Starting phenix.real_space_refine on Sat Mar 16 11:23:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo6_13006/03_2024/7oo6_13006_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo6_13006/03_2024/7oo6_13006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo6_13006/03_2024/7oo6_13006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo6_13006/03_2024/7oo6_13006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo6_13006/03_2024/7oo6_13006_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo6_13006/03_2024/7oo6_13006_updated.pdb" } resolution = 3.1 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= 0.000 sd= 0.012 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 42 5.16 5 C 9408 2.51 5 N 2443 2.21 5 O 2646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14546 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain: "B" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain: "C" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain: "D" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain: "E" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain: "F" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain: "G" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'LMT': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'LMT': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'LMT': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'LMT': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'LMT': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'LMT': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'LMT': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.89, per 1000 atoms: 0.54 Number of scatterers: 14546 At special positions: 0 Unit cell: (97.842, 97.842, 142.509, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 7 15.00 O 2646 8.00 N 2443 7.00 C 9408 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: 5.55 Conformation dependent library (CDL) restraints added in 2.3 seconds 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 14 sheets defined 51.7% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 23 through 58 Processing helix chain 'A' and resid 63 through 89 Processing helix chain 'A' and resid 94 through 127 removed outlier: 4.701A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 246 through 264 Processing helix chain 'B' and resid 23 through 58 Processing helix chain 'B' and resid 63 through 89 Processing helix chain 'B' and resid 94 through 127 removed outlier: 4.701A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 198 through 211 Processing helix chain 'B' and resid 246 through 264 Processing helix chain 'C' and resid 23 through 58 Processing helix chain 'C' and resid 63 through 89 Processing helix chain 'C' and resid 94 through 127 removed outlier: 4.702A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 198 through 211 Processing helix chain 'C' and resid 246 through 264 Processing helix chain 'D' and resid 23 through 58 Processing helix chain 'D' and resid 63 through 89 Processing helix chain 'D' and resid 94 through 127 removed outlier: 4.701A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 198 through 211 Processing helix chain 'D' and resid 246 through 264 Processing helix chain 'E' and resid 23 through 58 Processing helix chain 'E' and resid 63 through 89 Processing helix chain 'E' and resid 94 through 127 removed outlier: 4.701A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 198 through 211 Processing helix chain 'E' and resid 246 through 264 Processing helix chain 'F' and resid 23 through 58 Processing helix chain 'F' and resid 63 through 89 Processing helix chain 'F' and resid 94 through 127 removed outlier: 4.700A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 246 through 264 Processing helix chain 'G' and resid 23 through 58 Processing helix chain 'G' and resid 63 through 89 Processing helix chain 'G' and resid 94 through 127 removed outlier: 4.702A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 171 Processing helix chain 'G' and resid 198 through 211 Processing helix chain 'G' and resid 246 through 264 Processing sheet with id= A, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.820A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.220A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.821A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.221A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 175 through 177 removed outlier: 3.820A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.220A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 175 through 177 removed outlier: 3.821A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.220A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 175 through 177 removed outlier: 3.821A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.220A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 175 through 177 removed outlier: 3.820A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.221A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 175 through 177 removed outlier: 3.820A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.221A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) 931 hydrogen bonds defined for protein. 