Starting phenix.real_space_refine on Fri Sep 27 09:02:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/09_2024/8amx_15528.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/09_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_15528/09_2024/8amx_15528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/09_2024/8amx_15528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/09_2024/8amx_15528.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/09_2024/8amx_15528.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 10.06, per 1000 atoms: 0.64 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 - 3.00 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: 3.43 Conformation dependent library (CDL) restraints added in 2.0 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: 1.48 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: 4.45 Time building geometry restraints manager: 4.07 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: 0.00 - 1.14: 20641 1.14 - 2.28: 905 2.28 - 3.42: 189 3.42 - 4.56: 68 4.56 - 5.70: 37 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 3.120 nonbonded pdb=" OD2 ASP A 230 " pdb=" O HOH A 401 " model vdw 2.414 3.040 nonbonded pdb=" NH2 ARG D 229 " pdb=" O HOH D 401 " model vdw 2.417 3.120 nonbonded pdb=" NH2 ARG F 229 " pdb=" O HOH F 401 " model vdw 2.418 3.120 nonbonded pdb=" NH2 ARG B 229 " pdb=" O HOH B 401 " model vdw 2.419 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 2.750 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: 0.120 Set scattering table: 0.140 Process input model: 35.360 Find NCS groups from input model: 0.520 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:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.920 ------------------------------------------------------------------------------- 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 : 1.719 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: 1.6414 time to fit residues: 368.7671 Evaluate side-chains 197 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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: 2.9990 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 E 245 GLN F 165 HIS G 165 HIS G 245 GLN H 245 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0645 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= 0.230 Angle : 0.614 5.466 21840 Z= 0.342 Chirality : 0.043 0.155 2448 Planarity : 0.005 0.039 2712 Dihedral : 4.826 18.460 2160 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.29 % Favored : 96.36 % 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: 2.38 (0.19), residues: 2008 helix: 2.26 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.16 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 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 G 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 206 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 1.625 Fit side-chains REVERT: A 147 MET cc_start: 0.8292 (mmm) cc_final: 0.8086 (mmp) REVERT: A 244 LYS cc_start: 0.8412 (pttt) cc_final: 0.8056 (pttm) REVERT: B 147 MET cc_start: 0.8291 (mmm) cc_final: 0.8083 (mmp) REVERT: B 244 LYS cc_start: 0.8482 (pttt) cc_final: 0.8102 (pttm) REVERT: C 36 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: C 147 MET cc_start: 0.8299 (mmm) cc_final: 0.8094 (mmp) REVERT: C 244 LYS cc_start: 0.8438 (pttt) cc_final: 0.8061 (pttm) REVERT: D 147 MET cc_start: 0.8301 (mmm) cc_final: 0.8096 (mmp) REVERT: D 244 LYS cc_start: 0.8453 (pttt) cc_final: 0.8065 (pttm) REVERT: E 147 MET cc_start: 0.8302 (mmm) cc_final: 0.8096 (mmp) REVERT: E 244 LYS cc_start: 0.8450 (pttt) cc_final: 0.8062 (pttm) REVERT: F 147 MET cc_start: 0.8295 (mmm) cc_final: 0.8094 (mmp) REVERT: F 244 LYS cc_start: 0.8453 (pttt) cc_final: 0.8065 (pttm) REVERT: G 147 MET cc_start: 0.8292 (mmm) cc_final: 0.8089 (mmp) REVERT: G 175 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7832 (mm-30) REVERT: G 244 LYS cc_start: 0.8429 (pttt) cc_final: 0.8057 (pttm) REVERT: H 147 MET cc_start: 0.8290 (mmm) cc_final: 0.8087 (mmp) REVERT: H 244 LYS cc_start: 0.8427 (pttt) cc_final: 0.8058 (pttm) outliers start: 17 outliers final: 8 residues processed: 189 average time/residue: 1.5620 time to fit residues: 320.5292 Evaluate side-chains 193 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 184 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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: 0.5980 chunk 50 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN C 245 GLN D 245 GLN E 245 GLN F 245 GLN G 245 GLN H 245 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 16032 Z= 0.475 Angle : 0.777 6.353 21840 Z= 0.428 Chirality : 0.054 0.185 2448 Planarity : 0.007 0.046 2712 Dihedral : 5.284 19.364 2160 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.54 % Favored : 96.12 % Rotamer: Outliers : 1.95 % Allowed : 8.35 % Favored : 89.70 % 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: 1.78 (0.19), residues: 2008 helix: 2.09 (0.13), residues: 1376 sheet: None (None), residues: 0 loop : -0.89 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 