Starting phenix.real_space_refine on Wed Jun 3 14:38:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zd5_74052/06_2026/9zd5_74052.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zd5_74052/06_2026/9zd5_74052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zd5_74052/06_2026/9zd5_74052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zd5_74052/06_2026/9zd5_74052.map" model { file = "/net/cci-nas-00/data/ceres_data/9zd5_74052/06_2026/9zd5_74052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zd5_74052/06_2026/9zd5_74052.cif" } resolution = 2.2 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= 0.000 sd= 0.004 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 8 5.49 5 S 24 5.16 5 C 4168 2.51 5 N 1000 2.21 5 O 1140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6340 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1467 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1467 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1467 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1467 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "I" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 118 Unusual residues: {'PLC': 1, 'PLM': 3, 'S1P': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 118 Unusual residues: {'PLC': 1, 'PLM': 3, 'S1P': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {'PLM': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 185 Unusual residues: {'PLC': 2, 'PLM': 3, 'S1P': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.92, per 1000 atoms: 0.30 Number of scatterers: 6340 At special positions: 0 Unit cell: (112.455, 84.133, 84.966, 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 24 16.00 P 8 15.00 O 1140 8.00 N 1000 7.00 C 4168 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 312.0 milliseconds 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 52.6% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'I' and resid 5 through 11 removed outlier: 3.524A pdb=" N UNK I 9 " --> pdb=" O UNK I 5 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N UNK I 11 " --> pdb=" O UNK I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 15 Processing helix chain 'I' and resid 28 through 45 Processing helix chain 'I' and resid 45 through 53 removed outlier: 3.673A pdb=" N ILE I 50 " --> pdb=" O PHE I 46 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TRP I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N MET I 52 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 135 Processing helix chain 'I' and resid 138 through 157 Processing helix chain 'I' and resid 159 through 166 Processing helix chain 'I' and resid 166 through 183 removed outlier: 3.732A pdb=" N THR I 177 " --> pdb=" O ASN I 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 12 Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 28 through 45 Processing helix chain 'E' and resid 45 through 53 removed outlier: 5.906A pdb=" N TRP E 51 " --> pdb=" O PRO E 47 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N MET E 52 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 135 Processing helix chain 'E' and resid 138 through 157 Processing helix chain 'E' and resid 159 through 166 Processing helix chain 'E' and resid 166 through 183 removed outlier: 3.756A pdb=" N THR E 177 " --> pdb=" O ASN E 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 11 Processing helix chain 'G' and resid 12 through 15 Processing helix chain 'G' and resid 28 through 45 Processing helix chain 'G' and resid 45 through 53 removed outlier: 5.779A pdb=" N TRP G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET G 52 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 135 Processing helix chain 'G' and resid 138 through 157 Processing helix chain 'G' and resid 159 through 166 Processing helix chain 'G' and resid 166 through 183 removed outlier: 3.694A pdb=" N THR G 177 " --> pdb=" O ASN G 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 12 Processing helix chain 'H' and resid 13 through 19 removed outlier: 3.585A pdb=" N UNK H 18 " --> pdb=" O UNK H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 45 Processing helix chain 'H' and resid 45 through 53 removed outlier: 5.505A pdb=" N TRP H 51 " --> pdb=" O PRO H 47 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N MET H 52 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 135 Processing helix chain 'H' and resid 138 through 158 Processing helix chain 'H' and resid 159 through 166 Processing helix chain 'H' and resid 166 through 183 removed outlier: 3.719A pdb=" N THR H 177 " --> pdb=" O ASN H 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 54 through 57 Processing sheet with id=AA2, first strand: chain 'I' and resid 61 through 66 Processing sheet with id=AA3, first strand: chain 'I' and resid 99 through 109 removed outlier: 3.788A pdb=" N GLY I 120 " --> pdb=" O ILE I 103 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL I 118 " --> pdb=" O PRO I 105 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLU