Starting phenix.real_space_refine on Mon Jun 9 07:11:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ckx_16705/06_2025/8ckx_16705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ckx_16705/06_2025/8ckx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ckx_16705/06_2025/8ckx_16705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ckx_16705/06_2025/8ckx_16705.map" model { file = "/net/cci-nas-00/data/ceres_data/8ckx_16705/06_2025/8ckx_16705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ckx_16705/06_2025/8ckx_16705.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.050 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'ASN:plan1': 1} 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: {'GLN:plan1': 1, 'ASN: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: {'GLN:plan1': 2, 'ASN:plan1': 1} 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: {'GLN:plan1': 2, 'ASN:plan1': 1} 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: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 7.16, per 1000 atoms: 0.73 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: 3.79 Conformation dependent library (CDL) restraints added in 980.9 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: 0.87 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: 2.61 Time building geometry restraints manager: 4.23 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: 6.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.120 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.004 TRP B 117 HIS 0.011 0.004 HIS B 84 PHE 0.021 0.004 PHE B 40 TYR 0.021 0.006 TYR B 164 ARG 0.022 0.003 ARG F 167 Details of bonding type rmsd hydrogen bonds : bond 0.11723 ( 636) hydrogen bonds : angle 6.52378 ( 1878) covalent geometry : bond 0.00494 (10067) covalent geometry : angle 0.86705 (13675) *********************** 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 : 1.143 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: 1.5232 time to fit residues: 331.7423 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 : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.6980 chunk 95 optimal weight: 0.0570 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 98 optimal weight: 0.0970 chunk 38 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS B 193 ASN B 195 ASN C 193 ASN C 195 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.204546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.170004 restraints weight = 9315.880| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.03 r_work: 0.3783 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10067 Z= 0.123 Angle : 0.533 5.753 13675 Z= 0.274 Chirality : 0.042 0.166 1545 Planarity : 0.005 0.039 1769 Dihedral : 4.786 28.379 1337 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 2.07 % Allowed : 7.04 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.23), residues: 1241 helix: 1.06 (0.17), residues: 881 sheet: -1.09 (0.79), residues: 27 loop : 0.99 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 117 HIS 0.002 0.001 HIS E 120 PHE 0.013 0.002 PHE D 32 TYR 0.014 0.001 TYR E 169 ARG 0.005 0.001 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 636) hydrogen bonds : angle 4.22673 ( 1878) covalent geometry : bond 0.00286 (10067) covalent geometry : angle 0.53312 (13675) *********************** 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 163 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.061 Fit side-chains REVERT: A 70 LYS cc_start: 0.8474 (ttmm) cc_final: 0.7830 (tttp) REVERT: A 75 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7384 (pt0) REVERT: A 79 GLU cc_start: 0.7482 (tt0) cc_final: 0.6961 (mt-10) REVERT: A 163 ASP cc_start: 0.7990 (m-30) cc_final: 0.7778 (m-30) REVERT: A 170 LYS cc_start: 0.8398 (tttp) cc_final: 0.8172 (tptp) REVERT: A 212 GLU cc_start: 0.7691 (tt0) cc_final: 0.6626 (pm20) REVERT: B 165 VAL cc_start: 0.8191 (t) cc_final: 0.7888 (m) REVERT: B 170 LYS cc_start: 0.8271 (tttm) cc_final: 0.7942 (tptt) REVERT: B 214 MET cc_start: 0.7161 (mtp) cc_final: 0.6914 (mtp) REVERT: C 39 MET cc_start: 0.8379 (tpt) cc_final: 0.7991 (tpt) REVERT: C 81 ASP cc_start: 0.8540 (m-30) cc_final: 0.8320 (m-30) REVERT: C 118 MET