255 HIS 0.006 0.002 HIS E 57 PHE 0.019 0.003 PHE D 236 TYR 0.023 0.003 TYR G 223 ARG 0.003 0.001 ARG F 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 238 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 1.766 Fit side-chains REVERT: A 147 MET cc_start: 0.8262 (mmm) cc_final: 0.8043 (mmp) REVERT: A 244 LYS cc_start: 0.8477 (pttt) cc_final: 0.8118 (pttm) REVERT: B 29 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7501 (tp) REVERT: B 33 MET cc_start: 0.7546 (mmm) cc_final: 0.7289 (tpt) REVERT: B 147 MET cc_start: 0.8260 (mmm) cc_final: 0.8044 (mmp) REVERT: B 244 LYS cc_start: 0.8501 (pttt) cc_final: 0.8142 (pttm) REVERT: C 36 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: C 147 MET cc_start: 0.8270 (mmm) cc_final: 0.8053 (mmp) REVERT: C 244 LYS cc_start: 0.8488 (pttt) cc_final: 0.8123 (pttm) REVERT: D 147 MET cc_start: 0.8271 (mmm) cc_final: 0.8055 (mmp) REVERT: D 244 LYS cc_start: 0.8493 (pttt) cc_final: 0.8127 (pttm) REVERT: D 251 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7511 (pt0) REVERT: E 147 MET cc_start: 0.8270 (mmm) cc_final: 0.8054 (mmp) REVERT: E 244 LYS cc_start: 0.8492 (pttt) cc_final: 0.8124 (pttm) REVERT: F 147 MET cc_start: 0.8267 (mmm) cc_final: 0.8051 (mmp) REVERT: F 244 LYS cc_start: 0.8494 (pttt) cc_final: 0.8127 (pttm) REVERT: F 251 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7505 (pt0) REVERT: G 147 MET cc_start: 0.8260 (mmm) cc_final: 0.8043 (mmp) REVERT: G 244 LYS cc_start: 0.8480 (pttt) cc_final: 0.8118 (pttm) REVERT: H 147 MET cc_start: 0.8261 (mmm) cc_final: 0.8044 (mmp) REVERT: H 244 LYS cc_start: 0.8480 (pttt) cc_final: 0.8120 (pttm) outliers start: 31 outliers final: 8 residues processed: 219 average time/residue: 1.5501 time to fit residues: 368.3697 Evaluate side-chains 210 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 198 time to evaluate : 1.784 ------------------------------------------------------------------------------- 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 36 GLU 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 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: 0.9990 chunk 136 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 122 optimal weight: 0.2980 chunk 182 optimal weight: 0.6980 chunk 193 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 173 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN C 245 GLN D 245 GLN E 245 GLN F 245 GLN H 245 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16032 Z= 0.156 Angle : 0.553 5.390 21840 Z= 0.308 Chirality : 0.040 0.146 2448 Planarity : 0.005 0.040 2712 Dihedral : 4.692 18.118 2160 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.49 % Favored : 97.16 % Rotamer: Outliers : 1.07 % Allowed : 10.62 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.19), residues: 2008 helix: 2.45 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.21 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 169 HIS 0.004 0.001 HIS B 57 PHE 0.010 0.001 PHE C 236 TYR 0.018 0.002 TYR G 223 ARG 0.001 0.000 ARG B 31 *********************** 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 182 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 1.780 Fit side-chains REVERT: A 147 MET cc_start: 0.8226 (mmm) cc_final: 0.8026 (mmp) REVERT: A 244 LYS cc_start: 0.8429 (pttt) cc_final: 0.8073 (pttm) REVERT: A 251 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7582 (pt0) REVERT: B 244 LYS cc_start: 0.8470 (pttt) cc_final: 0.8103 (pttm) REVERT: C 36 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: C 244 LYS cc_start: 0.8440 (pttt) cc_final: 0.8075 (pttm) REVERT: D 244 LYS cc_start: 0.8442 (pttt) cc_final: 0.8075 (pttm) REVERT: D 251 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7507 (pt0) REVERT: E 244 LYS cc_start: 0.8441 (pttt) cc_final: 0.8075 (pttm) REVERT: F 244 LYS cc_start: 0.8441 (pttt) cc_final: 0.8074 (pttm) REVERT: F 251 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7504 (pt0) REVERT: G 244 LYS cc_start: 0.8429 (pttt) cc_final: 0.8069 (pttm) REVERT: H 244 LYS cc_start: 0.8430 (pttt) cc_final: 0.8072 (pttm) REVERT: H 251 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7521 (pt0) outliers start: 17 outliers final: 1 residues processed: 175 average time/residue: 1.4769 time to fit residues: 283.1250 Evaluate side-chains 171 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain H residue 251 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 133 optimal weight: 0.0030 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 173 optimal weight: 0.0970 chunk 48 optimal weight: 0.2980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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: 0.8215 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16032 Z= 0.133 Angle : 0.509 5.536 21840 Z= 0.280 Chirality : 0.039 0.133 2448 Planarity : 0.005 0.035 2712 Dihedral : 4.337 17.065 2160 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.59 % Favored : 96.07 % Rotamer: Outliers : 1.13 % Allowed : 11.56 % Favored : 87.31 % 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: 3.04 (0.20), residues: 