Starting phenix.real_space_refine on Wed Mar 4 03:07:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ckx_16705/03_2026/8ckx_16705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ckx_16705/03_2026/8ckx_16705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ckx_16705/03_2026/8ckx_16705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ckx_16705/03_2026/8ckx_16705.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ckx_16705/03_2026/8ckx_16705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ckx_16705/03_2026/8ckx_16705.map" } resolution = 2.97 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= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 726 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 6224 2.51 5 N 1709 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9857 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1650 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1641 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1649 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1637 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1637 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1643 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 2.40, per 1000 atoms: 0.24 Number of scatterers: 9857 At special positions: 0 Unit cell: (113.46, 109.74, 77.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 1853 8.00 N 1709 7.00 C 6224 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=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 501.2 milliseconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 6 sheets defined 73.0% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.562A pdb=" N LYS A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 173 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.292A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'B' and resid 16 through 31 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 176 removed outlier: 3.560A pdb=" N ALA B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.246A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 125 through 146 removed outlier: 3.600A pdb=" N MET C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.793A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.207A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 119 Processing helix chain 'D' and resid 125 through 146 removed outlier: 3.619A pdb=" N LYS D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.736A pdb=" N ALA D 174 " --> pdb=" O LYS D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.368A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 146 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 174 removed outlier: 3.916A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.190A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'F' and resid 16 through 31 Processing helix chain 'F' and resid 35 through 43 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 175 removed outlier: 3.864A pdb=" N ALA F 174 " --> pdb=" O LYS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.213A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 Processing helix chain 'F' and resid 210 through 218 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 4 636 hydrogen bonds defined for protein. 1878 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: 1.77 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3263 1.34 - 1.46: 1252 1.46 - 1.58: 5422 1.58 - 1.70: 0 1.70 - 1.81: 130 Bond restraints: 10067 Sorted by residual: bond pdb=" CB PRO A 1 " pdb=" CG PRO A 1 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.50e+00 bond pdb=" CB PRO C 1 " pdb=" CG PRO C 1 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.32e+00 bond pdb=" CB PRO B 1 " pdb=" CG PRO B 1 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.31e+00 bond pdb=" CB PRO F 1 " pdb=" CG PRO F 1 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.86e+00 bond pdb=" CB PRO D 1 " pdb=" CG PRO D 1 " ideal model delta sigma weight residual 1.492 1.553 -0.061 5.00e-02 4.00e+02 1.47e+00 ... (remaining 10062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 13569 3.20 - 6.40: 104 6.40 - 9.59: 0 9.59 - 12.79: 1 12.79 - 15.99: 1 Bond angle restraints: 13675 Sorted by residual: angle pdb=" CB LEU D 6 " pdb=" CG LEU D 6 " pdb=" CD1 LEU D 6 " ideal model delta sigma weight residual 110.70 126.69 -15.99 3.00e+00 1.11e-01 2.84e+01 angle pdb=" CA LEU F 111 " pdb=" CB LEU F 111 " pdb=" CG LEU F 111 " ideal model delta sigma weight residual 116.30 126.71 -10.41 3.50e+00 8.16e-02 8.84e+00 angle pdb=" CB GLU E 28 " pdb=" CG GLU E 28 " pdb=" CD GLU E 28 " ideal model delta sigma weight residual 112.60 117.27 -4.67 1.70e+00 3.46e-01 7.55e+00 angle pdb=" CA TYR A 169 " pdb=" CB TYR A 169 " pdb=" CG TYR A 169 " ideal model