2772 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: 4.64 Time building geometry restraints manager: 6.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2319 1.32 - 1.44: 3561 1.44 - 1.56: 8743 1.56 - 1.68: 14 1.68 - 1.80: 84 Bond restraints: 14721 Sorted by residual: bond pdb=" C4 PCW G 801 " pdb=" O4P PCW G 801 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" C4 PCW A 801 " pdb=" O4P PCW A 801 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C4 PCW C 801 " pdb=" O4P PCW C 801 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.53e+00 bond pdb=" C4 PCW B 801 " pdb=" O4P PCW B 801 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C4 PCW D 801 " pdb=" O4P PCW D 801 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.49e+00 ... (remaining 14716 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.27: 286 107.27 - 113.96: 8944 113.96 - 120.65: 5831 120.65 - 127.34: 4749 127.34 - 134.03: 63 Bond angle restraints: 19873 Sorted by residual: angle pdb=" O3P PCW E 801 " pdb=" P PCW E 801 " pdb=" O4P PCW E 801 " ideal model delta sigma weight residual 96.85 104.00 -7.15 3.00e+00 1.11e-01 5.67e+00 angle pdb=" O3P PCW D 801 " pdb=" P PCW D 801 " pdb=" O4P PCW D 801 " ideal model delta sigma weight residual 96.85 103.99 -7.14 3.00e+00 1.11e-01 5.67e+00 angle pdb=" O3P PCW F 801 " pdb=" P PCW F 801 " pdb=" O4P PCW F 801 " ideal model delta sigma weight residual 96.85 103.98 -7.13 3.00e+00 1.11e-01 5.64e+00 angle pdb=" O3P PCW A 801 " pdb=" P PCW A 801 " pdb=" O4P PCW A 801 " ideal model delta sigma weight residual 96.85 103.97 -7.12 3.00e+00 1.11e-01 5.63e+00 angle pdb=" O3P PCW B 801 " pdb=" P PCW B 801 " pdb=" O4P PCW B 801 " ideal model delta sigma weight residual 96.85 103.96 -7.11 3.00e+00 1.11e-01 5.62e+00 ... (remaining 19868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 8869 21.12 - 42.24: 252 42.24 - 63.37: 91 63.37 - 84.49: 0 84.49 - 105.61: 14 Dihedral angle restraints: 9226 sinusoidal: 3990 harmonic: 5236 Sorted by residual: dihedral pdb=" N PCW B 801 " pdb=" C4 PCW B 801 " pdb=" C5 PCW B 801 " pdb=" O4P PCW B 801 " ideal model delta sinusoidal sigma weight residual -66.66 -172.27 105.61 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" N PCW C 801 " pdb=" C4 PCW C 801 " pdb=" C5 PCW C 801 " pdb=" O4P PCW C 801 " ideal model delta sinusoidal sigma weight residual -66.66 -172.25 105.59 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" N PCW F 801 " pdb=" C4 PCW F 801 " pdb=" C5 PCW F 801 " pdb=" O4P PCW F 801 " ideal model delta sinusoidal sigma weight residual -66.66 -172.24 105.58 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 9223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1975 0.051 - 0.103: 344 0.103 - 0.154: 84 0.154 - 0.205: 12 0.205 - 0.256: 7 Chirality restraints: 2422 Sorted by residual: chirality pdb=" C2 PCW D 801 " pdb=" C1 PCW D 801 " pdb=" C3 PCW D 801 " pdb=" O2 PCW D 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C2 PCW B 801 " pdb=" C1 PCW B 801 " pdb=" C3 PCW B 801 " pdb=" O2 PCW B 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C2 PCW A 801 " pdb=" C1 PCW A 801 " pdb=" C3 PCW A 801 " pdb=" O2 PCW A 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2419 not shown) Planarity restraints: 2457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 111 " 0.004 2.00e-02 2.50e+03 8.31e-03 6.90e-01 pdb=" C LEU E 111 " -0.014 2.00e-02 2.50e+03 pdb=" O LEU E 111 " 0.005 2.00e-02 2.50e+03 pdb=" N GLN E 112 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 111 " 0.004 2.00e-02 2.50e+03 8.28e-03 6.86e-01 pdb=" C LEU B 111 " -0.014 2.00e-02 2.50e+03 pdb=" O LEU B 111 " 0.005 2.00e-02 2.50e+03 pdb=" N GLN B 112 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 270 " 0.014 5.00e-02 4.00e+02 2.07e-02 6.86e-01 pdb=" N PRO C 271 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO C 271 