2008 helix: 2.81 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.09 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 169 HIS 0.004 0.001 HIS H 57 PHE 0.008 0.001 PHE B 236 TYR 0.016 0.001 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 197 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 1.765 Fit side-chains REVERT: B 244 LYS cc_start: 0.8426 (pttt) cc_final: 0.8072 (pttm) REVERT: C 251 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7458 (pt0) REVERT: D 251 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7505 (pt0) REVERT: E 251 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7458 (pt0) REVERT: F 251 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7500 (pt0) REVERT: H 251 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7490 (pt0) outliers start: 18 outliers final: 0 residues processed: 190 average time/residue: 1.3306 time to fit residues: 278.5122 Evaluate side-chains 185 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 180 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain E residue 251 GLU Chi-restraints excluded: chain F residue 251 GLU 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: 3.9990 chunk 174 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.8353 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16032 Z= 0.285 Angle : 0.633 5.645 21840 Z= 0.349 Chirality : 0.045 0.160 2448 Planarity : 0.006 0.041 2712 Dihedral : 4.859 18.473 2160 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.59 % Favored : 96.07 % Rotamer: Outliers : 1.76 % Allowed : 10.93 % Favored : 87.31 % 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: 2.42 (0.19), residues: 2008 helix: 2.56 (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 0.009 0.002 TRP A 169 HIS 0.005 0.001 HIS F 57 PHE 0.016 0.002 PHE D 236 TYR 0.022 0.002 TYR G 223 ARG 0.002 0.000 ARG F 234 *********************** 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 216 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 1.642 Fit side-chains REVERT: A 244 LYS cc_start: 0.8452 (pttt) cc_final: 0.8092 (pttm) REVERT: B 29 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7541 (tp) REVERT: B 33 MET cc_start: 0.7363 (mmm) cc_final: 0.7074 (tpt) REVERT: B 244 LYS cc_start: 0.8451 (pttt) cc_final: 0.8095 (pttm) REVERT: C 36 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: C 244 LYS cc_start: 0.8463 (pttt) cc_final: 0.8094 (pttm) REVERT: D 147 MET cc_start: 0.8229 (mmm) cc_final: 0.8021 (mmp) REVERT: D 244 LYS cc_start: 0.8473 (pttt) cc_final: 0.8104 (pttm) REVERT: E 147 MET cc_start: 0.8226 (mmm) cc_final: 0.8021 (mmp) REVERT: E 244 LYS cc_start: 0.8466 (pttt) cc_final: 0.8095 (pttm) REVERT: F 29 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7171 (tp) REVERT: F 244 LYS cc_start: 0.8473 (pttt) cc_final: 0.8103 (pttm) REVERT: G 36 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7712 (mt-10) REVERT: G 147 MET cc_start: 0.8218 (mmm) cc_final: 0.8006 (mmp) REVERT: G 244 LYS cc_start: 0.8456 (pttt) cc_final: 0.8093 (pttm) REVERT: H 29 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7245 (tp) REVERT: H 244 LYS cc_start: 0.8452 (pttt) cc_final: 0.8089 (pttm) outliers start: 28 outliers final: 9 residues processed: 197 average time/residue: 1.4958 time to fit residues: 320.9226 Evaluate side-chains 201 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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 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 29 LEU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 149 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 192 optimal weight: 0.0570 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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: 0.8246 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16032 Z= 0.140 Angle : 0.523 5.512 21840 Z= 0.289 Chirality : 0.039 0.140 2448 Planarity : 0.005 0.037 2712 Dihedral : 4.456 17.436 2160 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.39 % Favored : 97.26 % Rotamer: Outliers : 0.63 % Allowed : 12.63 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.19), residues: 2008 helix: 2.71 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.34 (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 F 57 PHE 0.009 0.001 PHE B 236 TYR 0.018 0.001 TYR G 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 175 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 1.617 Fit side-chains REVERT: B 29 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7444 (tp) REVERT: B 244 LYS cc_start: 0.8410 (pttt) cc_final: 0.8069 (pttm) outliers start: 10 outliers final: 2 residues processed: 173 average time/residue: 1.4667 time to fit residues: 277.0389 Evaluate side-chains 168 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 149 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 131 optimal weight: 0.0770 chunk 95 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16032 Z= 0.148 Angle : 0.523 5.556 21840 Z= 0.288 Chirality : 0.039 0.140 2448 Planarity : 0.005 0.036 2712 Dihedral : 4.394 17.243 2160 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.34 % Favored : 96.31 % Rotamer: Outliers : 0.57 % Allowed : 12.50 % Favored : 86.93 % 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: 2.87 (0.19), residues: 2008 helix: 2.93 (0.13), residues: 1392 sheet: None (None), residues: 0 loop : -0.62 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.004 0.001 HIS E 57 PHE 0.010 0.001 PHE D 236 TYR 0.018 0.001 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 176 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 167 time to evaluate : 1.588 Fit side-chains REVERT: B 29 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7425 (tp) REVERT: B 32 LYS cc_start: 0.6540 (OUTLIER) cc_final: 0.6222 (tttp) REVERT: B 244 LYS cc_start: 0.8414 (pttt) cc_final: 0.8070 (pttm) outliers start: 9 outliers final: 5 residues processed: 174 average time/residue: 1.4344 time to fit residues: 272.8374 Evaluate side-chains 174 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 217 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain H residue 217 LEU 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: 1.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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: 0.1020 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 : 0.618 5.579 21840 Z= 0.340 Chirality : 0.044 0.156 2448 Planarity : 0.005 0.039 2712 Dihedral : 4.777 18.426 2160 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.54 % Favored : 96.12 % Rotamer: Outliers : 1.07 % Allowed : 12.00 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.19), residues: 2008 helix: 2.62 (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 0.007 0.002 TRP F 169 HIS 0.005 0.001 HIS F 57 PHE 0.015 0.002 PHE H 236 TYR 0.022 0.002 TYR G 223 ARG 0.002 0.000 ARG E 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 204 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 1.652 Fit side-chains REVERT: B 29 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7498 (tp) REVERT: B 33 MET cc_start: 0.7356 (mmm) cc_final: 0.7099 (tpt) REVERT: B 244 LYS cc_start: 0.8439 (pttt) cc_final: 0.8084 (pttm) REVERT: C 36 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7718 (mt-10) REVERT: H 29 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7394 (tp) outliers start: 17 outliers final: 11 residues processed: 194 average time/residue: 1.5178 time to fit residues: 320.1645 Evaluate side-chains 200 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 187 time to evaluate : 1.632 ------------------------------------------------------------------------------- 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 29 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 149 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: 4.9990 chunk 90 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 199 optimal weight: 0.5980 chunk 183 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8274 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16032 Z= 0.162 Angle : 0.540 5.524 21840 Z= 0.298 Chirality : 0.040 0.145 2448 Planarity : 0.005 0.036 2712 Dihedral : 4.530 17.730 2160 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.74 % Favored : 96.91 % Rotamer: Outliers : 0.31 % Allowed : 12.81 % 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: 2.69 (0.19), residues: 2008 helix: 2.80 (0.13), residues: 1392 sheet: None (None), residues: 0 loop : -0.71 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 169 HIS 0.004 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 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 174 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 169 time to evaluate : 1.613 Fit side-chains REVERT: B 29 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7425 (tp) REVERT: B 244 LYS cc_start: 0.8438 (pttt) cc_final: 0.8092 (pttm) outliers start: 5 outliers final: 4 residues processed: 171 average time/residue: 1.4624 time to fit residues: 273.4143 Evaluate side-chains 174 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 169 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 149 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.9990 chunk 146 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.132189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111853 restraints weight = 16561.271| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.42 r_work: 0.3173 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16032 Z= 0.159 Angle : 0.534 5.543 21840 Z= 0.294 Chirality : 0.040 0.142 2448 Planarity : 0.005 0.036 2712 Dihedral : 4.454 17.336 2160 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.24 % Favored : 96.41 % Rotamer: Outliers : 0.63 % Allowed : 12.56 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.19), residues: 2008 helix: 2.87 (0.13), residues: 1392 sheet: None (None), residues: 0 loop : -0.68 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.004 0.001 HIS C 57 PHE 0.011 0.001 PHE B 236 TYR 0.019 0.002 TYR G 223 ARG 0.001 0.000 ARG A 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5412.05 seconds wall clock time: 95 minutes 33.59 seconds (5733.59 seconds total)