Starting phenix.real_space_refine on Wed Feb 4 14:21:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i7t_52661/02_2026/9i7t_52661.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i7t_52661/02_2026/9i7t_52661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i7t_52661/02_2026/9i7t_52661.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i7t_52661/02_2026/9i7t_52661.map" model { file = "/net/cci-nas-00/data/ceres_data/9i7t_52661/02_2026/9i7t_52661.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i7t_52661/02_2026/9i7t_52661.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 sd= 0.049 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 11 5.49 5 S 34 5.16 5 C 7316 2.51 5 N 1817 2.21 5 O 2160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11338 Number of models: 1 Model: "" Number of chains: 20 Chain: "C" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 718 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "E" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 326 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "G" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 298 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "I" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 46} Chain: "K" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1093 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "A" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2466 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 305} Chain breaks: 1 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 718 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "F" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 326 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "H" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 298 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "J" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 46} Chain: "L" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1093 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "B" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2466 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 305} Chain breaks: 1 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'DU0': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'DU0': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 175 Unusual residues: {'DU0': 2, 'PC1': 2, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'DU0': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "H" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'DU0': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 133 Unusual residues: {'DU0': 2, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Time building chain proxies: 2.80, per 1000 atoms: 0.25 Number of scatterers: 11338 At special positions: 0 Unit cell: (149.823, 149.823, 108.81, 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 34 16.00 P 11 15.00 O 2160 8.00 N 1817 7.00 C 7316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 519.4 milliseconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2552 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 52.1% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 45 through 57 removed outlier: 3.578A pdb=" N LEU C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 117 Proline residue: C 100 - end of helix Processing helix chain 'E' and resid 11 through 50 Proline residue: E 40 - end of helix removed outlier: 3.964A pdb=" N PHE E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 26 removed outlier: 3.537A pdb=" N ASN G 22 " --> pdb=" O THR G 18 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 48 Processing helix chain 'G' and resid 49 through 56 removed outlier: 3.560A pdb=" N SER G 56 " --> pdb=" O GLU G 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 57 removed outlier: 5.490A pdb=" N LEU I 46 " --> pdb=" O HIS I 42 " (cutoff:3.500A) Proline residue: I 47 - end of helix Processing helix chain 'I' and resid 64 through 68 removed outlier: 3.636A pdb=" N LEU I 67 " --> pdb=" O ILE I 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 36 Processing helix chain 'K' and resid 36 through 80 Processing helix chain 'K' and resid 84 through 104 Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 108 through 123 Processing helix chain 'K' and resid 125 through 137 Processing helix chain 'K' and resid 138 through 152 Processing helix chain 'A' and resid 22 through 34 Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 45 through 57 removed outlier: 3.578A pdb=" N LEU D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL D 57 " --> pdb=" O LEU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 117 Proline residue: D 100 - end of helix Processing helix chain 'F' and resid 11 through 50 Proline residue: F 40 - end of helix removed outlier: 3.964A pdb=" N PHE F 50 " --> pdb=" O VAL F 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 26 removed outlier: 3.537A pdb=" N ASN