Starting phenix.real_space_refine on Sun Dec 10 12:57:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo6_13006/12_2023/7oo6_13006_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo6_13006/12_2023/7oo6_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_13006/12_2023/7oo6_13006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo6_13006/12_2023/7oo6_13006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo6_13006/12_2023/7oo6_13006_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo6_13006/12_2023/7oo6_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-1.21rc1-5172/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: 7.61, per 1000 atoms: 0.52 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: 5.93 Conformation dependent library (CDL) restraints added in 2.7 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: 2.48 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: 4.42 Time building geometry restraints manager: 6.36 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.570 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 40.350 Find NCS groups from input model: 0.940 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.040 ------------------------------------------------------------------------------- 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 : 1.636 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2866 time to fit residues: 101.9536 Evaluate side-chains 207 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0925 ------------------------------------------------------------------------------- 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: 0.8980 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7669 moved from start: 0.0940 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= 0.157 Angle : 0.417 6.731 19873 Z= 0.221 Chirality : 0.041 0.141 2422 Planarity : 0.002 0.024 2457 Dihedral : 12.795 107.214 2730 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.23 % Allowed : 8.26 % Favored : 89.51 % 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: 3.14 (0.15), residues: 1015 sheet: -0.37 (0.29), residues: 259 loop : -0.53 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 240 PHE 0.010 0.001 PHE F 188 TYR 0.003 0.001 TYR A 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 249 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 1.672 Fit side-chains outliers start: 33 outliers final: 19 residues processed: 233 average time/residue: 0.2899 time to fit residues: 96.7940 Evaluate side-chains 217 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1241 time to fit residues: 6.6170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 0.0040 chunk 137 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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: 0.7665 moved from start: 0.1078 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= 0.137 Angle : 0.383 6.051 19873 Z= 0.206 Chirality : 0.040 0.136 2422 Planarity : 0.002 0.021 2457 Dihedral : 12.533 101.161 2730 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.74 % Allowed : 10.77 % Favored : 88.49 % 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: 2.41 (0.19), residues: 1813 helix: 3.17 (0.15), residues: 1015 sheet: -0.37 (0.28), residues: 259 loop : -0.55 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 240 PHE 0.008 0.001 PHE D 188 TYR 0.002 0.000 TYR F 250 ARG 0.005 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 206 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 1.652 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 202 average time/residue: 0.3194 time to fit residues: 92.1178 Evaluate side-chains 189 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1437 time to fit residues: 2.8783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 18 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7680 moved from start: 0.1246 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= 0.160 Angle : 0.407 8.469 19873 Z= 0.214 Chirality : 0.041 0.141 2422 Planarity : 0.002 0.021 2457 Dihedral : 12.158 97.624 2730 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.22 % Allowed : 11.31 % Favored : 87.47 % 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: 2.39 (0.19), residues: 1813 helix: 3.15 (0.15), residues: 1008 sheet: -0.34 (0.27), residues: 294 loop : -0.52 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 240 PHE 0.008 0.001 PHE E 188 TYR 0.003 0.001 TYR A 250 ARG 0.004 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 219 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 1.719 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 209 average time/residue: 0.3079 time to fit residues: 90.9643 Evaluate side-chains 201 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 193 time to evaluate : 1.509 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1208 time to fit residues: 3.8981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 130 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.7714 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14721 Z= 0.232 Angle : 0.438 7.909 19873 Z= 0.231 Chirality : 0.042 0.141 2422 Planarity : 0.002 0.021 2457 Dihedral : 11.782 94.737 2730 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.22 % Allowed : 13.00 % Favored : 85.78 % 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: 2.97 (0.15), residues: 1008 sheet: -0.26 (0.27), residues: 294 loop : -0.58 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 240 PHE 0.010 0.001 PHE D 188 TYR 0.004 0.001 TYR A 250 ARG 0.006 0.000 ARG G 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 220 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 202 time to evaluate : 1.618 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 215 average time/residue: 0.3064 time to fit residues: 93.5631 Evaluate side-chains 200 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 192 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1317 time to fit residues: 4.0553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.7706 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14721 Z= 0.202 Angle : 0.435 9.095 19873 Z= 0.229 Chirality : 0.041 0.139 2422 Planarity : 0.002 0.021 2457 Dihedral : 11.472 90.365 2730 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.81 % Allowed : 13.95 % Favored : 85.24 % 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: 