I 107 " --> pdb=" O ILE I 116 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE I 116 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR I 115 " --> pdb=" O LYS I 198 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS I 198 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER I 117 " --> pdb=" O ASP I 196 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP I 196 " --> pdb=" O SER I 117 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP I 119 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE I 194 " --> pdb=" O ASP I 119 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL I 121 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL I 192 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR I 123 " --> pdb=" O GLU I 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AA5, first strand: chain 'E' and resid 61 through 66 Processing sheet with id=AA6, first strand: chain 'E' and resid 99 through 109 removed outlier: 3.802A pdb=" N GLY E 120 " --> pdb=" O ILE E 103 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL E 118 " --> pdb=" O PRO E 105 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLU E 107 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE E 116 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR E 115 " --> pdb=" O LYS E 198 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS E 198 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER E 117 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP E 196 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASP E 119 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE E 194 " --> pdb=" O ASP E 119 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL E 121 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL E 192 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR E 123 " --> pdb=" O GLU E 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'G' and resid 61 through 66 Processing sheet with id=AA9, first strand: chain 'G' and resid 99 through 109 removed outlier: 5.406A pdb=" N SER G 100 " --> pdb=" O TYR G 124 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR G 124 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ASP G 102 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL G 122 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY G 120 " --> pdb=" O PRO G 104 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR G 115 " --> pdb=" O LYS G 198 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS G 198 " --> pdb=" O THR G 115 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER G 117 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP G 196 " --> pdb=" O SER G 117 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP G 119 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE G 194 " --> pdb=" O ASP G 119 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL G 121 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL G 192 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR G 123 " --> pdb=" O GLU G 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 54 through 57 Processing sheet with id=AB2, first strand: chain 'H' and resid 61 through 66 Processing sheet with id=AB3, first strand: chain 'H' and resid 99 through 109 removed outlier: 3.755A pdb=" N GLY H 120 " --> pdb=" O ILE H 103 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL H 118 " --> pdb=" O PRO H 105 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU H 107 " --> pdb=" O ILE H 116 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE H 116 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR H 115 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS H 198 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER H 117 " --> pdb=" O ASP H 196 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASP H 196 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP H 119 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE H 194 " --> pdb=" O ASP H 119 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL H 121 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL H 192 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR H 123 " --> pdb=" O GLU H 190 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 855 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: 1.00 Time building geometry restraints manager: 0.78 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: 1059 1.32 - 1.44: 1456 1.44 - 1.56: 3853 1.56 - 1.68: 12 1.68 - 1.80: 36 Bond restraints: 6416 Sorted by residual: bond pdb=" O1 S1P H 307 " pdb=" P22 S1P H 307 " ideal model delta sigma weight residual 1.677 1.612 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O1 S1P E1005 " pdb=" P22 S1P E1005 " ideal model delta sigma weight residual 1.677 1.614 0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O1 S1P I1005 " pdb=" P22 S1P I1005 " ideal model delta sigma weight residual 1.677 1.614 0.063 2.00e-02 2.50e+03 9.96e+00 bond pdb=" O1 S1P H 306 " pdb=" P22 S1P H 306 " ideal model delta sigma weight residual 1.677 1.614 