H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 48 Processing helix chain 'H' and resid 49 through 56 removed outlier: 3.560A pdb=" N SER H 56 " --> pdb=" O GLU H 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 57 removed outlier: 5.490A pdb=" N LEU J 46 " --> pdb=" O HIS J 42 " (cutoff:3.500A) Proline residue: J 47 - end of helix Processing helix chain 'J' and resid 64 through 68 removed outlier: 3.636A pdb=" N LEU J 67 " --> pdb=" O ILE J 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 36 Processing helix chain 'L' and resid 36 through 80 Processing helix chain 'L' and resid 84 through 104 Processing helix chain 'L' and resid 105 through 107 No H-bonds generated for 'chain 'L' and resid 105 through 107' Processing helix chain 'L' and resid 108 through 123 Processing helix chain 'L' and resid 125 through 137 Processing helix chain 'L' and resid 138 through 152 Processing helix chain 'B' and resid 22 through 34 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 332 through 337 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 73 removed outlier: 6.406A pdb=" N PHE A 78 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE A 128 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA A 146 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 174 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 175 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 213 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 73 removed outlier: 6.406A pdb=" N PHE B 78 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE B 128 " --> pdb=" O TRP B 124 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA B 146 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR B 174 " --> pdb=" O PRO B 166 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 175 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 213 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) 812 hydrogen bonds defined for protein. 2370 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: 1.67 Time building geometry restraints manager: 1.16 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: 1826 1.32 - 1.44: 3030 1.44 - 1.56: 6635 1.56 - 1.68: 28 1.68 - 1.80: 64 Bond restraints: 11583 Sorted by residual: bond pdb=" CB PRO F 8 " pdb=" CG PRO F 8 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.80e+00 bond pdb=" CB PRO E 8 " pdb=" CG PRO E 8 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.80e+00 bond pdb=" CB PRO F 10 " pdb=" CG PRO F 10 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.24e+00 bond pdb=" CB PRO E 10 " pdb=" CG PRO E 10 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.24e+00 bond pdb=" CB ARG A 285 " pdb=" CG ARG A 285 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.92e+00 ... (remaining 11578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 15464 2.90 - 5.79: 225 5.79 - 8.69: 10 8.69 - 11.58: 0 11.58 - 14.48: 2 Bond angle restraints: 15701 Sorted by residual: angle pdb=" N GLY A 142 " pdb=" CA GLY A 142 " pdb=" C GLY A 142 " ideal model delta sigma weight residual 113.18 98.70 14.48 2.37e+00 1.78e-01 3.73e+01 angle pdb=" N GLY B 142 " pdb=" CA GLY B 142 " pdb=" C GLY B 142 " ideal model delta sigma weight residual 113.18 98.70 14.48 2.37e+00 1.78e-01 3.73e+01 angle pdb=" CA PRO F 40 " pdb=" N PRO F 40 " pdb=" CD PRO F 40 " ideal model delta sigma weight residual 112.00 107.49 4.51 1.40e+00 5.10e-01 1.04e+01 angle pdb=" CA PRO E 40 " pdb=" N PRO E 40 " pdb=" CD PRO E 40 " ideal model delta sigma weight residual 112.00 107.49 4.51 1.40e+00 5.10e-01 1.04e+01 angle pdb=" N ALA F 39 " pdb=" CA ALA F 39 " pdb=" C ALA F 39 " ideal model delta sigma weight residual 113.45 117.79 -4.34 1.39e+00 5.18e-01 9.73e+00 ... (remaining 15696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.30: 7238 26.30 - 52.60: 260 52.60 - 78.90: 58 78.90 - 105.20: 43 105.20 - 131.51: 22 Dihedral angle restraints: 7621 sinusoidal: 3667 harmonic: 3954 Sorted by residual: dihedral pdb=" C3 PLC A 404 " pdb=" C1 PLC A 404 " pdb=" C2 PLC A 404 " pdb=" O3P PLC A 404 " ideal model delta sinusoidal sigma weight residual 67.16 -64.35 131.51 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" O2 PLC A 404 " pdb=" C1 PLC A 404 " pdb=" C2 PLC A 404 " pdb=" O3P PLC A 404 " ideal model delta sinusoidal sigma weight residual 304.29 175.90 128.39 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C09 DU0 A 403 " pdb=" C11 DU0 A 403 " pdb=" O10 DU0 A 403 " pdb=" C12 DU0 A 403 " ideal model delta sinusoidal sigma weight residual 58.49 -62.93 121.42 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 7618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1250 0.045 - 0.090: 338 0.090 - 0.135: 115 0.135 - 0.181: 18 0.181 - 0.226: 6 Chirality restraints: 1727 Sorted by residual: chirality pdb=" CA PRO E 40 " pdb=" N PRO E 40 " pdb=" C PRO E 40 " pdb=" CB PRO E 40 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA PRO F 40 " pdb=" N PRO F 40 " pdb=" C PRO F 40 " pdb=" CB