delta sigma weight residual 113.90 109.28 4.62 1.80e+00 3.09e-01 6.59e+00 angle pdb=" CA GLU E 28 " pdb=" CB GLU E 28 " pdb=" CG GLU E 28 " ideal model delta sigma weight residual 114.10 119.16 -5.06 2.00e+00 2.50e-01 6.40e+00 ... (remaining 13670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5720 17.90 - 35.79: 356 35.79 - 53.69: 72 53.69 - 71.58: 12 71.58 - 89.48: 5 Dihedral angle restraints: 6165 sinusoidal: 2514 harmonic: 3651 Sorted by residual: dihedral pdb=" CA ASN A 121 " pdb=" C ASN A 121 " pdb=" N PRO A 122 " pdb=" CA PRO A 122 " ideal model delta harmonic sigma weight residual 180.00 150.69 29.31 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA PHE D 32 " pdb=" C PHE D 32 " pdb=" N SER D 33 " pdb=" CA SER D 33 " ideal model delta harmonic sigma weight residual 180.00 150.96 29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N SER E 33 " pdb=" CA SER E 33 " ideal model delta harmonic sigma weight residual 180.00 151.34 28.66 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 6162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.235: 1544 0.235 - 0.471: 0 0.471 - 0.706: 0 0.706 - 0.941: 0 0.941 - 1.176: 1 Chirality restraints: 1545 Sorted by residual: chirality pdb=" CG LEU D 6 " pdb=" CB LEU D 6 " pdb=" CD1 LEU D 6 " pdb=" CD2 LEU D 6 " both_signs ideal model delta sigma weight residual False -2.59 -1.41 -1.18 2.00e-01 2.50e+01 3.46e+01 chirality pdb=" CA PHE E 32 " pdb=" N PHE E 32 " pdb=" C PHE E 32 " pdb=" CB PHE E 32 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA PHE D 32 " pdb=" N PHE D 32 " pdb=" C PHE D 32 " pdb=" CB PHE D 32 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.76e-01 ... (remaining 1542 not shown) Planarity restraints: 1769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 154 " 0.295 9.50e-02 1.11e+02 1.32e-01 1.11e+01 pdb=" NE ARG F 154 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG F 154 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG F 154 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG F 154 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 173 " -0.285 9.50e-02 1.11e+02 1.28e-01 1.00e+01 pdb=" NE ARG D 173 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG D 173 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 173 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 173 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 173 " 0.276 9.50e-02 1.11e+02 1.24e-01 9.62e+00 pdb=" NE ARG C 173 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG C 173 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 173 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 173 " 0.007 2.00e-02 2.50e+03 ... (remaining 1766 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 4236 2.94 - 3.43: 10602 3.43 - 3.92: 17251 3.92 - 4.41: 19436 4.41 - 4.90: 31359 Nonbonded interactions: 82884 Sorted by model distance: nonbonded pdb=" OD1 ASP D 103 " pdb=" OG1 THR D 108 " model vdw 2.453 3.040 nonbonded pdb=" OD1 ASN E 53 " pdb=" OH TYR E 130 " model vdw 2.488 3.040 nonbonded pdb=" OD1 ASN A 53 " pdb=" OH TYR A 130 " model vdw 2.492 3.040 nonbonded pdb=" OD1 ASN D 53 " pdb=" OH TYR D 130 " model vdw 2.495 3.040 nonbonded pdb=" OD1 ASP E 103 " pdb=" OG1 THR E 108 " model vdw 2.496 3.040 ... (remaining 82879 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 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 85 or resid 97 through 221)) \ selection = (chain 'B' and (resid 1 through 5 or (resid 6 through 7 and (name N or name CA o \ r name C or name O or name CB )) or (resid 8 through 11 and (name N or name CA o \ r name C or name O or name CB )) or resid 12 through 85 or resid 97 through 221) \ ) selection = (chain 'C' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 or (resid 9 through 11 and (name N o \ r name CA or name C or name O or name CB )) or resid 12 through 85 or resid 97 t \ hrough 221)) selection = (chain 'D' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or (resid 8 through 11 and (name N or name CA o \ r name C or name O or name CB )) or resid 12 through 221)) selection = (chain 'E' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or (resid 8 through 11 and (name N or name CA o \ r name C or name O or name CB )) or resid 12 through 221)) selection = (chain 'F' and (resid 1 through 3 or (resid 4 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 85 or resid 97 through 221)) \ } 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: 5.