0.063 2.00e-02 2.50e+03 9.92e+00 bond pdb=" C6 S1P E1005 " pdb=" C7 S1P E1005 " ideal model delta sigma weight residual 1.540 1.493 0.047 2.00e-02 2.50e+03 5.52e+00 ... (remaining 6411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 8159 1.62 - 3.25: 325 3.25 - 4.87: 80 4.87 - 6.49: 17 6.49 - 8.11: 11 Bond angle restraints: 8592 Sorted by residual: angle pdb=" C LEU G 85 " pdb=" N PRO G 86 " pdb=" CA PRO G 86 " ideal model delta sigma weight residual 119.28 124.67 -5.39 1.10e+00 8.26e-01 2.40e+01 angle pdb=" C LEU E 85 " pdb=" N PRO E 86 " pdb=" CA PRO E 86 " ideal model delta sigma weight residual 119.47 124.70 -5.23 1.16e+00 7.43e-01 2.03e+01 angle pdb=" CA CYS G 53 " pdb=" C CYS G 53 " pdb=" O CYS G 53 " ideal model delta sigma weight residual 119.27 123.91 -4.64 1.17e+00 7.31e-01 1.57e+01 angle pdb=" CA CYS I 53 " pdb=" C CYS I 53 " pdb=" O CYS I 53 " ideal model delta sigma weight residual 119.60 123.94 -4.34 1.17e+00 7.31e-01 1.38e+01 angle pdb=" CA CYS H 87 " pdb=" C CYS H 87 " pdb=" O CYS H 87 " ideal model delta sigma weight residual 119.27 123.58 -4.31 1.17e+00 7.31e-01 1.36e+01 ... (remaining 8587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 3722 35.50 - 71.00: 228 71.00 - 106.51: 8 106.51 - 142.01: 25 142.01 - 177.51: 5 Dihedral angle restraints: 3988 sinusoidal: 1744 harmonic: 2244 Sorted by residual: dihedral pdb=" O2 PLC I1004 " pdb=" C1 PLC I1004 " pdb=" C2 PLC I1004 " pdb=" O3P PLC I1004 " ideal model delta sinusoidal sigma weight residual -55.71 121.80 -177.51 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PLC I1004 " pdb=" C1 PLC I1004 " pdb=" C2 PLC I1004 " pdb=" O3P PLC I1004 " ideal model delta sinusoidal sigma weight residual 67.16 -115.79 -177.05 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 PLC H 301 " pdb=" C1 PLC H 301 " pdb=" C2 PLC H 301 " pdb=" O3P PLC H 301 " ideal model delta sinusoidal sigma weight residual -55.71 121.31 -177.02 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 3985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 610 0.033 - 0.067: 228 0.067 - 0.100: 83 0.100 - 0.134: 68 0.134 - 0.167: 15 Chirality restraints: 1004 Sorted by residual: chirality pdb=" CA CYS I 30 " pdb=" N CYS I 30 " pdb=" C CYS I 30 " pdb=" CB CYS I 30 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA PHE E 46 " pdb=" N PHE E 46 " pdb=" C PHE E 46 " pdb=" CB PHE E 46 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA PHE H 46 " pdb=" N PHE H 46 " pdb=" C PHE H 46 " pdb=" CB PHE H 46 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 1001 not shown) Planarity restraints: 1028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 51 " -0.007 2.00e-02 2.50e+03 7.76e-03 1.51e+00 pdb=" CG TRP E 51 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP E 51 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP E 51 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 51 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 51 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 51 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 51 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 51 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 51 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 125 " 0.082 9.50e-02 1.11e+02 3.72e-02 1.05e+00 pdb=" NE ARG G 125 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG G 125 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG G 125 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 125 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 S1P H 306 " 0.010 2.00e-02 2.50e+03 9.56e-03 9.14e-01 pdb=" C4 S1P H 306 " -0.009 2.00e-02 2.50e+03 pdb=" C5 S1P H 306 " -0.010 2.00e-02 2.50e+03 pdb=" C6 S1P H 306 " 0.010 2.00e-02 2.50e+03 ... (remaining 1025 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 2923 2.97 - 3.46: 6213 3.46 - 3.94: 10599 3.94 - 4.42: 12023 4.42 - 4.90: 19352 Nonbonded interactions: 51110 Sorted by model distance: nonbonded pdb=" N GLU H 168 " pdb=" OE1 GLU H 168 " model vdw 2.492 3.120 nonbonded pdb=" N UNK G 15 " pdb=" N UNK G 16 " model vdw 2.496 2.560 nonbonded pdb=" N UNK E 15 " pdb=" N UNK E 16 " model vdw 2.512 2.560 nonbonded pdb=" N UNK I 15 " pdb=" N UNK I 16 " model vdw 2.522 2.560 nonbonded pdb=" N UNK G 18 " pdb=" N UNK G 19 " model vdw 2.560 2.560 ... (remaining 51105 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 'E' and (resid 5 through 200 or resid 1003)) selection = (chain 'G' and (resid 5 through 200 or resid 1003)) selection = (chain 'H' and (resid 5 through 200 or resid 303)) selection = (chain 'I' and (resid 5 through 200 or resid 1003)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.000 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.170 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:8.