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 271 " 0.012 5.00e-02 4.00e+02 ... (remaining 2454 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4528 2.84 - 3.36: 14092 3.36 - 3.87: 23903 3.87 - 4.39: 26707 4.39 - 4.90: 48180 Nonbonded interactions: 117410 Sorted by model distance: nonbonded pdb=" OE1 GLU C 212 " pdb=" NH2 ARG C 256 " model vdw 2.327 2.520 nonbonded pdb=" OE1 GLU G 212 " pdb=" NH2 ARG G 256 " model vdw 2.327 2.520 nonbonded pdb=" OE1 GLU A 212 " pdb=" NH2 ARG A 256 " model vdw 2.327 2.520 nonbonded pdb=" OE1 GLU E 212 " pdb=" NH2 ARG E 256 " model vdw 2.327 2.520 nonbonded pdb=" OE1 GLU F 212 " pdb=" NH2 ARG F 256 " model vdw 2.327 2.520 ... (remaining 117405 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' } 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: 0.850 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: 4.560 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 39.420 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.110 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 14721 Z= 0.265 Angle : 0.566 7.146 19873 Z= 0.282 Chirality : 0.044 0.256 2422 Planarity : 0.002 0.021 2457 Dihedral : 12.218 105.611 5852 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: 2.48 (0.19), residues: 1813 helix: 3.25 (0.15), residues: 1008 sheet: -0.29 (0.31), residues: 259 loop : -0.52 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 251 PHE 0.006 0.001 PHE C 277 TYR 0.003 0.001 TYR F 250 ARG 0.002 0.000 ARG E 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.572 Fit side-chains REVERT: A 125 VAL cc_start: 0.8512 (t) cc_final: 0.8253 (t) REVERT: C 47 MET cc_start: 0.4892 (mmt) cc_final: 0.4575 (tmm) REVERT: C 227 GLU cc_start: 0.8155 (pt0) cc_final: 0.7909 (pt0) REVERT: E 97 ILE cc_start: 0.7973 (mt) cc_final: 0.7756 (mt) REVERT: F 155 MET cc_start: 0.8604 (ptt) cc_final: 0.8382 (ptt) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2796 time to fit residues: 99.0012 Evaluate side-chains 208 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14721 Z= 0.166 Angle : 0.416 6.539 19873 Z= 0.222 Chirality : 0.041 0.145 2422 Planarity : 0.002 0.022 2457 Dihedral : 12.842 107.940 2730 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.10 % Allowed : 8.33 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.19), residues: 1813 helix: 3.16 (0.15), residues: 1015 sheet: -0.33 (0.29), residues: 259 loop : -0.52 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 240 PHE 0.010 0.001 PHE G 188 TYR 0.003 0.001 TYR B 250 ARG 0.005 0.000 ARG G 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 214 time to evaluate : 1.587 Fit side-chains REVERT: A 154 THR cc_start: 0.8431 (p) cc_final: 0.8088 (m) REVERT: C 47 MET cc_start: 0.4940 (mmt) cc_final: 0.4631 (tmm) REVERT: C 221 MET cc_start: 0.8406 (mtm) cc_final: 0.7957 (mtm) REVERT: D 47 MET cc_start: 0.5262 (tmm) cc_final: 0.4528 (mmm) REVERT: D 210 GLN cc_start: 0.7961 (mm110) cc_final: 0.7702 (mm110) REVERT: E 210 GLN cc_start: 0.8113 (mm110) cc_final: 0.7847 (mm-40) REVERT: F 154 THR cc_start: 0.8588 (p) cc_final: 0.8228 (m) REVERT: G 47 MET cc_start: 0.5236 (tmm) cc_final: 0.4272 (mmt) outliers start: 31 outliers final: 20 residues processed: 230 average time/residue: 0.2896 time to fit residues: 94.9673 Evaluate side-chains 218 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 198 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 213 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7686 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14721 Z= 0.163 Angle : 0.403 6.890 19873 Z= 0.214 Chirality : 0.041 0.138 2422 Planarity : 0.002 0.021 2457 Dihedral : 12.626 101.996 2730 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.17 % Allowed : 10.70 % Favored : 87.14 % 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: 1813 helix: 3.16 (0.15), residues: 1008 sheet: -0.40 (0.27), residues: 294 loop : -0.51 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 240 PHE 0.008 0.001 PHE D 188 TYR 0.003 0.001 TYR A 250 ARG 0.006 0.000 ARG G 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 207 time to evaluate : 1.527 Fit side-chains REVERT: A 47 MET cc_start: 0.5369 (tmm) cc_final: 0.4373 (mmm) REVERT: A 154 THR cc_start: 0.8512 (p) cc_final: 0.8249 (m) REVERT: A 187 GLU cc_start: 0.8051 (tt0) cc_final: 0.7800 (tt0) REVERT: C 47 MET cc_start: 0.5048 (mmt) cc_final: 0.4757 (tmm) REVERT: C 221 MET cc_start: 0.8373 (mtm) cc_final: 0.8005 (mtm) REVERT: D 154 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8349 (m) REVERT: E 169 LYS cc_start: 0.8480 (ttpp) cc_final: 0.8198 (ttpp) REVERT: E 210 GLN cc_start: 0.8079 (mm110) cc_final: 0.7806 (mm-40) REVERT: F 47 MET cc_start: 0.5044 (tmm) cc_final: 0.4571 (mmt) REVERT: F 154 THR cc_start: 0.8532 (p) cc_final: 0.8313 (m) REVERT: G 47 MET cc_start: 0.5004 (tmm) cc_final: 0.4796 (tmm) outliers start: 32 outliers final: 23 residues processed: 228 average time/residue: 0.3000 time to fit residues: 97.4208 Evaluate side-chains 221 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 197 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 213 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 175 optimal weight: 0.0670 chunk 86 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- 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: 0.7695 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14721 Z= 0.175 Angle : 0.406 6.766 19873 Z= 0.215 Chirality : 0.041 0.140 2422 Planarity : 0.002 0.021 2457 Dihedral : 12.279 99.398 2730 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.64 % Allowed : 11.71 % Favored : 85.65 % 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: 2.31 (0.19), residues: 1813 helix: 3.09 (0.15), residues: 1008 sheet: -0.38 (0.27), residues: 294 loop : -0.53 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 240 PHE 0.009 0.001 PHE D 188 TYR 0.003 0.001 TYR A 250 ARG 0.003 0.000 ARG G 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 201 time to evaluate : 1.536 Fit side-chains REVERT: A 154 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8280 (m) REVERT: C 47 MET cc_start: 0.4852 (mmt) cc_final: 0.4638 (tmm) REVERT: D 47 MET cc_start: 0.5665 (tmm) cc_final: 0.4756 (mmm) REVERT: D 154 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8349 (m) REVERT: E 83 ILE cc_start: 0.7367 (pt) cc_final: 0.7037 (pt) REVERT: E 210 GLN cc_start: 0.8037 (mm110) cc_final: 0.7768 (mm-40) REVERT: E 273 MET cc_start: 0.8192 (ttm) cc_final: 0.7904 (ttm) REVERT: F 154 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8335 (m) REVERT: G 47 MET cc_start: 0.5035 (tmm) cc_final: 0.4824 (tmm) outliers start: 39 outliers final: 24 residues processed: 225 average time/residue: 0.2923 time to fit residues: 93.1026 Evaluate side-chains 219 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 192 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 213 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 130 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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: 0.7715 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14721 Z= 0.212 Angle : 0.436 7.575 19873 Z= 0.229 Chirality : 0.042 0.142 2422 Planarity : 0.002 0.021 2457 Dihedral : 11.788 96.577 2730 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.91 % Allowed : 12.53 % Favored : 84.56 % 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: 2.19 (0.19), residues: 1813 helix: 2.96 (0.15), residues: 1008 sheet: -0.34 (0.27), residues: 294 loop : -0.57 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 240 PHE 0.010 0.001 PHE F 188 TYR 0.004 0.001 TYR B 250 ARG 0.004 0.000 ARG C 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 206 time to evaluate : 1.642 Fit side-chains REVERT: A 154 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8253 (m) REVERT: C 47 MET cc_start: 0.4845 (mmt) cc_final: 0.4595 (tmm) REVERT: C 97 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7601 (mt) REVERT: D 47 MET cc_start: 0.5658 (tmm) cc_final: 0.4726 (mmm) REVERT: D 154 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8366 (m) REVERT: E 83 ILE cc_start: 0.7499 (pt) cc_final: 0.7171 (pt) REVERT: E 221 MET cc_start: 0.8459 (mtm) cc_final: 0.8228 (mtm) REVERT: F 154 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8371 (m) REVERT: G 47 MET cc_start: 0.5108 (tmm) cc_final: 0.4851 (tmm) outliers start: 43 outliers final: 28 residues processed: 233 average time/residue: 0.2893 time to fit residues: 96.0460 Evaluate side-chains 234 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 202 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 213 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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: 0.7729 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14721 Z= 0.239 Angle : 0.448 7.714 19873 Z= 0.235 Chirality : 0.042 0.143 2422 Planarity : 0.003 0.021 2457 Dihedral : 11.520 93.172 2730 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.71 % Allowed : 13.41 % Favored : 83.89 % 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: 2.05 (0.19), residues: 1813 helix: 