PRO F 40 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C22 DU0 G 101 " pdb=" C21 DU0 G 101 " pdb=" C75 DU0 G 101 " pdb=" O23 DU0 G 101 " both_signs ideal model delta sigma weight residual False 2.46 2.67 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1724 not shown) Planarity restraints: 1930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA F 39 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO F 40 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO F 40 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO F 40 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 39 " 0.074 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO E 40 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO E 40 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO E 40 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 11 " 0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO F 12 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO F 12 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO F 12 " 0.053 5.00e-02 4.00e+02 ... (remaining 1927 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 964 2.74 - 3.28: 10911 3.28 - 3.82: 17937 3.82 - 4.36: 20982 4.36 - 4.90: 37569 Nonbonded interactions: 88363 Sorted by model distance: nonbonded pdb=" NE2 GLN B 147 " pdb=" OE2 GLU B 149 " model vdw 2.194 3.120 nonbonded pdb=" NE2 GLN A 147 " pdb=" OE2 GLU A 149 " model vdw 2.194 3.120 nonbonded pdb=" O ALA E 29 " pdb=" OG1 THR E 32 " model vdw 2.234 3.040 nonbonded pdb=" O ALA F 29 " pdb=" OG1 THR F 32 " model vdw 2.234 3.040 nonbonded pdb=" NH2 ARG B 301 " pdb=" O ALA B 304 " model vdw 2.260 3.120 ... (remaining 88358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 21 through 403) selection = (chain 'B' and resid 21 through 403) } ncs_group { reference = (chain 'C' and (resid 28 through 118 or (resid 201 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C2A or name C3 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or n \ ame O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 \ or name P )))) selection = (chain 'D' and resid 28 through 201) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.750 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 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 : 0.007 0.084 11585 Z= 0.286 Angle : 0.837 14.476 15701 Z= 0.419 Chirality : 0.048 0.226 1727 Planarity : 0.009 0.110 1930 Dihedral : 17.422 131.505 5069 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.35 % Favored : 98.50 % Rotamer: Outliers : 0.18 % Allowed : 1.26 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.22), residues: 1330 helix: 1.60 (0.19), residues: 638 sheet: 1.02 (0.25), residues: 402 loop : -0.10 (0.40), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.003 ARG L 34 TYR 0.014 0.002 TYR B 93 PHE 0.014 0.002 PHE B 72 TRP 0.014 0.002 TRP D 88 HIS 0.005 0.002 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00653 (11583) covalent geometry : angle 0.83746 (15701) hydrogen bonds : bond 0.19988 ( 812) hydrogen bonds : angle 7.03319 ( 2370) Misc. bond : bond 0.00292 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 380 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 LYS cc_start: 0.8784 (mttt) cc_final: 0.8426 (tmtt) REVERT: E 28 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7309 (mmt180) REVERT: G 24 LEU cc_start: 0.8848 (tp) cc_final: 0.8585 (tt) REVERT: G 25 PHE cc_start: 0.8322 (m-80) cc_final: 0.8100 (t80) REVERT: I 68 SER cc_start: 0.7940 (m) cc_final: 0.7563 (p) REVERT: A 117 SER cc_start: 0.8954 (m) cc_final: 0.8598 (t) REVERT: A 168 PHE cc_start: 0.7994 (t80) cc_final: 0.7629 (t80) REVERT: A 198 GLN cc_start: 0.8793 (mt0) cc_final: 0.8546 (mt0) REVERT: D 78 LYS cc_start: 0.8783 (mttt) cc_final: 0.8424 (tmtt) REVERT: F 28 ARG cc_start: 0.8168 (mtt180) cc_final: 0.7311 (mmt180) REVERT: H 24 LEU cc_start: 0.8845 (tp) cc_final: 0.8584 (tt) REVERT: H 25 PHE cc_start: 0.8325 (m-80) cc_final: 0.8099 (t80) REVERT: J 68 SER cc_start: 0.7941 (m) cc_final: 0.7564 (p) REVERT: B 117 SER cc_start: 0.8950 (m) cc_final: 0.8594 (t) REVERT: B 168 PHE cc_start: 0.7995 (t80) cc_final: 0.7632 (t80) REVERT: B 198 GLN cc_start: 0.8789 (mt0) cc_final: 0.8542 (mt0) outliers start: 2 outliers final: 0 residues processed: 380 average time/residue: 0.1190 time to fit residues: 60.5025 Evaluate side-chains 230 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN I 27 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN A 228 GLN D 116 GLN J 27 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 GLN B 228 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.166402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.130216 restraints weight = 22295.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.126923 restraints weight = 23483.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.128851 restraints weight = 20019.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.131352 restraints weight = 12356.