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 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 : 0.006 0.065 6428 Z= 0.310 Angle : 0.820 8.113 8592 Z= 0.441 Chirality : 0.050 0.167 1004 Planarity : 0.003 0.037 1028 Dihedral : 24.211 177.509 2524 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.27 % Allowed : 24.02 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.30), residues: 696 helix: 0.94 (0.30), residues: 308 sheet: 0.67 (0.35), residues: 164 loop : -0.19 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 125 TYR 0.007 0.001 TYR H 123 PHE 0.014 0.002 PHE G 101 TRP 0.021 0.002 TRP E 51 HIS 0.003 0.001 HIS I 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.27 ( 6416) covalent geometry : angle 0.81964 / 0.44 ( 8592) hydrogen bonds : bond 0.11268 / 7.26 ( 301) hydrogen bonds : angle 6.38501 / 4.37 ( 855) Misc. bond : bond 0.03392 / 1.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 166 average time/residue: 0.6750 time to fit residues: 116.4706 Evaluate side-chains 74 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 173 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 159 ASN G 138 ASN H 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.213394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.135450 restraints weight = 10674.191| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 4.42 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 6428 Z= 0.357 Angle : 0.790 9.312 8592 Z= 0.386 Chirality : 0.054 0.209 1004 Planarity : 0.005 0.050 1028 Dihedral : 23.934 178.975 1227 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.76 % Allowed : 27.78 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.31), residues: 696 helix: 1.07 (0.30), residues: 308 sheet: 0.20 (0.33), residues: 192 loop : -0.11 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 191 TYR 0.015 0.002 TYR E 60 PHE 0.022 0.003 PHE E 82 TRP 0.017 0.002 TRP G 51 HIS 0.001 0.000 HIS E 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00845 / 0.36 ( 6416) covalent geometry : angle 0.79008 / 0.39 ( 8592) hydrogen bonds : bond 0.04070 / 2.55 ( 301) hydrogen bonds : angle 4.92899 / 3.33 ( 855) Misc. bond : bond 0.00122 / 0.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 179 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7895 (p0) REVERT: G 50 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9103 (pp) REVERT: G 55 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8524 (mmmt) REVERT: G 67 ARG cc_start: 0.7554 (tpp80) cc_final: 0.7230 (tpp80) REVERT: G 93 LYS cc_start: 0.8791 (tptt) cc_final: 0.8517 (tptm) REVERT: G 107 GLU cc_start: 0.8782 (mp0) cc_final: 0.8346 (mp0) REVERT: H 41 PHE cc_start: 0.9242 (t80) cc_final: 0.8884 (t80) REVERT: H 101 PHE cc_start: 0.7280 (t80) cc_final: 0.7056 (t80) REVERT: H 107 GLU cc_start: 0.5111 (pm20) cc_final: 0.4224 (tm-30) outliers start: 23 outliers final: 11 residues processed: 112 average time/residue: 0.6802 time to fit residues: 79.3677 Evaluate side-chains 81 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 165 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 19 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 53 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 106 GLN G 173 ASN H 159 ASN ** H 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.214494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.138953 restraints weight = 10377.458| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 4.36 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6428 Z= 0.188 Angle : 0.629 7.496 8592 Z= 0.313 Chirality : 0.049 0.175 1004 Planarity : 0.004 0.041 1028 Dihedral : 21.376 174.805 1220 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.92 % Allowed : 28.59 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.31), residues: 696 helix: 1.09 (0.30), residues: 308 sheet: 0.39 (0.34), residues: 192 loop : -0.01 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 144 TYR 0.011 0.001 TYR E 60 PHE 0.013 0.002 PHE E 91 TRP 0.011 0.001 TRP I 51 HIS 0.002 0.001 HIS E 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 6416) covalent geometry : angle 0.62855 / 0.31 ( 8592) hydrogen bonds : bond 0.03499 / 2.20 ( 301) hydrogen bonds : angle 4.77683 / 3.21 ( 855) Misc. bond : bond 0.00064 / 0.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 106 GLN cc_start: 0.3239 (OUTLIER) cc_final: 0.2709 (tt0) REVERT: I 188 LYS cc_start: 0.8661 (tptp) cc_final: 0.8363 (tptp) REVERT: G 27 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7641 (tp) REVERT: G 32 TRP cc_start: 0.7725 (m100) cc_final: 0.7348 (m100) REVERT: G 55 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8426 (mmpt) REVERT: G 67 ARG cc_start: 0.7427 (tpp80) cc_final: 0.6990 (tpp80) REVERT: G 83 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.6508 (p90) REVERT: G 93 LYS cc_start: 0.8873 (tptt) cc_final: 0.8614 (tptp) REVERT: G 101 PHE cc_start: 0.6305 (t80) cc_final: 0.5968 (t80) REVERT: G 138 ASN cc_start: 0.7755 (t0) cc_final: 0.7101 (t0) REVERT: G 144 ARG cc_start: 0.8053 (ptp-110) cc_final: 0.7794 (ptp-110) REVERT: G 160 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6366 (mp) REVERT: H 41 PHE cc_start: 0.9305 (t80) cc_final: 0.8953 (t80) REVERT: H 52 MET cc_start: 0.8786 (mpm) cc_final: 0.8567 (mpm) REVERT: H 55 LYS cc_start: 0.7058 (mmmt) cc_final: 0.6436 (mmmm) REVERT: H 107 GLU cc_start: 0.5071 (pm20) cc_final: 0.4295 (tm-30) outliers start: 24 outliers final: 11 residues processed: 100 average time/residue: 0.6449 time to fit residues: 67.1598 Evaluate side-chains 84 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 106 GLN Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 165 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 159 ASN H 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.214078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.137515 restraints weight = 10483.407| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 4.43 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6428 Z= 0.195 Angle : 0.629 7.598 8592 Z= 0.313 Chirality : 0.049 0.186 1004 Planarity : 0.004 0.029 1028 Dihedral : 20.449 174.236 1217 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.58 % Allowed : 27.78 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.78 (0.31), residues: 696 helix: 1.17 (0.30), residues: 308 sheet: 0.34 (0.35), residues: 192 loop : -0.11 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 144 TYR 0.011 0.001 TYR E 60 PHE 0.014 0.001 PHE E 91 TRP 0.010 0.001 TRP I 32 HIS 0.001 0.000 HIS H 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 6416) covalent geometry : angle 0.62901 / 0.31 ( 8592) hydrogen bonds : bond 0.03305 / 2.09 ( 301) hydrogen bonds : angle 4.63389 / 3.10 ( 855) Misc. bond : bond 0.00066 / 0.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 136 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8815 (tp) REVERT: E 174 MET cc_start: 0.8545 (mmm) cc_final: 0.8218 (mmt) REVERT: E 188 LYS cc_start: 0.9233 (tppp) cc_final: 0.8744 (tptp) REVERT: G 27 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7646 (tp) REVERT: G 32 TRP cc_start: 0.7766 (m100) cc_final: 0.7320 (m100) REVERT: G 52 MET cc_start: 0.8991 (mpp) cc_final: 0.8790 (mmm) REVERT: G 67 ARG cc_start: 0.7479 (tpp80) cc_final: 0.6959 (tpp80) REVERT: G 83 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6559 (p90) REVERT: G 93 LYS cc_start: 0.8882 (tptt) cc_final: 0.8631 (tptp) REVERT: G 101 PHE cc_start: 0.6462 (t80) cc_final: 0.6045 (t80) REVERT: G 107 GLU cc_start: 0.8572 (mp0) cc_final: 0.8150 (tp30) REVERT: G 138 ASN cc_start: 0.7568 (t0) cc_final: 0.7296 (t0) REVERT: G 160 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6287 (mp) REVERT: G 188 LYS cc_start: 0.8877 (tppp) cc_final: 0.8664 (mmmm) REVERT: H 41 PHE cc_start: 0.9317 (t80) cc_final: 0.8955 (t80) REVERT: H 52 MET cc_start: 0.8825 (mpm) cc_final: 0.8566 (mpm) REVERT: H 55 LYS cc_start: 0.7041 (mmmt) cc_final: 0.6285 (mmmm) REVERT: H 107 GLU cc_start: 0.5223 (pm20) cc_final: 0.4417 (tm-30) REVERT: H 195 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7794 (mmmm) outliers start: 28 outliers final: 16 residues processed: 105 average time/residue: 0.6059 time to fit residues: 66.5212 Evaluate side-chains 90 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 123 TYR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 165 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 53 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 67 optimal weight: 0.0060 chunk 47 optimal weight: 0.4980 chunk 44 optimal weight: 0.0070 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 106 GLN G 173 ASN H 159 ASN H 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.216495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.142917 restraints weight = 10779.426| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 4.42 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6428 Z= 0.118 Angle : 0.575 7.843 8592 Z= 0.290 Chirality : 0.047 0.172 1004 Planarity : 0.003 0.038 1028 Dihedral : 19.378 171.922 1217 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.41 % Allowed : 27.61 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.87 (0.31), residues: 696 helix: 1.20 (0.30), residues: 308 sheet: 0.43 (0.35), residues: 192 loop : -0.06 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 144 TYR 0.005 0.001 TYR E 60 PHE 0.031 0.001 PHE I 46 TRP 0.009 0.001 TRP H 51 HIS 0.001 0.000 HIS G 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 6416) covalent geometry : angle 0.57456 / 0.29 ( 8592) hydrogen bonds : bond 0.02939 / 1.86 ( 301) hydrogen bonds : angle 4.52247 / 3.04 ( 855) Misc. bond : bond 0.00027 / 0.