2.83 (0.15), residues: 1008 sheet: -0.33 (0.26), residues: 294 loop : -0.65 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 240 PHE 0.011 0.001 PHE G 188 TYR 0.004 0.001 TYR A 250 ARG 0.004 0.000 ARG C 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 204 time to evaluate : 1.508 Fit side-chains REVERT: A 154 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8299 (m) REVERT: C 47 MET cc_start: 0.4867 (mmt) cc_final: 0.4597 (tmm) REVERT: E 47 MET cc_start: 0.5338 (tmm) cc_final: 0.4344 (mmt) REVERT: E 83 ILE cc_start: 0.7549 (pt) cc_final: 0.7187 (pt) REVERT: G 47 MET cc_start: 0.5015 (tmm) cc_final: 0.4784 (tmm) outliers start: 40 outliers final: 32 residues processed: 230 average time/residue: 0.2864 time to fit residues: 93.0410 Evaluate side-chains 235 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 202 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 213 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 100 optimal weight: 0.0870 chunk 128 optimal weight: 0.0970 chunk 99 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 175 optimal weight: 0.1980 chunk 109 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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: 0.7673 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14721 Z= 0.118 Angle : 0.395 7.483 19873 Z= 0.209 Chirality : 0.040 0.133 2422 Planarity : 0.002 0.026 2457 Dihedral : 10.761 81.405 2730 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.37 % Allowed : 14.29 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.19), residues: 1813 helix: 3.05 (0.15), residues: 1008 sheet: -0.35 (0.26), residues: 294 loop : -0.56 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 251 PHE 0.009 0.001 PHE D 188 TYR 0.002 0.000 TYR B 250 ARG 0.009 0.000 ARG G 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 209 time to evaluate : 1.563 Fit side-chains REVERT: A 72 LEU cc_start: 0.3916 (OUTLIER) cc_final: 0.3628 (tt) REVERT: B 39 ILE cc_start: 0.6754 (mm) cc_final: 0.6546 (mm) REVERT: B 88 ARG cc_start: 0.7760 (tpt90) cc_final: 0.7512 (tpt170) REVERT: B 154 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8301 (m) REVERT: B 169 LYS cc_start: 0.8546 (ttpp) cc_final: 0.8216 (ttpp) REVERT: C 47 MET cc_start: 0.4849 (mmt) cc_final: 0.4622 (tmm) REVERT: C 97 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7546 (mt) REVERT: D 47 MET cc_start: 0.5739 (tmm) cc_final: 0.4840 (mmm) REVERT: F 47 MET cc_start: 0.5418 (tmm) cc_final: 0.4695 (mmt) outliers start: 35 outliers final: 25 residues processed: 229 average time/residue: 0.2750 time to fit residues: 90.7838 Evaluate side-chains 226 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 198 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 213 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 111 optimal weight: 0.0670 chunk 119 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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: 0.7688 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14721 Z= 0.163 Angle : 0.419 8.506 19873 Z= 0.218 Chirality : 0.041 0.138 2422 Planarity : 0.002 0.026 2457 Dihedral : 10.455 71.265 2730 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.57 % Allowed : 14.49 % Favored : 82.94 % 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: 2.23 (0.19), residues: 1813 helix: 2.99 (0.15), residues: 1008 sheet: -0.31 (0.26), residues: 294 loop : -0.56 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP G 240 PHE 0.009 0.001 PHE B 188 TYR 0.002 0.000 TYR F 250 ARG 0.005 0.000 ARG G 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 199 time to evaluate : 1.575 Fit side-chains REVERT: A 72 LEU cc_start: 0.3845 (OUTLIER) cc_final: 0.3550 (tt) REVERT: B 39 ILE cc_start: 0.6789 (mm) cc_final: 0.6578 (mm) REVERT: B 88 ARG cc_start: 0.7781 (tpt90) cc_final: 0.7524 (tpt170) REVERT: C 47 MET cc_start: 0.4841 (mmt) cc_final: 0.4634 (tmm) REVERT: C 97 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7561 (mt) REVERT: D 47 MET cc_start: 0.5568 (tmm) cc_final: 0.4669 (mmm) REVERT: E 47 MET cc_start: 0.5213 (tmm) cc_final: 0.4263 (mmt) REVERT: G 47 MET cc_start: 0.5522 (tmm) cc_final: 0.4554 (mmt) outliers start: 38 outliers final: 30 residues processed: 222 average time/residue: 0.2801 time to fit residues: 89.0524 Evaluate side-chains 229 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 197 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 213 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 154 optimal weight: 0.0570 chunk 162 optimal weight: 0.5980 