Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 19:09:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/04_2023/8amx_15528.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/04_2023/8amx_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_15528/04_2023/8amx_15528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/04_2023/8amx_15528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/04_2023/8amx_15528.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amx_15528/04_2023/8amx_15528.pdb" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 8.21, per 1000 atoms: 0.53 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: 5.96 Conformation dependent library (CDL) restraints added in 2.5 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: 0.61 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: 4.83 Time building geometry restraints manager: 6.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 3.950 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: 14.960 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 40.300 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.180 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.996 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 1.6018 time to fit residues: 360.0168 Evaluate side-chains 191 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.775 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3439 ------------------------------------------------------------------------------- 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: 0.7980 chunk 116 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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: 0.8346 moved from start: 0.0665 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= 0.255 Angle : 0.630 5.576 21840 Z= 0.350 Chirality : 0.044 0.158 2448 Planarity : 0.006 0.040 2712 Dihedral : 4.887 18.567 2160 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.44 % Favored : 96.22 % Rotamer Outliers : 1.57 % 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: 2.35 (0.19), residues: 2008 helix: 2.30 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : -0.28 (0.28), residues: 592 *********************** 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 210 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 185 time to evaluate : 1.928 Fit side-chains outliers start: 25 outliers final: 8 residues processed: 185 average time/residue: 1.5448 time to fit residues: 311.1340 Evaluate side-chains 193 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 1.606 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1307 time to fit residues: 4.1269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 180 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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: 0.8345 moved from start: 0.0804 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= 0.252 Angle : 0.621 5.630 21840 Z= 0.344 Chirality : 0.044 0.161 2448 Planarity : 0.005 0.040 2712 Dihedral : 4.865 18.610 2160 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.39 % Favored : 96.26 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.19), residues: 2008 helix: 2.27 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.14 (0.29), residues: 576 *********************** 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 210 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 1.751 Fit side-chains outliers start: 22 outliers final: 3 residues processed: 197 average time/residue: 1.4985 time to fit residues: 322.4609 Evaluate side-chains 191 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 188 time to evaluate : 1.754 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1362 time to fit residues: 3.1499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 95 optimal weight: 0.0040 chunk 173 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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: 0.8263 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 16032 Z= 0.152 Angle : 0.533 5.541 21840 Z= 0.295 Chirality : 0.040 0.142 2448 Planarity : 0.005 0.036 2712 Dihedral : 4.511 17.624 2160 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.54 % Favored : 97.11 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.20), residues: 2008 helix: 2.64 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : 0.02 (0.30), residues: 576 *********************** 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 170 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 1.720 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 164 average time/residue: 1.5072 time to fit residues: 270.8272 Evaluate side-chains 164 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 159 time to evaluate : 2.016 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1468 time to fit residues: 4.0738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 2 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 164 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8250 moved from start: 0.1236 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 : 0.522 5.589 21840 Z= 0.288 Chirality : 0.039 0.140 2448 Planarity : 0.005 0.035 2712 Dihedral : 4.384 17.168 2160 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.14 % Favored : 96.51 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.20), residues: 2008 helix: 2.75 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.03 (0.29), residues: 576 *********************** 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 188 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 1.877 Fit side-chains outliers start: 22 outliers final: 0 residues processed: 180 average time/residue: 1.4381 time to fit residues: 283.8231 Evaluate side-chains 166 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.8317 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 16032 Z= 0.218 Angle : 0.585 5.502 21840 Z= 0.322 Chirality : 0.042 0.152 2448 Planarity : 0.005 0.037 2712 Dihedral : 4.658 18.027 2160 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.74 % Favored : 95.92 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.20), residues: 2008 helix: 2.53 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.16 (0.29), residues: 576 *********************** 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 199 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 186 time to evaluate : 1.616 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 196 average time/residue: 1.5438 time to fit residues: 329.7821 Evaluate side-chains 189 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 1.766 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1395 time to fit residues: 2.6384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 192 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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: 0.8358 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 16032 Z= 0.286 Angle : 0.642 5.751 21840 Z= 0.353 Chirality : 0.045 0.163 2448 Planarity : 0.005 0.039 2712 Dihedral : 4.903 18.694 2160 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.88 % Favored : 95.77 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.19), residues: 2008 helix: 2.45 (0.14), residues: 1392 sheet: None (None), residues: 0 loop : -0.66 (0.28), residues: 616 *********************** 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 210 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 1.774 Fit side-chains outliers start: 26 outliers final: 8 residues processed: 201 average time/residue: 1.4880 time to fit residues: 328.0227 Evaluate side-chains 194 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 186 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.3726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.0030 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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: 0.8251 moved from start: 0.1313 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= 0.146 Angle : 0.527 5.553 21840 Z= 0.290 Chirality : 0.039 0.141 2448 Planarity : 0.005 0.035 2712 Dihedral : 4.469 17.525 2160 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.39 % Favored : 97.26 % Rotamer Outliers : 0.75 % 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: 2.85 (0.20), residues: 2008 helix: 2.67 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.18 (0.29), residues: 576 *********************** 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 179 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 1.759 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 175 average time/residue: 1.4879 time to fit residues: 285.1041 Evaluate side-chains 177 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 1.606 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.1344 time to fit residues: 2.7224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 162 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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: 0.8336 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 16032 Z= 0.251 Angle : 0.610 5.503 21840 Z= 0.335 Chirality : 0.044 0.154 2448 Planarity : 0.005 0.038 2712 Dihedral : 4.771 18.347 2160 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.88 % Favored : 95.77 % Rotamer Outliers : 1.07 % 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: 2.53 (0.20), residues: 2008 helix: 2.43 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.28 (0.29), residues: 576 *********************** 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 209 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 1.673 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 209 average time/residue: 1.5478 time to fit residues: 352.8335 Evaluate side-chains 202 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 192 time to evaluate : 1.770 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 2.3703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8278 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 16032 Z= 0.164 Angle : 0.545 5.534 21840 Z= 0.300 Chirality : 0.040 0.147 2448 Planarity : 0.005 0.036 2712 Dihedral : 4.550 17.768 2160 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.59 % Favored : 97.06 % Rotamer Outliers : 0.94 % 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: 2.75 (0.20), residues: 2008 helix: 2.61 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.24 (0.29), residues: 576 ********************** 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 186 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.883 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 181 average time/residue: 1.5292 time to fit residues: 303.7437 Evaluate side-chains 186 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 171 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 0.1463 time to fit residues: 3.6108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.0170 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 163 optimal weight: 0.0370 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.122929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.100530 restraints weight = 15616.867| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.36 r_work: 0.3001 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1431 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= 0.138 Angle : 0.512 5.607 21840 Z= 0.281 Chirality : 0.039 0.136 2448 Planarity : 0.005 0.034 2712 Dihedral : 4.320 17.152 2160 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.24 % Favored : 96.41 % Rotamer Outliers : 0.63 % 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: 3.03 (0.20), residues: 2008 helix: 2.83 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -0.17 (0.29), residues: 576 =============================================================================== Job complete usr+sys time: 5200.21 seconds wall clock time: 93 minutes 2.81 seconds (5582.81 seconds total)