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 106 GLN cc_start: 0.2984 (OUTLIER) cc_final: 0.2448 (tt0) REVERT: I 193 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7358 (tt0) REVERT: G 27 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7718 (tp) REVERT: G 32 TRP cc_start: 0.7693 (m100) cc_final: 0.7201 (m100) REVERT: G 52 MET cc_start: 0.8998 (mpp) cc_final: 0.8586 (mmp) REVERT: G 55 LYS cc_start: 0.8668 (mmpt) cc_final: 0.8335 (mmmt) REVERT: G 67 ARG cc_start: 0.7348 (tpp80) cc_final: 0.6852 (tpp80) REVERT: G 101 PHE cc_start: 0.6639 (t80) cc_final: 0.6419 (t80) REVERT: G 107 GLU cc_start: 0.8583 (mp0) cc_final: 0.8229 (tp30) REVERT: G 160 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6338 (mp) REVERT: G 198 LYS cc_start: 0.4988 (mmtt) cc_final: 0.4747 (mppt) REVERT: H 41 PHE cc_start: 0.9353 (t80) cc_final: 0.8976 (t80) REVERT: H 52 MET cc_start: 0.8793 (mpm) cc_final: 0.8559 (mpm) REVERT: H 55 LYS cc_start: 0.7027 (mmmt) cc_final: 0.6535 (mmmm) REVERT: H 101 PHE cc_start: 0.8093 (t80) cc_final: 0.7807 (t80) REVERT: H 107 GLU cc_start: 0.5008 (pm20) cc_final: 0.4222 (tm-30) REVERT: H 173 ASN cc_start: 0.9315 (t0) cc_final: 0.9079 (p0) REVERT: H 195 LYS cc_start: 0.8119 (ttpp) cc_final: 0.7763 (mmmm) outliers start: 27 outliers final: 12 residues processed: 103 average time/residue: 0.6483 time to fit residues: 69.6522 Evaluate side-chains 86 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 106 GLN Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 123 TYR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 165 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 42 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.215327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.138764 restraints weight = 10603.073| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 4.51 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6428 Z= 0.155 Angle : 0.619 7.714 8592 Z= 0.309 Chirality : 0.048 0.184 1004 Planarity : 0.004 0.032 1028 Dihedral : 18.826 169.952 1216 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.25 % Allowed : 27.61 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.83 (0.32), residues: 696 helix: 1.19 (0.30), residues: 308 sheet: 0.38 (0.35), residues: 192 loop : -0.07 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 144 TYR 0.009 0.001 TYR E 60 PHE 0.028 0.002 PHE I 46 TRP 0.008 0.001 TRP I 32 HIS 0.001 0.000 HIS G 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 6416) covalent geometry : angle 0.61880 / 0.31 ( 8592) hydrogen bonds : bond 0.02993 / 1.91 ( 301) hydrogen bonds : angle 4.46756 / 3.01 ( 855) Misc. bond : bond 0.00047 / 0.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.443 Fit side-chains REVERT: E 107 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6563 (pp20) REVERT: E 136 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8830 (tp) REVERT: E 174 MET cc_start: 0.8598 (mmm) cc_final: 0.8385 (mmt) REVERT: E 188 LYS cc_start: 0.9246 (tppp) cc_final: 0.8807 (tptp) REVERT: G 27 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7733 (tp) REVERT: G 32 TRP cc_start: 0.7679 (m100) cc_final: 0.7152 (m100) REVERT: G 52 MET cc_start: 0.9016 (mpp) cc_final: 0.8802 (mpp) REVERT: G 55 LYS cc_start: 0.8570 (mmpt) cc_final: 0.8363 (mmmt) REVERT: G 67 ARG cc_start: 0.7396 (tpp80) cc_final: 0.6975 (tpp80) REVERT: G 83 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.6734 (p90) REVERT: G 107 GLU cc_start: 0.8493 (mp0) cc_final: 0.8233 (tp30) REVERT: G 160 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6379 (mp) REVERT: H 41 PHE cc_start: 0.9395 (t80) cc_final: 0.9016 (t80) REVERT: H 55 LYS cc_start: 0.7028 (mmmt) cc_final: 0.6532 (mmmm) REVERT: H 101 PHE cc_start: 0.8141 (t80) cc_final: 0.7843 (t80) REVERT: H 107 GLU cc_start: 0.5074 (pm20) cc_final: 0.4230 (tm-30) REVERT: H 195 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7921 (mmmm) outliers start: 26 outliers final: 16 residues processed: 96 average time/residue: 0.6257 time to fit residues: 62.7607 Evaluate side-chains 88 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain H residue 165 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 64 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.212309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.135612 restraints weight = 10479.693| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 4.35 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 6428 Z= 0.318 Angle : 0.749 9.205 8592 Z= 0.366 Chirality : 0.051 0.228 1004 Planarity : 0.004 0.040 1028 Dihedral : 19.049 167.981 1216 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.27 % Allowed : 28.92 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.64 (0.31), residues: 696 helix: 1.09 (0.31), residues: 308 sheet: 0.25 (0.35), residues: 192 loop : -0.24 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 152 TYR 0.017 0.002 TYR E 60 PHE 0.037 0.002 PHE I 46 TRP 0.022 0.002 TRP I 32 HIS 0.002 0.001 HIS H 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.32 ( 6416) covalent geometry : angle 0.74888 / 0.37 ( 8592) hydrogen bonds : bond 0.03337 / 2.10 ( 301) hydrogen bonds : angle 4.57354 / 3.09 ( 855) Misc. bond : bond 0.00107 / 0.