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.840 Find NCS groups from input model: 0.230 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:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 0.005 0.079 10067 Z= 0.238 Angle : 0.867 15.988 13675 Z= 0.514 Chirality : 0.059 1.176 1545 Planarity : 0.013 0.132 1769 Dihedral : 12.698 89.480 3791 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.19 % Allowed : 0.75 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: -1.11 (0.20), residues: 1241 helix: -0.92 (0.14), residues: 881 sheet: -1.34 (0.78), residues: 27 loop : 0.49 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.003 ARG F 167 TYR 0.021 0.006 TYR B 164 PHE 0.021 0.004 PHE B 40 TRP 0.020 0.004 TRP B 117 HIS 0.011 0.004 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00494 (10067) covalent geometry : angle 0.86705 (13675) hydrogen bonds : bond 0.11723 ( 636) hydrogen bonds : angle 6.52378 ( 1878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.342 Fit side-chains REVERT: A 68 MET cc_start: 0.8669 (mtp) cc_final: 0.8403 (mtp) REVERT: A 74 ASN cc_start: 0.8129 (m-40) cc_final: 0.7863 (m-40) REVERT: A 79 GLU cc_start: 0.7073 (tt0) cc_final: 0.6686 (mt-10) REVERT: A 163 ASP cc_start: 0.7895 (m-30) cc_final: 0.7646 (m-30) REVERT: A 212 GLU cc_start: 0.7374 (tt0) cc_final: 0.6767 (pm20) REVERT: B 170 LYS cc_start: 0.7759 (tttm) cc_final: 0.7535 (tptt) REVERT: B 192 GLN cc_start: 0.7559 (mt0) cc_final: 0.7321 (mm110) REVERT: C 81 ASP cc_start: 0.8662 (m-30) cc_final: 0.8428 (m-30) REVERT: C 118 MET cc_start: 0.8591 (mtp) cc_final: 0.8286 (mtp) REVERT: C 154 ARG cc_start: 0.7313 (mtt-85) cc_final: 0.7087 (mtp-110) REVERT: C 170 LYS cc_start: 0.8576 (tttm) cc_final: 0.8282 (tttp) REVERT: C 179 GLN cc_start: 0.7378 (tp40) cc_final: 0.7083 (mm-40) REVERT: C 212 GLU cc_start: 0.7132 (tt0) cc_final: 0.6349 (tp30) REVERT: D 140 LYS cc_start: 0.8485 (mttt) cc_final: 0.8262 (mttm) REVERT: D 170 LYS cc_start: 0.8432 (tttm) cc_final: 0.7826 (ttpp) REVERT: D 212 GLU cc_start: 0.7142 (tt0) cc_final: 0.6769 (pm20) REVERT: E 68 MET cc_start: 0.8318 (mtp) cc_final: 0.8082 (mtp) REVERT: E 200 THR cc_start: 0.7516 (m) cc_final: 0.7231 (p) REVERT: E 212 GLU cc_start: 0.7525 (tt0) cc_final: 0.6530 (mt-10) REVERT: E 216 THR cc_start: 0.7842 (m) cc_final: 0.7567 (p) REVERT: F 55 MET cc_start: 0.8562 (mtp) cc_final: 0.8208 (mtp) REVERT: F 74 ASN cc_start: 0.8697 (m-40) cc_final: 0.8402 (m-40) REVERT: F 102 SER cc_start: 0.8451 (m) cc_final: 0.8170 (p) REVERT: F 151 LEU cc_start: 0.8818 (mt) cc_final: 0.8574 (mm) REVERT: F 216 THR cc_start: 0.8268 (m) cc_final: 0.7786 (p) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.7049 time to fit residues: 153.3341 Evaluate side-chains 152 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.0010 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 HIS B 193 ASN B 195 ASN C 193 ASN C 195 ASN D 193 ASN F 195 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.201906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.167285 restraints weight = 9420.090| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.03 r_work: 0.3751 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10067 Z= 0.141 Angle : 0.552 5.625 13675 Z= 0.285 Chirality : 0.043 0.166 1545 Planarity : 0.005 0.038 1769 Dihedral : 4.957 28.360 1337 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 2.07 % Allowed : 7.23 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: 1.16 (0.23), residues: 1241 helix: 0.91 (0.17), residues: 878 sheet: -1.01 (0.79), residues: 27 loop : 0.94 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 143 TYR 0.016 0.002 TYR E 169 PHE 0.015 0.003 PHE D 32 TRP 0.010 0.001 TRP B 117 HIS 0.003 0.001 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00345 (10067) covalent geometry : angle 0.55231 (13675) hydrogen bonds : bond 0.04207 ( 636) hydrogen bonds : angle 4.37661 ( 1878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.361 Fit side-chains REVERT: A 75 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7268 (pt0) REVERT: A 79 GLU cc_start: 0.7604 (tt0) cc_final: 0.7075 (mt-10) REVERT: A 163 ASP cc_start: 0.8059 (m-30) cc_final: 0.7842 (m-30) REVERT: A 170 LYS cc_start: 0.8438 (tttp) cc_final: 0.8205 (tptp) REVERT: A 212 GLU cc_start: 0.7705 (tt0) cc_final: 0.6642 (pm20) REVERT: B 112 GLN cc_start: 0.6567 (mm-40) cc_final: 0.5692 (tp40) REVERT: B 170 LYS cc_start: 0.8262 (tttm) cc_final: 0.7959 (tptt) REVERT: B 192 GLN cc_start: 0.7649 (mt0) cc_final: 0.7320 (mm110) REVERT: B 214 MET cc_start: 0.7415 (mtp) cc_final: 0.7174 (mtp) REVERT: C 81 ASP cc_start: 0.8559 (m-30) cc_final: 0.8318 (m-30) REVERT: C 118 MET cc_start: 0.8622 (mtp) cc_final: 0.8268 (mtp) REVERT: C 154 ARG cc_start: 0.7537 (mtt-85) cc_final: 0.7195 (mtp-110) REVERT: C 170 LYS cc_start: 0.8803 (tttm) cc_final: 0.8418 (tttp) REVERT: C 179 GLN cc_start: 0.7488 (tp40) cc_final: 0.7256 (tp-100) REVERT: C 212 GLU cc_start: 0.7313 (tt0) cc_final: 0.6635 (tp30) REVERT: D 140 LYS cc_start: 0.8653 (mttt) cc_final: 0.8356 (mttm) REVERT: D 170 LYS cc_start: 0.8626 (tttm) cc_final: 0.7741 (ttpp) REVERT: D 212 GLU cc_start: 0.7456 (tt0) cc_final: 0.6860 (pt0) REVERT: E 151 LEU cc_start: 0.8415 (mp) cc_final: 0.8197 (mm) REVERT: E 170 LYS cc_start: 0.8648 (tttm) cc_final: 0.8336 (tttt) REVERT: E 187 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: E 212 GLU cc_start: 0.7708 (tt0) cc_final: 0.7483 (tt0) REVERT: F 55 MET cc_start: 0.8623 (mtp) cc_final: 0.8299 (mtp) REVERT: F 74 ASN cc_start: 0.8530 (m-40) cc_final: 0.8242 (m-40) REVERT: F 75 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.7003 (pt0) REVERT: F 143 ARG cc_start: 0.7274 (ttp80) cc_final: 0.6607 (mtt90) REVERT: F 151 LEU cc_start: 0.8826 (mt) cc_final: 0.8545 (mm) outliers start: 22 outliers final: 5 residues processed: 159 average time/residue: 0.7379 time to fit residues: 123.8119 Evaluate side-chains 145 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain F residue 75 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 0.0000 chunk 8 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 176 GLN B 193 ASN D 193 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.200686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.166679 restraints weight = 9496.608| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.02 r_work: 0.3687 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10067 Z= 0.132 Angle : 0.517 7.987 13675 Z= 0.262 Chirality : 0.042 0.152 1545 Planarity : 0.005 0.038 1769 Dihedral : 4.466 29.354 1337 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 2.07 % Allowed : 8.08 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: 1.62 (0.23), residues: 1241 helix: 1.28 (0.17), residues: 881 sheet: -0.90 (0.80), residues: 27 loop : 1.00 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 143 TYR 0.015 0.001 TYR E 169 PHE 0.013 0.002 PHE C 32 TRP 0.007 0.001 TRP B 117 HIS 0.002 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00326 (10067) covalent geometry : angle 0.51740 (13675) hydrogen bonds : bond 0.03659 ( 636) hydrogen bonds : angle 4.01832 ( 1878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.380 Fit side-chains REVERT: A 75 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7328 (pt0) REVERT: A 79 GLU cc_start: 0.7663 (tt0) cc_final: 0.7218 (mt-10) REVERT: A 163 ASP cc_start: 0.8066 (m-30) cc_final: 0.7866 (m-30) REVERT: A 212 GLU cc_start: 0.7647 (tt0) cc_final: 0.6646 (pm20) REVERT: B 112 GLN cc_start: 0.6603 (mm-40) cc_final: 0.5905 (tp40) REVERT: B 170 LYS cc_start: 0.8373 (tttm) cc_final: 0.8077 (tptt) REVERT: B 192 GLN cc_start: 0.7736 (mt0) cc_final: 0.7360 (mm-40) REVERT: C 50 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: C 118 MET cc_start: 0.8670 (mtp) cc_final: 0.8232 (mtp) REVERT: C 154 ARG cc_start: 0.7596 (mtt-85) cc_final: 0.7326 (mtp-110) REVERT: C 170 LYS cc_start: 0.8828 (tttm) cc_final: 0.8482 (tttp) REVERT: D 140 LYS cc_start: 0.8732 (mttt) cc_final: 0.8408 (mttm) REVERT: D 170 LYS cc_start: 0.8652 (tttm) cc_final: 0.7780 (ttpp) REVERT: D 212 GLU cc_start: 0.7511 (tt0) cc_final: 0.6611 (pm20) REVERT: E 144 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7475 (ttm) REVERT: E 151 LEU cc_start: 0.8478 (mp) cc_final: 0.8180 (mm) REVERT: E 170 LYS cc_start: 0.8742 (tttm) cc_final: 0.8438 (tttt) REVERT: E 187 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: F 55 MET cc_start: 0.8634 (mtp) cc_final: 0.8396 (mtp) REVERT: F 75 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7149 (pt0) REVERT: F 151 LEU cc_start: 0.8834 (mt) cc_final: 0.8618 (mp) outliers start: 22 outliers final: 7 residues processed: 156 average time/residue: 0.7609 time to fit residues: 125.1156 Evaluate side-chains 145 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 0.0270 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.198617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164987 restraints weight = 9569.581| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.01 r_work: 0.3672 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10067 Z= 0.157 Angle : 0.529 7.994 13675 Z= 0.266 Chirality : 0.043 0.151 1545 Planarity : 0.005 0.040 1769 Dihedral : 4.383 29.416 1337 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.25 % Allowed : 8.45 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: 1.62 (0.23), residues: 1241 helix: 1.30 (0.17), residues: 882 sheet: -0.86 (0.82), residues: 27 loop : 0.94 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 143 TYR 0.015 0.002 TYR E 169 PHE 0.013 0.002 PHE C 32 TRP 0.007 0.001 TRP D 184 HIS 0.003 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00395 (10067) covalent geometry : angle 0.52941 (13675) hydrogen bonds : bond 0.03634 ( 636) hydrogen bonds : angle 3.97904 ( 1878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7296 (pt0) REVERT: A 79 GLU cc_start: 0.7628 (tt0) cc_final: 