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.131663 restraints weight = 10252.926| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11585 Z= 0.197 Angle : 0.784 11.844 15701 Z= 0.385 Chirality : 0.046 0.217 1727 Planarity : 0.005 0.062 1930 Dihedral : 14.295 113.145 2581 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.44 % Allowed : 9.39 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.24), residues: 1330 helix: 2.23 (0.20), residues: 654 sheet: 1.13 (0.26), residues: 398 loop : 0.11 (0.43), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 62 TYR 0.026 0.002 TYR L 133 PHE 0.020 0.001 PHE L 116 TRP 0.011 0.001 TRP B 197 HIS 0.010 0.002 HIS L 109 Details of bonding type rmsd covalent geometry : bond 0.00423 (11583) covalent geometry : angle 0.78428 (15701) hydrogen bonds : bond 0.05158 ( 812) hydrogen bonds : angle 5.05941 ( 2370) Misc. bond : bond 0.00083 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 243 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 LYS cc_start: 0.8711 (mttt) cc_final: 0.8392 (tmtt) REVERT: E 28 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7217 (mmt180) REVERT: I 36 ILE cc_start: 0.8878 (pt) cc_final: 0.8397 (mm) REVERT: I 68 SER cc_start: 0.8241 (m) cc_final: 0.7828 (p) REVERT: K 133 TYR cc_start: 0.6762 (m-10) cc_final: 0.6270 (m-80) REVERT: A 25 TYR cc_start: 0.7187 (t80) cc_final: 0.6886 (t80) REVERT: A 117 SER cc_start: 0.8854 (m) cc_final: 0.8572 (t) REVERT: A 168 PHE cc_start: 0.7722 (t80) cc_final: 0.7303 (t80) REVERT: D 67 HIS cc_start: 0.8671 (t70) cc_final: 0.8470 (t-90) REVERT: D 78 LYS cc_start: 0.8704 (mttt) cc_final: 0.8387 (tmtt) REVERT: F 28 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7216 (mmt180) REVERT: J 36 ILE cc_start: 0.8866 (pt) cc_final: 0.8385 (mm) REVERT: J 68 SER cc_start: 0.8244 (m) cc_final: 0.7835 (p) REVERT: L 133 TYR cc_start: 0.6769 (m-10) cc_final: 0.6270 (m-80) REVERT: B 25 TYR cc_start: 0.7182 (t80) cc_final: 0.6885 (t80) REVERT: B 117 SER cc_start: 0.8830 (m) cc_final: 0.8553 (t) REVERT: B 168 PHE cc_start: 0.7727 (t80) cc_final: 0.7311 (t80) outliers start: 16 outliers final: 8 residues processed: 251 average time/residue: 0.1080 time to fit residues: 37.5318 Evaluate side-chains 214 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 206 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain B residue 203 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 0 optimal weight: 30.0000 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN A 230 GLN D 116 GLN B 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.164186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.128122 restraints weight = 22477.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.127625 restraints weight = 25798.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.129075 restraints weight = 23179.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.130029 restraints weight = 13402.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.131623 restraints weight = 11637.927| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11585 Z= 0.230 Angle : 0.746 9.510 15701 Z= 0.369 Chirality : 0.046 0.244 1727 Planarity : 0.005 0.042 1930 Dihedral : 12.793 111.685 2581 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.99 % Allowed : 11.19 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.24), residues: 1330 helix: 2.06 (0.20), residues: 662 sheet: 0.98 (0.25), residues: 402 loop : 0.19 (0.45), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 29 TYR 0.013 0.001 TYR B 25 PHE 0.022 0.002 PHE C 82 TRP 0.011 0.001 TRP A 197 HIS 0.007 0.001 HIS L 109 Details of bonding type rmsd covalent geometry : bond 0.00515 (11583) covalent geometry : angle 0.74642 (15701) hydrogen bonds : bond 0.04416 ( 812) hydrogen bonds : angle 4.79866 ( 2370) Misc. bond : bond 0.00294 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 LYS cc_start: 0.8721 (mttt) cc_final: 0.8428 (tmtt) REVERT: E 28 ARG cc_start: 0.7729 (mtt180) cc_final: 0.7423 (mmt180) REVERT: I 28 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: I 32 LYS cc_start: 0.8941 (mttt) cc_final: 0.8728 (tptt) REVERT: I 36 ILE cc_start: 0.8853 (pt) cc_final: 0.8552 (mm) REVERT: K 133 TYR cc_start: 0.6526 (m-10) cc_final: 0.5972 (m-80) REVERT: A 117 SER cc_start: 0.8784 (m) cc_final: 0.8555 (t) REVERT: A 168 PHE cc_start: 0.7692 (t80) cc_final: 0.7291 (t80) REVERT: D 78 LYS cc_start: 0.8707 (mttt) cc_final: 0.8410 (tmtt) REVERT: F 28 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7423 (mmt180) REVERT: J 28 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: J 32 LYS cc_start: 0.8939 (mttt) cc_final: 0.8725 (tptt) REVERT: J 36 ILE cc_start: 0.8850 (pt) cc_final: 0.8546 (mm) REVERT: L 133 TYR cc_start: 0.6543 (m-10) cc_final: 0.5988 (m-80) REVERT: B 117 SER cc_start: 0.8765 (m) cc_final: 0.8542 (t) REVERT: B 168 PHE cc_start: 0.7702 (t80) cc_final: 0.7307 (t80) outliers start: 22 outliers final: 14 residues processed: 228 average time/residue: 0.1097 time to fit residues: 34.1482 Evaluate side-chains 205 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 224 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 GLN K 46 ASN K 65 GLN A 344 ASN D 116 GLN L 46 ASN L 65 GLN B 344 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.163823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.127218 restraints weight = 22867.