2.18 (0.19), residues: 1813 helix: 2.94 (0.15), residues: 1008 sheet: -0.24 (0.27), residues: 294 loop : -0.61 (0.25), residues: 511 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 G 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 212 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 200 time to evaluate : 2.153 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 206 average time/residue: 0.3082 time to fit residues: 91.2473 Evaluate side-chains 203 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 1.593 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1251 time to fit residues: 4.0479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.7703 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14721 Z= 0.188 Angle : 0.411 7.583 19873 Z= 0.220 Chirality : 0.041 0.140 2422 Planarity : 0.002 0.021 2457 Dihedral : 11.074 80.891 2730 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.47 % Allowed : 14.08 % Favored : 85.44 % 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: 2.17 (0.19), residues: 1813 helix: 2.92 (0.15), residues: 1008 sheet: -0.22 (0.27), residues: 294 loop : -0.62 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 240 PHE 0.010 0.001 PHE D 188 TYR 0.003 0.001 TYR A 250 ARG 0.004 0.000 ARG E 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 203 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 196 time to evaluate : 1.581 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 202 average time/residue: 0.3013 time to fit residues: 87.8652 Evaluate side-chains 190 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1210 time to fit residues: 2.6354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 30.0000 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 111 optimal weight: 0.0370 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 137 optimal weight: 0.0370 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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: 0.7683 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14721 Z= 0.147 Angle : 0.428 9.744 19873 Z= 0.222 Chirality : 0.040 0.136 2422 Planarity : 0.002 0.021 2457 Dihedral : 10.614 68.978 2730 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.27 % Allowed : 14.96 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.19), residues: 1813 helix: 3.00 (0.15), residues: 1008 sheet: -0.20 (0.27), residues: 294 loop : -0.58 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 240 PHE 0.009 0.001 PHE D 188 TYR 0.002 0.000 TYR F 250 ARG 0.004 0.000 ARG C 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 195 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 191 time to evaluate : 1.557 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 194 average time/residue: 0.2899 time to fit residues: 80.6108 Evaluate side-chains 192 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.688 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1281 time to fit residues: 2.7299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 6.9990 chunk 168 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 0.0770 chunk 128 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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: 0.7677 moved from start: 0.1654 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= 0.145 Angle : 0.390 6.718 19873 Z= 0.208 Chirality : 0.040 0.137 2422 Planarity : 0.002 0.021 2457 Dihedral : 10.135 58.872 2730 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.27 % Allowed : 15.30 % Favored : 84.43 % 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: 2.29 (0.19), residues: 1813 helix: 3.02 (0.15), residues: 1008 sheet: -0.16 (0.27), residues: 294 loop : -0.58 (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 B 188 TYR 0.002 0.000 TYR F 250 ARG 0.004 0.000 ARG C 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 203 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 1.619 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 199 average time/residue: 0.2981 time to fit residues: 84.4880 Evaluate side-chains 196 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 193 time to evaluate : 1.564 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1397 time to fit residues: 2.8924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.7691 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14721 Z= 0.179 Angle : 0.431 10.209 19873 Z= 0.223 Chirality : 0.041 0.138 2422 Planarity : 0.002 0.021 2457 Dihedral : 9.978 59.799 2730 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.14 % Allowed : 15.57 % Favored : 84.29 % 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: 2.24 (0.19), residues: 1813 helix: 2.97 (0.15), residues: 1008 sheet: -0.14 (0.27), residues: 294 loop : -0.62 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 240 PHE 0.010 0.001 PHE F 188 TYR 0.003 0.001 TYR G 250 ARG 0.004 0.000 ARG C 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 208 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 206 time to evaluate : 1.557 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 206 average time/residue: 0.3091 time to fit residues: 91.2022 Evaluate side-chains 207 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 1.545 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1259 time to fit residues: 2.5325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 21 optimal weight: 0.0040 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.154522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.111162 restraints weight = 15589.799| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.49 r_work: 0.3017 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1739 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= 0.157 Angle : 0.405 9.566 19873 Z= 0.213 Chirality : 0.040 0.137 2422 Planarity : 0.002 0.021 2457 Dihedral : 9.713 58.642 2730 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.14 % Allowed : 15.78 % Favored : 84.09 % 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: 2.25 (0.19), residues: 1813 helix: 2.98 (0.15), residues: 1008 sheet: -0.14 (0.26), residues: 294 loop : -0.62 (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 B 188 TYR 0.002 0.001 TYR F 250 ARG 0.004 0.000 ARG C 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3038.35 seconds wall clock time: 55 minutes 39.68 seconds (3339.68 seconds total)