cc_start: 0.8551 (mtp) cc_final: 0.8194 (mtp) REVERT: C 154 ARG cc_start: 0.7515 (mtt-85) cc_final: 0.7240 (mtp-110) REVERT: C 170 LYS cc_start: 0.8741 (tttm) cc_final: 0.8366 (tttp) REVERT: C 179 GLN cc_start: 0.7467 (tp40) cc_final: 0.7197 (tp-100) REVERT: D 140 LYS cc_start: 0.8619 (mttt) cc_final: 0.8318 (mttm) REVERT: D 170 LYS cc_start: 0.8602 (tttm) cc_final: 0.7712 (ttpp) REVERT: D 212 GLU cc_start: 0.7424 (tt0) cc_final: 0.6856 (pt0) REVERT: E 170 LYS cc_start: 0.8665 (tttm) cc_final: 0.8465 (tptt) REVERT: E 187 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: F 55 MET cc_start: 0.8594 (mtp) cc_final: 0.8235 (mtp) REVERT: F 74 ASN cc_start: 0.8493 (m-40) cc_final: 0.8211 (m-40) REVERT: F 75 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6984 (pt0) REVERT: F 143 ARG cc_start: 0.7236 (ttp80) cc_final: 0.6559 (mtt90) outliers start: 22 outliers final: 4 residues processed: 151 average time/residue: 1.8548 time to fit residues: 295.3838 Evaluate side-chains 140 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU 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 42 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 103 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 120 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN B 193 ASN D 193 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.201430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.166941 restraints weight = 9473.783| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.04 r_work: 0.3690 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2197 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= 0.139 Angle : 0.524 7.603 13675 Z= 0.265 Chirality : 0.042 0.152 1545 Planarity : 0.005 0.038 1769 Dihedral : 4.450 29.264 1337 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 2.16 % Allowed : 8.26 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.23), residues: 1241 helix: 1.37 (0.18), residues: 879 sheet: -0.89 (0.81), residues: 27 loop : 0.99 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 117 HIS 0.003 0.001 HIS E 120 PHE 0.011 0.002 PHE C 32 TYR 0.016 0.002 TYR E 169 ARG 0.004 0.000 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 636) hydrogen bonds : angle 4.02915 ( 1878) covalent geometry : bond 0.00346 (10067) covalent geometry : angle 0.52388 (13675) *********************** 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 164 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.083 Fit side-chains REVERT: A 75 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: A 79 GLU cc_start: 0.7678 (tt0) cc_final: 0.7227 (mt-10) REVERT: A 163 ASP cc_start: 0.8094 (m-30) cc_final: 0.7889 (m-30) REVERT: A 212 GLU cc_start: 0.7672 (tt0) cc_final: 0.6672 (pm20) REVERT: B 112 GLN cc_start: 0.6600 (mm-40) cc_final: 0.5920 (tp40) REVERT: B 165 VAL cc_start: 0.8190 (t) cc_final: 0.7918 (m) REVERT: B 170 LYS cc_start: 0.8378 (tttm) cc_final: 0.8091 (tptt) REVERT: B 192 GLN cc_start: 0.7694 (mt0) cc_final: 0.7366 (mm110) REVERT: C 50 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: C 81 ASP cc_start: 0.8586 (m-30) cc_final: 0.8366 (m-30) REVERT: C 118 MET cc_start: 0.8687 (mtp) cc_final: 0.8241 (mtp) REVERT: C 154 ARG cc_start: 0.7560 (mtt-85) cc_final: 0.7337 (mtp-110) REVERT: C 170 LYS cc_start: 0.8830 (tttm) cc_final: 0.8499 (tttp) REVERT: D 140 LYS cc_start: 0.8735 (mttt) cc_final: 0.8415 (mttm) REVERT: D 170 LYS cc_start: 0.8650 (tttm) cc_final: 0.7783 (ttpp) REVERT: D 212 GLU cc_start: 0.7568 (tt0) cc_final: 0.6685 (pm20) REVERT: E 76 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7804 (mm-30) REVERT: E 144 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7476 (ttm) REVERT: E 170 LYS cc_start: 0.8780 (tttm) cc_final: 0.8460 (tttt) REVERT: E 187 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: E 212 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6736 (mt-10) REVERT: F 55 MET cc_start: 0.8639 (mtp) cc_final: 0.8406 (mtp) REVERT: F 75 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7123 (pt0) REVERT: F 151 LEU cc_start: 0.8839 (mt) cc_final: 0.8616 (mp) outliers start: 23 outliers final: 4 residues processed: 152 average time/residue: 1.8085 time to fit residues: 289.7943 