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.126990 restraints weight = 25386.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.128147 restraints weight = 22925.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.129495 restraints weight = 13319.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.130375 restraints weight = 11297.137| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11585 Z= 0.229 Angle : 0.741 12.191 15701 Z= 0.369 Chirality : 0.045 0.200 1727 Planarity : 0.005 0.041 1930 Dihedral : 12.647 108.822 2581 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.89 % Allowed : 14.80 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.24), residues: 1330 helix: 1.85 (0.19), residues: 662 sheet: 0.74 (0.25), residues: 402 loop : 0.06 (0.45), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 16 TYR 0.020 0.001 TYR B 25 PHE 0.019 0.002 PHE G 25 TRP 0.011 0.001 TRP A 197 HIS 0.003 0.001 HIS L 109 Details of bonding type rmsd covalent geometry : bond 0.00514 (11583) covalent geometry : angle 0.74064 (15701) hydrogen bonds : bond 0.04105 ( 812) hydrogen bonds : angle 4.73270 ( 2370) Misc. bond : bond 0.00224 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 LYS cc_start: 0.8722 (mttt) cc_final: 0.8390 (tmtt) REVERT: E 28 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7400 (mmt180) REVERT: I 28 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: I 32 LYS cc_start: 0.8940 (mttt) cc_final: 0.8689 (mttp) REVERT: I 36 ILE cc_start: 0.8961 (pt) cc_final: 0.8627 (mm) REVERT: A 60 MET cc_start: 0.8390 (tpp) cc_final: 0.7982 (mpp) REVERT: A 117 SER cc_start: 0.8761 (m) cc_final: 0.8542 (t) REVERT: A 168 PHE cc_start: 0.7727 (t80) cc_final: 0.7342 (t80) REVERT: D 78 LYS cc_start: 0.8710 (mttt) cc_final: 0.8386 (tmtt) REVERT: F 28 ARG cc_start: 0.7872 (mtt180) cc_final: 0.7399 (mmt180) REVERT: J 32 LYS cc_start: 0.8938 (mttt) cc_final: 0.8688 (mttp) REVERT: J 36 ILE cc_start: 0.8956 (pt) cc_final: 0.8622 (mm) REVERT: B 60 MET cc_start: 0.8395 (tpp) cc_final: 0.8018 (mpp) REVERT: B 117 SER cc_start: 0.8734 (m) cc_final: 0.8532 (t) REVERT: B 168 PHE cc_start: 0.7731 (t80) cc_final: 0.7346 (t80) outliers start: 32 outliers final: 24 residues processed: 230 average time/residue: 0.1095 time to fit residues: 34.6110 Evaluate side-chains 219 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain K residue 46 ASN Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain K residue 118 LYS Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain L residue 46 ASN Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 224 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 46 ASN ** K 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 ASN ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.165356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.128502 restraints weight = 22640.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.126685 restraints weight = 23308.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.127704 restraints weight = 21071.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.130443 restraints weight = 13546.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.130785 restraints weight = 9626.578| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11585 Z= 0.140 Angle : 0.698 12.547 15701 Z= 0.345 Chirality : 0.042 0.182 1727 Planarity : 0.005 0.051 1930 Dihedral : 12.089 104.864 2581 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.71 % Allowed : 14.80 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.24), residues: 1330 helix: 1.83 (0.20), residues: 658 sheet: 0.82 (0.25), residues: 400 loop : 0.04 (0.44), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 52 TYR 0.016 0.001 TYR L 133 PHE 0.021 0.001 PHE C 82 TRP 0.014 0.001 TRP A 197 HIS 0.001 0.000 HIS I 42 Details of bonding type rmsd covalent geometry : bond 0.00304 (11583) covalent geometry : angle 0.69806 (15701) hydrogen bonds : bond 0.03861 ( 812) hydrogen bonds : angle 4.54995 ( 2370) Misc. bond : bond 0.00075 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 MET cc_start: 0.7330 (ppp) cc_final: 0.7046 (ppp) REVERT: C 78 LYS cc_start: 0.8692 (mttt) cc_final: 0.8370 (tmtt) REVERT: E 28 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7319 (mmt180) REVERT: I 36 ILE cc_start: 0.8973 (pt) cc_final: 0.8659 (mm) REVERT: A 117 SER cc_start: 0.8717 (m) cc_final: 0.8473 (t) REVERT: A 168 PHE cc_start: 0.7755 (t80) cc_final: 0.7441 (t80) REVERT: A 183 GLN cc_start: 0.8337 (tp40) cc_final: 0.8087 (tm-30) REVERT: D 56 MET cc_start: 0.7328 (ppp) cc_final: 0.7046 (ppp) REVERT: D 78 LYS cc_start: 0.8679 (mttt) cc_final: 0.8363 (tmtt) REVERT: F 28 ARG cc_start: 0.7797 (mtt180) cc_final: 0.7323 (mmt180) REVERT: J 36 ILE cc_start: 0.8975 (pt) cc_final: 0.8660 (mm) REVERT: B 117 SER cc_start: 0.8696 (m) cc_final: 0.8469 (t) REVERT: B 168 PHE cc_start: 0.7754 (t80) cc_final: 0.7439 (t80) REVERT: B 183 GLN cc_start: 0.8325 (tp40) cc_final: 0.8077 (tm-30) outliers start: 30 outliers final: 18 residues processed: 223 average time/residue: 0.0921 time to fit residues: 29.6194 Evaluate side-chains 215 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 224 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 112 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4425 r_free = 0.4425 target = 0.164539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.128605 restraints weight = 22931.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.123596 restraints weight = 21865.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.125608 restraints weight = 20280.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.127771 restraints weight = 12519.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.128029 restraints weight = 10776.390| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11585 Z= 0.175 Angle : 0.726 13.668 15701 Z= 0.355 Chirality : 0.042 0.172 1727 Planarity : 0.005 0.051 1930 Dihedral : 11.893 102.110 2581 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.89 % Allowed : 16.16 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.24), residues: 1330 helix: 1.80 (0.20), residues: 658 sheet: 0.80 (0.25), residues: 400 loop : -0.05 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 16 TYR 0.016 0.001 TYR B 99 PHE 0.034 0.001 PHE H 25 TRP 0.013 0.001 TRP A 197 HIS 0.001 0.000 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00397 (11583) covalent geometry : angle 0.72634 (15701) hydrogen bonds : bond 0.03730 ( 812) hydrogen bonds : angle 4.53915 ( 2370) Misc. bond : bond 0.00125 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 56 MET cc_start: 0.7509 (ppp) cc_final: 0.7279 (ppp) REVERT: C 78 LYS cc_start: 0.8735 (mttt) cc_final: 0.8380 (tmtt) REVERT: E 28 ARG cc_start: 0.7968 (mtt180) cc_final: 0.7359 (mmt180) REVERT: I 36 ILE cc_start: 0.9010 (pt) cc_final: 0.8752 (mm) REVERT: I 54 TYR cc_start: 0.7682 (t80) cc_final: 0.7423 (t80) REVERT: A 117 SER cc_start: 0.8738 (m) cc_final: 0.8531 (t) REVERT: A 143 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7278 (mm-40) REVERT: A 168 PHE cc_start: 0.7821 (t80) cc_final: 0.7588 (t80) REVERT: D 56 MET cc_start: 0.7520 (ppp) cc_final: 0.7286 (ppp) REVERT: D 78 LYS cc_start: 0.8724 (mttt) cc_final: 0.8373 (tmtt) REVERT: F 28 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7357 (mmt180) REVERT: J 36 ILE cc_start: 0.9008 (pt) cc_final: 0.8750 (mm) REVERT: J 54 TYR cc_start: 0.7686 (t80) cc_final: 0.7426 (t80) REVERT: B 143 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7284 (mm-40) REVERT: B 168 PHE cc_start: 0.7829 (t80) cc_final: 0.7597 (t80) outliers start: 32 outliers final: 20 residues processed: 217 average time/residue: 0.1027 time to fit residues: 31.8780 Evaluate side-chains 209 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 224 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 8 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 105 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.165204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.128934 restraints weight = 22813.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.126829 restraints weight = 23783.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.128436 restraints weight = 21297.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.130639 restraints weight = 12879.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.130866 restraints weight = 10946.815| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11585 Z= 0.145 Angle : 0.710 14.654 15701 Z= 0.342 Chirality : 0.041 0.139 1727 Planarity : 0.005 0.044 1930 Dihedral : 11.531 98.376 2581 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.35 % Allowed : 16.06 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.23), residues: 1330 helix: 1.87 (0.20), residues: 658 sheet: 0.82 (0.25), residues: 400 loop : -0.06 (0.43), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 16 TYR 0.018 0.001 TYR L 133 PHE 0.027 0.001 PHE H 25 TRP 0.013 0.001 TRP A 197 HIS 0.001 0.000 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00325 (11583) covalent geometry : angle 0.71014 (15701) hydrogen bonds : bond 0.03517 ( 812) hydrogen bonds : angle 4.40328 ( 2370) Misc. bond : bond 0.00074 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 LYS cc_start: 0.8681 (mttt) cc_final: 0.8375 (tmtt) REVERT: E 28 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7320 (mmt180) REVERT: I 28 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: I 36 ILE cc_start: 