overall best weight: 0.7302 ------------------------------------------------------------------------------- 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: 0.7689 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14721 Z= 0.161 Angle : 0.414 8.398 19873 Z= 0.216 Chirality : 0.041 0.138 2422 Planarity : 0.002 0.025 2457 Dihedral : 10.063 58.604 2730 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.44 % Allowed : 14.90 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.19), residues: 1813 helix: 2.96 (0.15), residues: 1008 sheet: -0.29 (0.26), residues: 294 loop : -0.56 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 251 PHE 0.009 0.001 PHE D 188 TYR 0.003 0.001 TYR G 250 ARG 0.006 0.000 ARG G 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 194 time to evaluate : 1.362 Fit side-chains REVERT: A 72 LEU cc_start: 0.3850 (OUTLIER) cc_final: 0.3556 (tt) REVERT: B 39 ILE cc_start: 0.6786 (mm) cc_final: 0.6572 (mm) REVERT: B 88 ARG cc_start: 0.7789 (tpt90) cc_final: 0.7524 (tpt170) REVERT: B 279 ARG cc_start: 0.7986 (ttp-170) cc_final: 0.7636 (ttp-170) REVERT: C 47 MET cc_start: 0.4834 (mmt) cc_final: 0.4624 (tmm) REVERT: C 97 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7566 (mt) REVERT: D 47 MET cc_start: 0.5564 (tmm) cc_final: 0.4678 (mmm) REVERT: D 273 MET cc_start: 0.8315 (ttm) cc_final: 0.8096 (ttm) REVERT: F 47 MET cc_start: 0.5341 (tmm) cc_final: 0.4595 (mmt) REVERT: G 47 MET cc_start: 0.5582 (tmm) cc_final: 0.4568 (mmt) REVERT: G 126 MET cc_start: 0.7910 (ttp) cc_final: 0.7245 (mtm) outliers start: 36 outliers final: 28 residues processed: 219 average time/residue: 0.2865 time to fit residues: 89.9689 Evaluate side-chains 221 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 213 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.8980 chunk 172 optimal weight: 0.0030 chunk 105 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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: 0.7686 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14721 Z= 0.158 Angle : 0.416 9.359 19873 Z= 0.216 Chirality : 0.041 0.137 2422 Planarity : 0.002 0.026 2457 Dihedral : 9.771 57.862 2730 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.03 % Allowed : 15.30 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.19), residues: 1813 helix: 2.96 (0.15), residues: 1008 sheet: -0.27 (0.26), residues: 294 loop : -0.57 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 240 PHE 0.009 0.001 PHE E 188 TYR 0.002 0.000 TYR F 250 ARG 0.005 0.000 ARG G 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 197 time to evaluate : 1.519 Fit side-chains REVERT: A 72 LEU cc_start: 0.3852 (OUTLIER) cc_final: 0.3545 (tt) REVERT: B 39 ILE cc_start: 0.6783 (mm) cc_final: 0.6569 (mm) REVERT: B 88 ARG cc_start: 0.7795 (tpt90) cc_final: 0.7525 (tpt170) REVERT: B 279 ARG cc_start: 0.7994 (ttp-170) cc_final: 0.7650 (ttp-170) REVERT: C 97 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7560 (mt) REVERT: D 47 MET cc_start: 0.5587 (tmm) cc_final: 0.4712 (mmm) REVERT: D 273 MET cc_start: 0.8314 (ttm) cc_final: 0.8103 (ttm) REVERT: F 47 MET cc_start: 0.5495 (tmm) cc_final: 0.4695 (mmt) REVERT: G 47 MET cc_start: 0.5614 (tmm) cc_final: 0.4603 (mmt) outliers start: 30 outliers final: 27 residues processed: 217 average time/residue: 0.2842 time to fit residues: 87.8590 Evaluate side-chains 224 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 213 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 21 optimal weight: 0.0010 chunk 40 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 26 optimal weight: 20.0000 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.153401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.111288 restraints weight = 15642.216| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.45 r_work: 0.3143 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14721 Z= 0.146 Angle : 0.421 10.671 19873 Z= 0.217 Chirality : 0.040 0.136 2422 Planarity : 0.002 0.025 2457 Dihedral : 9.532 59.582 2730 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.03 % Allowed : 15.64 % Favored : 82.33 % 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: 2.20 (0.19), residues: 1813 helix: 2.92 (0.15), residues: 1015 sheet: -0.24 (0.26), residues: 294 loop : -0.60 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 240 PHE 0.009 0.001 PHE B 188 TYR 0.002 0.000 TYR F 250 ARG 0.005 0.000 ARG G 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3056.41 seconds wall clock time: 55 minutes 38.34 seconds (3338.34 seconds total)