0.7188 (mt-10) REVERT: A 212 GLU cc_start: 0.7565 (tt0) cc_final: 0.6614 (pm20) REVERT: B 112 GLN cc_start: 0.6649 (mm-40) cc_final: 0.5922 (tp40) REVERT: B 170 LYS cc_start: 0.8373 (tttm) cc_final: 0.8082 (tptt) REVERT: B 192 GLN cc_start: 0.7848 (mt0) cc_final: 0.7439 (mm110) REVERT: C 39 MET cc_start: 0.8430 (tpt) cc_final: 0.8088 (tpt) REVERT: C 50 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: C 118 MET cc_start: 0.8675 (mtp) cc_final: 0.8276 (mtp) REVERT: C 154 ARG cc_start: 0.7647 (mtt-85) cc_final: 0.7429 (mtp-110) REVERT: C 170 LYS cc_start: 0.8832 (tttm) cc_final: 0.8378 (tptp) REVERT: D 21 ASN cc_start: 0.8167 (m-40) cc_final: 0.7841 (m110) REVERT: D 103 ASP cc_start: 0.8654 (m-30) cc_final: 0.8410 (m-30) REVERT: D 140 LYS cc_start: 0.8750 (mttt) cc_final: 0.8424 (mttm) REVERT: D 170 LYS cc_start: 0.8633 (tttm) cc_final: 0.7789 (ttpp) REVERT: D 212 GLU cc_start: 0.7490 (tt0) cc_final: 0.6855 (pt0) REVERT: E 144 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7415 (ttm) REVERT: E 170 LYS cc_start: 0.8740 (tttm) cc_final: 0.8452 (tttt) REVERT: E 187 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: F 55 MET cc_start: 0.8629 (mtp) cc_final: 0.8381 (mtp) REVERT: F 75 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7137 (pt0) REVERT: F 151 LEU cc_start: 0.8866 (mt) cc_final: 0.8597 (mp) outliers start: 24 outliers final: 9 residues processed: 151 average time/residue: 0.7302 time to fit residues: 116.1895 Evaluate side-chains 147 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 120 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 119 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN D 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.200529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.166386 restraints weight = 9420.698| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.04 r_work: 0.3684 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10067 Z= 0.130 Angle : 0.496 8.348 13675 Z= 0.249 Chirality : 0.041 0.148 1545 Planarity : 0.005 0.042 1769 Dihedral : 4.200 29.291 1337 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.07 % Allowed : 9.39 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: 1.78 (0.24), residues: 1241 helix: 1.45 (0.17), residues: 886 sheet: -1.03 (0.85), residues: 27 loop : 0.91 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 143 TYR 0.013 0.001 TYR E 169 PHE 0.013 0.002 PHE C 32 TRP 0.004 0.001 TRP E 184 HIS 0.002 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00323 (10067) covalent geometry : angle 0.49551 (13675) hydrogen bonds : bond 0.03387 ( 636) hydrogen bonds : angle 3.85588 ( 1878) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.396 Fit side-chains REVERT: A 75 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7323 (pt0) REVERT: A 79 GLU cc_start: 0.7637 (tt0) cc_final: 0.7191 (mt-10) REVERT: A 212 GLU cc_start: 0.7543 (tt0) cc_final: 0.6641 (pm20) REVERT: B 112 GLN cc_start: 0.6633 (mm-40) cc_final: 0.5960 (tp40) REVERT: B 170 LYS cc_start: 0.8365 (tttm) cc_final: 0.8063 (tptt) REVERT: B 192 GLN cc_start: 0.7815 (mt0) cc_final: 0.7423 (mm110) REVERT: C 39 MET cc_start: 0.8369 (tpt) cc_final: 0.8021 (tpt) REVERT: C 50 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: C 118 MET cc_start: 0.8647 (mtp) cc_final: 0.8172 (mtp) REVERT: C 154 ARG cc_start: 0.7633 (mtt-85) cc_final: 0.7409 (mtp-110) REVERT: C 170 LYS cc_start: 0.8819 (tttm) cc_final: 0.8372 (tptp) REVERT: C 192 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: D 21 ASN cc_start: 0.8172 (m-40) cc_final: 0.7863 (m110) REVERT: D 103 ASP cc_start: 0.8668 (m-30) cc_final: 0.8435 (m-30) REVERT: D 140 LYS cc_start: 0.8790 (mttt) cc_final: 0.8565 (mttm) REVERT: D 170 LYS cc_start: 0.8631 (tttm) cc_final: 0.7774 (ttpp) REVERT: D 212 GLU cc_start: 0.7548 (tt0) cc_final: 0.6861 (pt0) REVERT: E 144 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7494 (ttm) REVERT: E 170 LYS cc_start: 0.8744 (tttm) cc_final: 0.8453 (tttt) REVERT: F 55 MET cc_start: 0.8621 (mtp) cc_final: 0.8295 (mtp) REVERT: F 75 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7102 (pt0) REVERT: F 151 LEU cc_start: 0.8869 (mt) cc_final: 0.8595 (mp) outliers start: 22 outliers final: 7 residues processed: 140 average time/residue: 0.7409 time to fit residues: 109.4002 Evaluate side-chains 140 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.1980 chunk 15 optimal weight: 0.0980 chunk 92 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.200855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.166719 restraints weight = 9467.431| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.04 r_work: 0.3688 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10067 Z= 0.125 Angle : 0.486 5.145 13675 Z= 0.244 Chirality : 0.041 0.148 