0.8948 (pt) cc_final: 0.8674 (mm) REVERT: I 54 TYR cc_start: 0.7588 (t80) cc_final: 0.7339 (t80) REVERT: A 117 SER cc_start: 0.8760 (m) cc_final: 0.8540 (t) REVERT: A 143 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7235 (mm-40) REVERT: A 168 PHE cc_start: 0.7765 (t80) cc_final: 0.7537 (t80) REVERT: D 78 LYS cc_start: 0.8665 (mttt) cc_final: 0.8367 (tmtt) REVERT: F 28 ARG cc_start: 0.7813 (mtt180) cc_final: 0.7315 (mmt180) REVERT: J 28 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8118 (pm20) REVERT: J 36 ILE cc_start: 0.8948 (pt) cc_final: 0.8671 (mm) REVERT: J 54 TYR cc_start: 0.7596 (t80) cc_final: 0.7348 (t80) REVERT: B 143 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7240 (mm-40) REVERT: B 168 PHE cc_start: 0.7777 (t80) cc_final: 0.7561 (t80) outliers start: 26 outliers final: 18 residues processed: 209 average time/residue: 0.0960 time to fit residues: 29.1539 Evaluate side-chains 211 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 224 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.8980 chunk 67 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 27 GLN A 228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.164048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.127095 restraints weight = 22566.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.124674 restraints weight = 23030.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.126094 restraints weight = 21072.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.128582 restraints weight = 12803.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.128738 restraints weight = 10412.264| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11585 Z= 0.183 Angle : 0.742 14.266 15701 Z= 0.359 Chirality : 0.042 0.144 1727 Planarity : 0.005 0.043 1930 Dihedral : 11.474 95.407 2581 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.99 % Allowed : 16.52 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.24), residues: 1330 helix: 1.89 (0.20), residues: 656 sheet: 0.74 (0.25), residues: 400 loop : -0.10 (0.43), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 16 TYR 0.014 0.001 TYR A 99 PHE 0.020 0.001 PHE G 25 TRP 0.011 0.001 TRP A 197 HIS 0.002 0.000 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00419 (11583) covalent geometry : angle 0.74239 (15701) hydrogen bonds : bond 0.03512 ( 812) hydrogen bonds : angle 4.48897 ( 2370) Misc. bond : bond 0.00130 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 LYS cc_start: 0.8719 (mttt) cc_final: 0.8384 (tmtt) REVERT: E 28 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7392 (mmt180) REVERT: I 36 ILE cc_start: 0.8974 (pt) cc_final: 0.8697 (mm) REVERT: I 54 TYR cc_start: 0.7709 (t80) cc_final: 0.7453 (t80) REVERT: A 117 SER cc_start: 0.8788 (m) cc_final: 0.8577 (t) REVERT: A 143 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7359 (mm-40) REVERT: A 168 PHE cc_start: 0.7850 (t80) cc_final: 0.7633 (t80) REVERT: D 78 LYS cc_start: 0.8706 (mttt) cc_final: 0.8376 (tmtt) REVERT: F 28 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7395 (mmt180) REVERT: J 36 ILE cc_start: 0.8974 (pt) cc_final: 0.8686 (mm) REVERT: J 54 TYR cc_start: 0.7717 (t80) cc_final: 0.7460 (t80) REVERT: B 143 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7334 (mm-40) REVERT: B 168 PHE cc_start: 0.7858 (t80) cc_final: 0.7636 (t80) outliers start: 22 outliers final: 16 residues processed: 207 average time/residue: 0.1012 time to fit residues: 30.1137 Evaluate side-chains 206 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 224 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 GLN B 228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.159875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.108224 restraints weight = 22599.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.111379 restraints weight = 15992.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.111487 restraints weight = 11568.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.111722 restraints weight = 11390.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.111983 restraints weight = 10707.952| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 11585 Z= 0.352 Angle : 0.880 16.479 15701 Z= 0.433 Chirality : 0.049 0.231 1727 Planarity : 0.005 0.040 1930 Dihedral : 12.303 93.064 2581 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.62 % Allowed : 17.51 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.23), residues: 1330 helix: 1.63 (0.20), residues: 656 sheet: 0.36 (0.25), residues: 402 loop : -0.36 (0.42), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 16 TYR 0.014 0.002 TYR E 47 PHE 0.018 0.002 PHE G 25 TRP 0.008 0.002 TRP A 221 HIS 0.005 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00797 (11583) covalent geometry : angle 0.87983 (15701) hydrogen bonds : bond 0.03929 ( 812) hydrogen bonds : angle 4.94300 ( 2370) Misc. bond : bond 0.00363 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 LYS