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.255 Fit side-chains REVERT: I 193 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7381 (tt0) REVERT: E 25 LYS cc_start: 0.7965 (tmmm) cc_final: 0.7432 (ttmm) REVERT: E 107 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6607 (pp20) REVERT: E 174 MET cc_start: 0.8638 (mmm) cc_final: 0.8361 (mmt) REVERT: E 193 GLU cc_start: 0.6619 (pm20) cc_final: 0.5101 (pp20) REVERT: G 32 TRP cc_start: 0.7702 (m100) cc_final: 0.7400 (m100) REVERT: G 52 MET cc_start: 0.9007 (mpp) cc_final: 0.8764 (mmp) REVERT: G 67 ARG cc_start: 0.7520 (tpp80) cc_final: 0.7080 (tpp80) REVERT: G 83 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.6741 (p90) REVERT: G 107 GLU cc_start: 0.8515 (mp0) cc_final: 0.8148 (tp30) REVERT: G 160 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6423 (mp) REVERT: G 198 LYS cc_start: 0.4016 (mmtt) cc_final: 0.3727 (mptt) REVERT: H 41 PHE cc_start: 0.9414 (t80) cc_final: 0.9034 (t80) REVERT: H 52 MET cc_start: 0.8747 (mpm) cc_final: 0.8440 (mpm) REVERT: H 55 LYS cc_start: 0.7046 (mmmt) cc_final: 0.6478 (mmmm) REVERT: H 195 LYS cc_start: 0.8291 (ttpp) cc_final: 0.7946 (mmmm) outliers start: 20 outliers final: 14 residues processed: 96 average time/residue: 0.6705 time to fit residues: 67.1989 Evaluate side-chains 86 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 165 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 53 optimal weight: 0.0970 chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 59 optimal weight: 40.0000 chunk 69 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 106 GLN ** G 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.214832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.140794 restraints weight = 10526.050| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 4.26 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6428 Z= 0.152 Angle : 0.667 10.256 8592 Z= 0.332 Chirality : 0.048 0.198 1004 Planarity : 0.004 0.055 1028 Dihedral : 18.290 166.129 1216 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.27 % Allowed : 29.74 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.31), residues: 696 helix: 1.13 (0.31), residues: 308 sheet: 0.58 (0.37), residues: 172 loop : -0.29 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 144 TYR 0.008 0.001 TYR E 60 PHE 0.034 0.002 PHE I 46 TRP 0.030 0.002 TRP G 51 HIS 0.001 0.000 HIS H 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 6416) covalent geometry : angle 0.66713 / 0.33 ( 8592) hydrogen bonds : bond 0.02981 / 1.90 ( 301) hydrogen bonds : angle 4.47907 / 3.00 ( 855) Misc. bond : bond 0.00036 / 0.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: I 106 GLN cc_start: 0.3061 (OUTLIER) cc_final: 0.2701 (tt0) REVERT: I 193 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7209 (tt0) REVERT: E 25 LYS cc_start: 0.8021 (tmmm) cc_final: 0.7585 (ttmm) REVERT: E 107 GLU cc_start: 0.7070 (tm-30) cc_final: 0.6744 (pp20) REVERT: E 174 MET cc_start: 0.8601 (mmm) cc_final: 0.8342 (mmt) REVERT: E 188 LYS cc_start: 0.9232 (tppp) cc_final: 0.8824 (tptp) REVERT: E 193 GLU cc_start: 0.6557 (pm20) cc_final: 0.5264 (pp20) REVERT: G 52 MET cc_start: 0.9020 (mpp) cc_final: 0.8812 (mpp) REVERT: G 67 ARG cc_start: 0.7360 (tpp80) cc_final: 0.6937 (tpp80) REVERT: G 107 GLU cc_start: 0.8559 (mp0) cc_final: 0.8291 (tm-30) REVERT: G 160 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6414 (mp) REVERT: G 198 LYS cc_start: 0.4033 (mmtt) cc_final: 0.3742 (mptt) REVERT: H 41 PHE cc_start: 0.9408 (t80) cc_final: 0.9026 (t80) REVERT: H 52 MET cc_start: 0.8758 (mpm) cc_final: 0.8445 (mpm) REVERT: H 55 LYS cc_start: 0.7048 (mmmt) cc_final: 0.6465 (mmmm) REVERT: H 107 GLU cc_start: 0.4698 (pm20) cc_final: 0.3349 (tm-30) REVERT: H 195 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7974 (mmmm) outliers start: 20 outliers final: 13 residues processed: 96 average time/residue: 0.6579 time to fit residues: 65.9012 Evaluate side-chains 88 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 106 GLN Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 165 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 66 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 0.0170 chunk 36 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.213551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.136528 restraints weight = 10667.893| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 4.48 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6428 Z= 0.198 Angle : 0.717 12.048 8592 Z= 0.355 Chirality : 0.049 0.224 1004 Planarity : 0.004 0.035 1028 Dihedral : 18.156 163.172 1216 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.45 % Allowed : 30.56 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.32), residues: 696 helix: 1.17 (0.31), residues: 308 sheet: 0.25 (0.36), residues: 192 loop : -0.20 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 152 TYR 0.012 0.001 TYR E 60 PHE 0.037 0.002 PHE I 46 TRP 0.033 0.002 TRP G 51 HIS 0.001 0.000 HIS H 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 ( 6416) covalent geometry : angle 0.71727 / 0.35 ( 8592) hydrogen bonds : bond 0.03066 / 1.94 ( 301) hydrogen bonds : angle 4.45836 / 2.99 ( 855) Misc. bond : bond 0.00052 / 0.