1545 Planarity : 0.005 0.043 1769 Dihedral : 4.105 28.905 1337 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.16 % Allowed : 10.52 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: 1.86 (0.24), residues: 1241 helix: 1.52 (0.17), residues: 886 sheet: -0.89 (0.84), residues: 27 loop : 0.91 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 143 TYR 0.014 0.001 TYR E 169 PHE 0.012 0.002 PHE C 32 TRP 0.004 0.001 TRP C 23 HIS 0.002 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00311 (10067) covalent geometry : angle 0.48551 (13675) hydrogen bonds : bond 0.03339 ( 636) hydrogen bonds : angle 3.82312 ( 1878) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.366 Fit side-chains REVERT: A 75 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7320 (pt0) REVERT: A 79 GLU cc_start: 0.7604 (tt0) cc_final: 0.7148 (mt-10) REVERT: A 212 GLU cc_start: 0.7637 (tt0) cc_final: 0.6676 (pm20) REVERT: B 112 GLN cc_start: 0.6650 (mm-40) cc_final: 0.5996 (tp40) REVERT: B 165 VAL cc_start: 0.8363 (t) cc_final: 0.7966 (m) REVERT: B 170 LYS cc_start: 0.8358 (tttm) cc_final: 0.8057 (tptt) REVERT: B 192 GLN cc_start: 0.7810 (mt0) cc_final: 0.7404 (mm110) REVERT: C 39 MET cc_start: 0.8355 (tpt) cc_final: 0.7959 (tpt) REVERT: C 50 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: C 118 MET cc_start: 0.8636 (mtp) cc_final: 0.8195 (mtp) REVERT: C 154 ARG cc_start: 0.7634 (mtt-85) cc_final: 0.7417 (mtp-110) REVERT: C 170 LYS cc_start: 0.8807 (tttm) cc_final: 0.8372 (tptp) REVERT: D 21 ASN cc_start: 0.8184 (m-40) cc_final: 0.7877 (m110) REVERT: D 103 ASP cc_start: 0.8672 (m-30) cc_final: 0.8450 (m-30) REVERT: D 140 LYS cc_start: 0.8785 (mttt) cc_final: 0.8550 (mttm) REVERT: D 170 LYS cc_start: 0.8643 (tttm) cc_final: 0.7796 (ttpp) REVERT: D 212 GLU cc_start: 0.7537 (tt0) cc_final: 0.6878 (pt0) REVERT: E 10 MET cc_start: 0.3434 (mmp) cc_final: 0.2803 (pp-130) REVERT: E 144 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7498 (ttm) REVERT: E 170 LYS cc_start: 0.8705 (tttm) cc_final: 0.8418 (tttt) REVERT: F 55 MET cc_start: 0.8614 (mtp) cc_final: 0.8271 (mtp) REVERT: F 75 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7067 (pt0) REVERT: F 151 LEU cc_start: 0.8899 (mt) cc_final: 0.8590 (mp) outliers start: 23 outliers final: 8 residues processed: 144 average time/residue: 0.7550 time to fit residues: 114.6975 Evaluate side-chains 138 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 102 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 23 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN D 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.199035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.164272 restraints weight = 9378.498| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.06 r_work: 0.3654 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10067 Z= 0.156 Angle : 0.518 6.999 13675 Z= 0.260 Chirality : 0.042 0.144 1545 Planarity : 0.005 0.043 1769 Dihedral : 4.202 28.792 1337 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.07 % Allowed : 11.08 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: 1.73 (0.23), residues: 1241 helix: 1.43 (0.17), residues: 884 sheet: -0.75 (0.82), residues: 27 loop : 0.82 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 154 TYR 0.015 0.002 TYR E 169 PHE 0.012 0.002 PHE C 32 TRP 0.005 0.001 TRP C 23 HIS 0.003 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00397 (10067) covalent geometry : angle 0.51767 (13675) hydrogen bonds : bond 0.03515 ( 636) hydrogen bonds : angle 3.91349 ( 1878) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.318 Fit side-chains REVERT: A 75 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7316 (pt0) REVERT: A 79 GLU cc_start: 0.7610 (tt0) cc_final: 0.7164 (mt-10) REVERT: A 212 GLU cc_start: 0.7656 (tt0) cc_final: 0.6685 (pm20) REVERT: B 112 GLN cc_start: 0.6680 (mm-40) cc_final: 0.5957 (tp40) REVERT: B 170 LYS cc_start: 0.8346 (tttm) cc_final: 0.8061 (tptt) REVERT: B 192 GLN cc_start: 0.7906 (mt0) cc_final: 0.7526 (mm-40) REVERT: C 50 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: C 118 MET cc_start: 0.8694 (mtp) cc_final: 0.8361 (mtm) REVERT: C 154 ARG cc_start: 0.7666 (mtt-85) cc_final: 0.7414 (mtp-110) REVERT: C 170 LYS cc_start: 0.8834 (tttm) cc_final: 0.8371 (tptp) REVERT: C 192 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7825 (mm-40) REVERT: D 21 ASN cc_start: 0.8209 (m-40) cc_final: 0.7893 (m110) REVERT: D 103 ASP cc_start: 0.8722 (m-30) cc_final: 0.8513 (m-30) REVERT: D 140 LYS cc_start: 0.8792 (mttt) cc_final: 0.8573 (mttm) REVERT: D 170 LYS cc_start: 0.8655 (tttm) cc_final: 0.7804 (ttpp) REVERT: D 212 GLU cc_start: 0.7557 (tt0) cc_final: 0.6883 (pt0) REVERT: E 10 MET cc_start: 0.3773 (mmp) cc_final: 0.2986 (pp-130) REVERT: E 144 