cc_start: 0.8796 (mttt) cc_final: 0.8381 (tmtt) REVERT: E 28 ARG cc_start: 0.8290 (mtt180) cc_final: 0.7482 (mmt180) REVERT: I 36 ILE cc_start: 0.9192 (pt) cc_final: 0.8954 (mm) REVERT: I 54 TYR cc_start: 0.8075 (t80) cc_final: 0.7846 (t80) REVERT: A 117 SER cc_start: 0.8844 (m) cc_final: 0.8466 (p) REVERT: D 78 LYS cc_start: 0.8796 (mttt) cc_final: 0.8374 (tmtt) REVERT: F 28 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7478 (mmt180) REVERT: J 32 LYS cc_start: 0.9215 (mttt) cc_final: 0.8894 (tptt) REVERT: J 36 ILE cc_start: 0.9206 (pt) cc_final: 0.8973 (mm) REVERT: J 54 TYR cc_start: 0.8058 (t80) cc_final: 0.7831 (t80) REVERT: B 143 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7372 (mm-40) outliers start: 18 outliers final: 17 residues processed: 199 average time/residue: 0.0979 time to fit residues: 28.3787 Evaluate side-chains 194 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 224 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 111 optimal weight: 0.1980 chunk 114 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN B 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.164929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.128501 restraints weight = 22730.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.124659 restraints weight = 24350.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.126981 restraints weight = 19791.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.128805 restraints weight = 12320.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.129200 restraints weight = 10952.885| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11585 Z= 0.149 Angle : 0.826 16.798 15701 Z= 0.402 Chirality : 0.045 0.255 1727 Planarity : 0.005 0.045 1930 Dihedral : 11.520 88.459 2581 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.62 % Allowed : 19.04 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1330 helix: 1.73 (0.20), residues: 658 sheet: 0.45 (0.25), residues: 402 loop : -0.16 (0.44), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 29 TYR 0.015 0.001 TYR A 99 PHE 0.017 0.001 PHE G 25 TRP 0.016 0.001 TRP A 197 HIS 0.001 0.000 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00340 (11583) covalent geometry : angle 0.82594 (15701) hydrogen bonds : bond 0.03623 ( 812) hydrogen bonds : angle 4.68577 ( 2370) Misc. bond : bond 0.00360 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 LYS cc_start: 0.8703 (mttt) cc_final: 0.8318 (tmtt) REVERT: E 28 ARG cc_start: 0.7906 (mtt180) cc_final: 0.7313 (mmt180) REVERT: I 32 LYS cc_start: 0.9004 (mttt) cc_final: 0.8768 (tptt) REVERT: I 36 ILE cc_start: 0.9014 (pt) cc_final: 0.8760 (mm) REVERT: I 54 TYR cc_start: 0.7624 (t80) cc_final: 0.7401 (t80) REVERT: A 117 SER cc_start: 0.8748 (m) cc_final: 0.8522 (t) REVERT: D 78 LYS cc_start: 0.8694 (mttt) cc_final: 0.8315 (tmtt) REVERT: F 28 ARG cc_start: 0.7878 (mtt180) cc_final: 0.7303 (mmt180) REVERT: J 32 LYS cc_start: 0.9050 (mttt) cc_final: 0.8829 (tptt) REVERT: J 36 ILE cc_start: 0.9026 (pt) cc_final: 0.8782 (mm) REVERT: J 54 TYR cc_start: 0.7632 (t80) cc_final: 0.7405 (t80) outliers start: 18 outliers final: 16 residues processed: 203 average time/residue: 0.0964 time to fit residues: 28.1290 Evaluate side-chains 193 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain K residue 117 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain L residue 117 TYR Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 224 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 34 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4435 r_free = 0.4435 target = 0.165468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.129981 restraints weight = 22649.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.127253 restraints weight = 25843.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.129003 restraints weight = 22257.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.131112 restraints weight = 13560.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.131410 restraints weight = 11219.427| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 11585 Z= 0.166 Angle : 0.879 16.491 15701 Z= 0.430 Chirality : 0.049 0.352 1727 Planarity : 0.005 0.043 1930 Dihedral : 11.296 84.135 2581 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.17 % Allowed : 18.50 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.23), residues: 1330 helix: 1.59 (0.20), residues: 660 sheet: 0.58 (0.25), residues: 400 loop : 0.04 (0.43), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 16 TYR 0.014 0.001 TYR A 99 PHE 0.011 0.001 PHE G 25 TRP 0.008 0.001 TRP B 197 HIS 0.001 0.000 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00388 (11583) covalent geometry : angle 0.87916 (15701) hydrogen bonds : bond 0.03661 ( 812) hydrogen bonds : angle 4.69454 ( 2370) Misc. bond : bond 0.01037 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1974.50 seconds wall clock time: 34 minutes 45.53 seconds (2085.53 seconds total)