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 166 ASP cc_start: 0.8148 (m-30) cc_final: 0.7926 (m-30) REVERT: I 193 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7167 (tt0) REVERT: E 25 LYS cc_start: 0.8032 (tmmm) cc_final: 0.7673 (ttmm) REVERT: E 169 GLU cc_start: 0.8302 (pm20) cc_final: 0.7887 (pm20) REVERT: E 188 LYS cc_start: 0.9272 (tppp) cc_final: 0.8868 (tptp) REVERT: G 52 MET cc_start: 0.9036 (mpp) cc_final: 0.8820 (mpp) REVERT: G 67 ARG cc_start: 0.7456 (tpp80) cc_final: 0.7032 (tpp80) REVERT: G 93 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8492 (tptt) REVERT: G 107 GLU cc_start: 0.8584 (mp0) cc_final: 0.8231 (tm-30) REVERT: G 160 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6439 (mp) REVERT: G 198 LYS cc_start: 0.4033 (mmtt) cc_final: 0.3742 (mptt) REVERT: H 41 PHE cc_start: 0.9424 (t80) cc_final: 0.9040 (t80) REVERT: H 52 MET cc_start: 0.8762 (mpm) cc_final: 0.8494 (mpm) REVERT: H 55 LYS cc_start: 0.7063 (mmmt) cc_final: 0.6476 (mmmm) REVERT: H 107 GLU cc_start: 0.4649 (pm20) cc_final: 0.3222 (tm-30) REVERT: H 195 LYS cc_start: 0.8293 (ttpp) cc_final: 0.8052 (mmmm) outliers start: 15 outliers final: 12 residues processed: 94 average time/residue: 0.6519 time to fit residues: 63.8505 Evaluate side-chains 88 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 165 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 31 optimal weight: 0.0970 chunk 41 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 30.0000 chunk 37 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.213619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.136341 restraints weight = 10561.106| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 4.46 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6428 Z= 0.215 Angle : 0.736 12.868 8592 Z= 0.362 Chirality : 0.049 0.221 1004 Planarity : 0.004 0.039 1028 Dihedral : 18.087 162.830 1216 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.78 % Allowed : 31.05 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.32), residues: 696 helix: 1.08 (0.31), residues: 308 sheet: 0.39 (0.37), residues: 172 loop : -0.30 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 152 TYR 0.012 0.001 TYR E 60 PHE 0.036 0.002 PHE I 46 TRP 0.034 0.002 TRP G 51 HIS 0.001 0.000 HIS H 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 ( 6416) covalent geometry : angle 0.73563 / 0.36 ( 8592) hydrogen bonds : bond 0.03124 / 1.96 ( 301) hydrogen bonds : angle 4.48288 / 3.00 ( 855) Misc. bond : bond 0.00050 / 0.03 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1392 Ramachandran restraints generated. 696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 166 ASP cc_start: 0.8122 (m-30) cc_final: 0.7899 (m-30) REVERT: I 193 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7152 (tt0) REVERT: E 25 LYS cc_start: 0.8059 (tmmm) cc_final: 0.7741 (ttmm) REVERT: E 101 PHE cc_start: 0.7935 (t80) cc_final: 0.7493 (t80) REVERT: E 102 ASP cc_start: 0.8639 (p0) cc_final: 0.8340 (p0) REVERT: E 188 LYS cc_start: 0.9244 (tppp) cc_final: 0.8806 (tptp) REVERT: E 193 GLU cc_start: 0.6542 (pm20) cc_final: 0.5193 (pp20) REVERT: G 52 MET cc_start: 0.9086 (mpp) cc_final: 0.8885 (mpp) REVERT: G 67 ARG cc_start: 0.7490 (tpp80) cc_final: 0.7069 (tpp80) REVERT: G 160 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6433 (mp) REVERT: G 198 LYS cc_start: 0.4018 (mmtt) cc_final: 0.3812 (mptp) REVERT: H 41 PHE cc_start: 0.9426 (t80) cc_final: 0.9043 (t80) REVERT: H 52 MET cc_start: 0.8732 (mpm) cc_final: 0.8428 (mpm) REVERT: H 55 LYS cc_start: 0.7104 (mmmt) cc_final: 0.6468 (mmmm) REVERT: H 107 GLU cc_start: 0.4574 (pm20) cc_final: 0.3203 (tm-30) REVERT: H 174 MET cc_start: 0.7782 (mmp) cc_final: 0.7527 (mmm) outliers start: 17 outliers final: 12 residues processed: 88 average time/residue: 0.5942 time to fit residues: 54.7784 Evaluate side-chains 81 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 165 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 26 optimal weight: 0.5980 chunk 69 optimal weight: 0.0070 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.215197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.140391 restraints weight = 10498.257| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 4.37 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6428 Z= 0.148 Angle : 0.694 13.210 8592 Z= 0.345 Chirality : 0.048 0.217 1004 Planarity : 0.004 0.033 1028 Dihedral : 17.638 163.480 1216 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.29 % Allowed : 31.86 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.32), residues: 696 helix: 1.11 (0.31), residues: 308 sheet: 0.38 (0.39), residues: 172 loop : -0.33 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 152 TYR 0.008 0.001 TYR H 123 PHE 0.038 0.002 PHE I 46 TRP 0.033 0.002 TRP G 51 HIS 0.002 0.001 HIS E 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 6416) covalent geometry : angle 0.69425 / 0.35 ( 8592) hydrogen bonds : bond 0.02982 / 1.85 ( 301) hydrogen bonds : angle 4.43902 / 2.95 ( 855) Misc. bond : bond 0.00028 / 0.01 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4108.57 seconds wall clock time: 71 minutes 7.91 seconds (4267.91 seconds total)