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7476 (ttm) REVERT: E 170 LYS cc_start: 0.8722 (tttm) cc_final: 0.8447 (tttt) REVERT: E 187 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: F 55 MET cc_start: 0.8659 (mtp) cc_final: 0.8404 (mtp) outliers start: 22 outliers final: 8 residues processed: 143 average time/residue: 0.7568 time to fit residues: 114.0807 Evaluate side-chains 141 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 187 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 84 optimal weight: 0.0000 chunk 3 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 121 optimal weight: 0.0170 chunk 102 optimal weight: 4.9990 chunk 2 optimal weight: 0.0370 chunk 80 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.2900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.202871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.168602 restraints weight = 9313.700| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.04 r_work: 0.3698 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10067 Z= 0.108 Angle : 0.474 5.570 13675 Z= 0.239 Chirality : 0.040 0.143 1545 Planarity : 0.005 0.044 1769 Dihedral : 3.995 28.226 1337 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.69 % Allowed : 11.64 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: 1.98 (0.24), residues: 1241 helix: 1.64 (0.17), residues: 887 sheet: -0.56 (0.85), residues: 27 loop : 0.82 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 154 TYR 0.011 0.001 TYR E 169 PHE 0.010 0.001 PHE C 32 TRP 0.005 0.001 TRP E 184 HIS 0.002 0.000 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00261 (10067) covalent geometry : angle 0.47398 (13675) hydrogen bonds : bond 0.03205 ( 636) hydrogen bonds : angle 3.77883 ( 1878) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.249 Fit side-chains REVERT: A 75 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7412 (pt0) REVERT: A 79 GLU cc_start: 0.7582 (tt0) cc_final: 0.7128 (mt-10) REVERT: A 212 GLU cc_start: 0.7624 (tt0) cc_final: 0.6675 (pm20) REVERT: B 112 GLN cc_start: 0.6606 (mm-40) cc_final: 0.6007 (tp40) REVERT: B 170 LYS cc_start: 0.8326 (tttm) cc_final: 0.8054 (tptt) REVERT: B 192 GLN cc_start: 0.7792 (mt0) cc_final: 0.7383 (mm-40) REVERT: C 50 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: C 102 SER cc_start: 0.8713 (m) cc_final: 0.8251 (p) REVERT: C 118 MET cc_start: 0.8620 (mtp) cc_final: 0.8328 (mtm) REVERT: C 154 ARG cc_start: 0.7669 (mtt-85) cc_final: 0.7420 (mtp-110) REVERT: C 170 LYS cc_start: 0.8801 (tttm) cc_final: 0.8345 (tptp) REVERT: D 21 ASN cc_start: 0.8197 (m-40) cc_final: 0.7882 (m110) REVERT: D 103 ASP cc_start: 0.8692 (m-30) cc_final: 0.8480 (m-30) REVERT: D 140 LYS cc_start: 0.8785 (mttt) cc_final: 0.8446 (mttm) REVERT: D 170 LYS cc_start: 0.8643 (tttm) cc_final: 0.7796 (ttpp) REVERT: E 10 MET cc_start: 0.3873 (mmp) cc_final: 0.3066 (pp-130) REVERT: E 144 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7472 (ttm) REVERT: F 55 MET cc_start: 0.8627 (mtp) cc_final: 0.8304 (mtp) outliers start: 18 outliers final: 7 residues processed: 140 average time/residue: 0.7459 time to fit residues: 110.0653 Evaluate side-chains 138 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 144 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 0.0270 chunk 73 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN D 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.200692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.166294 restraints weight = 9383.692| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.06 r_work: 0.3739 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10067 Z= 0.131 Angle : 0.501 7.720 13675 Z= 0.252 Chirality : 0.041 0.143 1545 Planarity : 0.005 0.044 1769 Dihedral : 4.047 28.009 1337 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.60 % Allowed : 11.92 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: 1.94 (0.24), residues: 1241 helix: 1.60 (0.17), residues: 887 sheet: -0.54 (0.85), residues: 27 loop : 0.83 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 143 TYR 0.015 0.001 TYR E 169 PHE 0.014 0.002 PHE C 32 TRP 0.006 0.001 TRP E 184 HIS 0.002 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00329 (10067) covalent geometry : angle 0.50098 (13675) hydrogen bonds : bond 0.03338 ( 636) hydrogen bonds : angle 3.83045 ( 1878) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.357 Fit side-chains REVERT: A 75 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7240 (pt0) REVERT: A 79 GLU cc_start: 0.7483 (tt0) cc_final: 0.7025 (mt-10) REVERT: A 212 GLU cc_start: 0.7533 (tt0) cc_final: 0.6625 (pm20) REVERT: B 112 GLN cc_start: 0.6444 (mm-40) cc_final: 0.5884 (tp40) REVERT: B 170 LYS cc_start: 0.8277 (tttm) cc_final: 0.7951 (tptt) REVERT: B 192 GLN cc_start: 0.7786 (mt0) cc_final: 0.7358 (mm110) REVERT: C 50 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: C 118 MET cc_start: 0.8589 (mtp) cc_final: 0.8329 (mtm) REVERT: C 154 ARG cc_start: 0.7556 (mtt-85) cc_final: 0.7319 (mtp-110) REVERT: C 170 LYS cc_start: 0.8763 (tttm) cc_final: 0.8294 (tptp) REVERT: D 21 ASN cc_start: 0.8154 (m-40) cc_final: 0.7838 (m110) REVERT: D 103 ASP cc_start: 0.8670 (m-30) cc_final: 0.8447 (m-30) REVERT: D 140 LYS cc_start: 0.8729 (mttt) cc_final: 0.8373 (mttm) REVERT: D 170 LYS cc_start: 0.8569 (tttm) cc_final: 0.7663 (ttpp) REVERT: E 10 MET cc_start: 0.3918 (mmp) cc_final: 0.3180 (pp-130) REVERT: E 144 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7494 (ttm) REVERT: F 55 MET cc_start: 0.8590 (mtp) cc_final: 0.8232 (mtp) outliers start: 17 outliers final: 7 residues processed: 138 average time/residue: 0.7239 time to fit residues: 105.5916 Evaluate side-chains 136 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 22 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 118 optimal weight: 0.4980 chunk 75 optimal weight: 0.0970 chunk 78 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.200927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.166481 restraints weight = 9291.102| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.06 r_work: 0.3734 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10067 Z= 0.129 Angle : 0.493 7.133 13675 Z= 0.248 Chirality : 0.041 0.142 1545 Planarity : 0.005 0.043 1769 Dihedral : 4.023 27.877 1337 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.22 % Allowed : 12.30 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: 1.93 (0.23), residues: 1241 helix: 1.59 (0.17), residues: 887 sheet: -0.54 (0.85), residues: 27 loop : 0.85 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 143 TYR 0.013 0.001 TYR E 169 PHE 0.011 0.002 PHE B 32 TRP 0.006 0.001 TRP E 184 HIS 0.002 0.001 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00323 (10067) covalent geometry : angle 0.49321 (13675) hydrogen bonds : bond 0.03343 ( 636) hydrogen bonds : angle 3.82759 ( 1878) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.374 Fit side-chains REVERT: A 75 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7340 (pt0) REVERT: A 79 GLU cc_start: 0.7484 (tt0) cc_final: 0.7027 (mt-10) REVERT: A 170 LYS cc_start: 0.8441 (tttp) cc_final: 0.8221 (tptp) REVERT: A 212 GLU cc_start: 0.7543 (tt0) cc_final: 0.6647 (pm20) REVERT: B 112 GLN cc_start: 0.6449 (mm-40) cc_final: 0.5859 (tp40) REVERT: B 170 LYS cc_start: 0.8283 (tttm) cc_final: 0.7964 (tptt) REVERT: B 192 GLN cc_start: 0.7786 (mt0) cc_final: 0.7353 (mm110) REVERT: C 50 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: C 102 SER cc_start: 0.8713 (m) cc_final: 0.8227 (p) REVERT: C 118 MET cc_start: 0.8587 (mtp) cc_final: 0.8319 (mtm) REVERT: C 154 ARG cc_start: 0.7555 (mtt-85) cc_final: 0.7334 (mtp-110) REVERT: C 170 LYS cc_start: 0.8766 (tttm) cc_final: 0.8300 (tptp) REVERT: D 21 ASN cc_start: 0.8134 (m-40) cc_final: 0.7815 (m110) REVERT: D 103 ASP cc_start: 0.8679 (m-30) cc_final: 0.8443 (m-30) REVERT: D 140 LYS cc_start: 0.8735 (mttt) cc_final: 0.8483 (mttm) REVERT: D 170 LYS cc_start: 0.8577 (tttm) cc_final: 0.7682 (ttpp) REVERT: E 10 MET cc_start: 0.4007 (mmp) cc_final: 0.3239 (pp-130) REVERT: E 144 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7442 (ttm) REVERT: F 55 MET cc_start: 0.8584 (mtp) cc_final: 0.8232 (mtp) outliers start: 13 outliers final: 7 residues processed: 132 average time/residue: 0.7472 time to fit residues: 104.1740 Evaluate side-chains 133 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 1 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 125 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.199275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.164934 restraints weight = 9379.999| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.05 r_work: 0.3728 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10067 Z= 0.148 Angle : 0.519 9.037 13675 Z= 0.259 Chirality : 0.042 0.142 1545 Planarity : 0.005 0.043 1769 Dihedral : 4.089 27.859 1337 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.31 % Allowed : 12.21 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: 1.87 (0.23), residues: 1241 helix: 1.53 (0.17), residues: 887 sheet: -0.57 (0.84), residues: 27 loop : 0.84 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 154 TYR 0.014 0.002 TYR E 169 PHE 0.012 0.002 PHE C 32 TRP 0.006 0.001 TRP E 184 HIS 0.003 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00375 (10067) covalent geometry : angle 0.51851 (13675) hydrogen bonds : bond 0.03450 ( 636) hydrogen bonds : angle 3.88904 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3047.38 seconds wall clock time: 52 minutes 41.53 seconds (3161.53 seconds total)