244 LYS cc_start: 0.8434 (pttt) cc_final: 0.8068 (pttm) REVERT: E 244 LYS cc_start: 0.8451 (pttt) cc_final: 0.8085 (pttm) REVERT: F 244 LYS cc_start: 0.8436 (pttt) cc_final: 0.8069 (pttm) REVERT: G 244 LYS cc_start: 0.8418 (pttt) cc_final: 0.8060 (pttm) REVERT: H 244 LYS cc_start: 0.8422 (pttt) cc_final: 0.8065 (pttm) outliers start: 13 outliers final: 2 residues processed: 199 average time/residue: 1.4513 time to fit residues: 315.3664 Evaluate side-chains 191 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 149 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 173 optimal weight: 0.0770 chunk 48 optimal weight: 2.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16032 Z= 0.253 Angle : 0.616 5.518 21840 Z= 0.340 Chirality : 0.044 0.159 2448 Planarity : 0.005 0.040 2712 Dihedral : 4.874 18.572 2160 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.88 % Favored : 95.77 % Rotamer: Outliers : 1.76 % Allowed : 9.99 % Favored : 88.25 % 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: 2.35 (0.19), residues: 2008 helix: 2.29 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.33 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 169 HIS 0.005 0.001 HIS C 57 PHE 0.015 0.002 PHE C 236 TYR 0.021 0.002 TYR G 223 ARG 0.002 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 1.518 Fit side-chains REVERT: A 244 LYS cc_start: 0.8451 (pttt) cc_final: 0.8098 (pttm) REVERT: A 251 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7554 (pt0) REVERT: B 29 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7452 (tp) REVERT: B 33 MET cc_start: 0.7388 (mmm) cc_final: 0.7098 (tpt) REVERT: B 244 LYS cc_start: 0.8476 (pttt) cc_final: 0.8116 (pttm) REVERT: C 244 LYS cc_start: 0.8434 (pttt) cc_final: 0.8067 (pttm) REVERT: D 244 LYS cc_start: 0.8436 (pttt) cc_final: 0.8068 (pttm) REVERT: D 251 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7543 (pt0) REVERT: E 244 LYS cc_start: 0.8457 (pttt) cc_final: 0.8092 (pttm) REVERT: F 244 LYS cc_start: 0.8438 (pttt) cc_final: 0.8069 (pttm) REVERT: F 251 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: G 244 LYS cc_start: 0.8425 (pttt) cc_final: 0.8062 (pttm) REVERT: G 251 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: H 244 LYS cc_start: 0.8425 (pttt) cc_final: 0.8064 (pttm) REVERT: H 251 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7556 (pt0) outliers start: 28 outliers final: 8 residues processed: 199 average time/residue: 1.4655 time to fit residues: 318.2309 Evaluate side-chains 203 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 189 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 251 GLU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 251 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16032 Z= 0.234 Angle : 0.603 5.542 21840 Z= 0.333 Chirality : 0.043 0.158 2448 Planarity : 0.005 0.039 2712 Dihedral : 4.829 18.506 2160 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.54 % Favored : 96.12 % Rotamer: Outliers : 1.57 % Allowed : 10.30 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.19), residues: 2008 helix: 2.34 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.35 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 169 HIS 0.005 0.001 HIS E 57 PHE 0.014 0.002 PHE H 236 TYR 0.020 0.002 TYR G 223 ARG 0.002 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.789 Fit side-chains REVERT: A 244 LYS cc_start: 0.8448 (pttt) cc_final: 0.8096 (pttm) REVERT: B 29 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7501 (tp) REVERT: B 33 MET cc_start: 0.7393 (mmm) cc_final: 0.7163 (tpt) REVERT: B 244 LYS cc_start: 0.8471 (pttt) cc_final: 0.8109 (pttm) REVERT: C 244 LYS cc_start: 0.8440 (pttt) cc_final: 0.8073 (pttm) REVERT: D 244 LYS cc_start: 0.8448 (pttt) cc_final: 0.8075 (pttm) REVERT: D 251 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7516 (pt0) REVERT: E 244 LYS cc_start: 0.8450 (pttt) cc_final: 0.8087 (pttm) REVERT: F 244 LYS cc_start: 0.8441 (pttt) cc_final: 0.8076 (pttm) REVERT: F 251 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7511 (pt0) REVERT: G 244 LYS cc_start: 0.8431 (pttt) cc_final: 0.8070 (pttm) REVERT: G 251 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7529 (pt0) REVERT: H 29 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7322 (tp) REVERT: H 244 LYS cc_start: 0.8431 (pttt) cc_final: 0.8070 (pttm) REVERT: H 251 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7525 (pt0) outliers start: 25 outliers final: 9 residues processed: 195 average time/residue: 1.5395 time to fit residues: 327.0477 Evaluate side-chains 204 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 251 GLU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 251 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 162 optimal weight: 0.0030 chunk 108 optimal weight: 1.9990 chunk 192 optimal weight: 0.0670 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 88 optimal weight: 0.0570 overall best weight: 0.3246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 245 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16032 Z= 0.123 Angle : 0.500 5.599 21840 Z= 0.274 Chirality : 0.038 0.132 2448 Planarity : 0.005 0.035 2712 Dihedral : 4.300 17.052 2160 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.24 % Favored : 97.41 % Rotamer: Outliers : 1.13 % Allowed : 11.62 % Favored : 87.25 % 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: 3.01 (0.20), residues: 2008 helix: 2.83 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.24 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.004 0.001 HIS E 57 PHE 0.008 0.001 PHE C 37 TYR 0.016 0.001 TYR H 223 ARG 0.001 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 1.704 Fit side-chains REVERT: B 244 LYS cc_start: 0.8438 (pttt) cc_final: 0.8098 (pttm) REVERT: D 251 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7432 (pt0) REVERT: F 29 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7180 (tp) REVERT: F 251 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7426 (pt0) REVERT: G 251 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: H 251 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7442 (pt0) outliers start: 18 outliers final: 11 residues processed: 185 average time/residue: 1.3551 time to fit residues: 275.5605 Evaluate side-chains 195 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 251 GLU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 251 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8259 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16032 Z= 0.159 Angle : 0.529 5.558 21840 Z= 0.290 Chirality : 0.039 0.142 2448 Planarity : 0.005 0.036 2712 Dihedral : 4.412 17.190 2160 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.84 % Favored : 96.81 % Rotamer: Outliers : 1.76 % Allowed : 11.18 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.20), residues: 2008 helix: 2.76 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.25 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.005 0.001 HIS E 57 PHE 0.011 0.001 PHE B 236 TYR 0.019 0.002 TYR G 223 ARG 0.001 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 1.646 Fit side-chains REVERT: B 244 LYS cc_start: 0.8432 (pttt) cc_final: 0.8087 (pttm) REVERT: D 251 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7487 (pt0) REVERT: F 251 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7483 (pt0) REVERT: G 251 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7500 (pt0) REVERT: H 251 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7498 (pt0) outliers start: 28 outliers final: 19 residues processed: 180 average time/residue: 1.3736 time to fit residues: 271.3477 Evaluate side-chains 188 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 251 GLU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 251 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 162 optimal weight: 0.0070 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- 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: 0.8342 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16032 Z= 0.261 Angle : 0.619 5.599 21840 Z= 0.340 Chirality : 0.044 0.158 2448 Planarity : 0.005 0.039 2712 Dihedral : 4.817 18.339 2160 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.69 % Favored : 95.97 % Rotamer: Outliers : 2.01 % Allowed : 10.99 % Favored : 87.00 % 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: 2.45 (0.19), residues: 2008 helix: 2.59 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -0.71 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 169 HIS 0.005 0.001 HIS E 57 PHE 0.015 0.002 PHE H 236 TYR 0.022 0.002 TYR G 223 ARG 0.001 0.000 ARG G 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 1.708 Fit side-chains REVERT: B 29 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7503 (tp) REVERT: B 33 MET cc_start: 0.7372 (mmm) cc_final: 0.7156 (tpt) REVERT: B 244 LYS cc_start: 0.8473 (pttt) cc_final: 0.8125 (pttm) REVERT: C 29 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7323 (tp) REVERT: C 244 LYS cc_start: 0.8468 (pttt) cc_final: 0.8098 (pttm) REVERT: D 29 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7349 (tp) REVERT: D 244 LYS cc_start: 0.8468 (pttt) cc_final: 0.8097 (pttm) REVERT: F 244 LYS cc_start: 0.8458 (pttt) cc_final: 0.8084 (pttm) REVERT: G 244 LYS cc_start: 0.8457 (pttt) cc_final: 0.8094 (pttm) REVERT: H 244 LYS cc_start: 0.8445 (pttt) cc_final: 0.8079 (pttm) outliers start: 32 outliers final: 23 residues processed: 206 average time/residue: 1.4296 time to fit residues: 321.8361 Evaluate side-chains 215 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 217 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 199 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.8281 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16032 Z= 0.170 Angle : 0.548 5.552 21840 Z= 0.302 Chirality : 0.040 0.146 2448 Planarity : 0.005 0.037 2712 Dihedral : 4.566 17.658 2160 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.84 % Favored : 96.81 % Rotamer: Outliers : 1.44 % Allowed : 11.37 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.19), residues: 2008 helix: 2.60 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.35 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 169 HIS 0.005 0.001 HIS B 57 PHE 0.011 0.001 PHE F 236 TYR 0.019 0.002 TYR G 223 ARG 0.001 0.000 ARG A 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 1.722 Fit side-chains REVERT: B 29 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7478 (tp) REVERT: B 244 LYS cc_start: 0.8464 (pttt) cc_final: 0.8111 (pttm) outliers start: 23 outliers final: 22 residues processed: 190 average time/residue: 1.4228 time to fit residues: 295.8142 Evaluate side-chains 198 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 217 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 158 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 163 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.134812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114382 restraints weight = 16451.555| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.43 r_work: 0.3241 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16032 Z= 0.141 Angle : 0.515 5.592 21840 Z= 0.283 Chirality : 0.039 0.137 2448 Planarity : 0.005 0.035 2712 Dihedral : 4.354 17.208 2160 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.84 % Favored : 96.81 % Rotamer: Outliers : 1.32 % Allowed : 11.81 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.20), residues: 2008 helix: 2.79 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.32 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.004 0.001 HIS B 57 PHE 0.009 0.001 PHE B 236 TYR 0.017 0.001 TYR G 223 ARG 0.001 0.000 ARG A 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5394.59 seconds wall clock time: 95 minutes 50.31 seconds (5750.31 seconds total)