Evaluate side-chains 142 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU 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 200 THR Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 212 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 42 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 22 optimal weight: 0.0010 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 = 0.198984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.165104 restraints weight = 9393.266| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.01 r_work: 0.3670 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10067 Z= 0.153 Angle : 0.528 8.134 13675 Z= 0.264 Chirality : 0.042 0.151 1545 Planarity : 0.005 0.040 1769 Dihedral : 4.350 29.436 1337 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.54 % Allowed : 8.54 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.23), residues: 1241 helix: 1.36 (0.17), residues: 882 sheet: -0.94 (0.83), residues: 27 loop : 0.96 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 184 HIS 0.003 0.001 HIS C 12 PHE 0.012 0.002 PHE C 32 TYR 0.015 0.002 TYR E 169 ARG 0.002 0.000 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 636) hydrogen bonds : angle 3.96567 ( 1878) covalent geometry : bond 0.00386 (10067) covalent geometry : angle 0.52832 (13675) *********************** 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 162 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 1.098 Fit side-chains REVERT: A 75 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7294 (pt0) REVERT: A 79 GLU cc_start: 0.7655 (tt0) cc_final: 0.7218 (mt-10) REVERT: A 212 GLU cc_start: 0.7585 (tt0) cc_final: 0.6660 (pm20) REVERT: B 112 GLN cc_start: 0.6651 (mm-40) cc_final: 0.5930 (tp40) REVERT: B 170 LYS cc_start: 0.8373 (tttm) cc_final: 0.8079 (tptt) REVERT: B 192 GLN cc_start: 0.7747 (mt0) cc_final: 0.7369 (mm110) REVERT: C 50 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: C 118 MET cc_start: 0.8680 (mtp) cc_final: 0.8281 (mtp) REVERT: C 154 ARG cc_start: 0.7613 (mtt-85) cc_final: 0.7411 (mtp-110) REVERT: C 170 LYS cc_start: 0.8824 (tttm) cc_final: 0.8376 (tptp) REVERT: D 21 ASN cc_start: 0.8142 (m-40) cc_final: 0.7813 (m110) REVERT: D 140 LYS cc_start: 0.8748 (mttt) cc_final: 0.8528 (mttm) REVERT: D 170 LYS cc_start: 0.8629 (tttm) cc_final: 0.7787 (ttpp) REVERT: D 212 GLU cc_start: 0.7509 (tt0) cc_final: 0.6858 (pt0) REVERT: E 144 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7429 (ttm) REVERT: E 170 LYS cc_start: 0.8731 (tttm) cc_final: 0.8444 (tttt) REVERT: E 187 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: F 55 MET cc_start: 0.8631 (mtp) cc_final: 0.8387 (mtp) REVERT: F 75 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7120 (pt0) REVERT: F 151 LEU cc_start: 0.8850 (mt) cc_final: 0.8583 (mp) outliers start: 27 outliers final: 5 residues processed: 151 average time/residue: 1.6193 time to fit residues: 258.6915 Evaluate side-chains 148 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU 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 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 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 0 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 63 optimal weight: 0.0570 chunk 20 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 chunk 113 optimal weight: 0.0670 chunk 8 optimal weight: 3.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.202598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.168420 restraints weight = 9307.713| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.03 r_work: 0.3700 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2677 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= 0.117 Angle : 0.486 8.207 13675 Z= 0.244 Chirality : 0.041 0.147 1545 Planarity : 0.005 0.042 1769 Dihedral : 4.134 29.219 1337 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.69 % Allowed : 9.58 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.24), residues: 1241 helix: 1.54 (0.17), residues: 886 sheet: -0.99 (0.86), residues: 27 loop : 0.92 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 184 HIS 0.002 0.000 HIS D 12 PHE 0.016 0.002 PHE C 32 TYR 0.012 0.001 TYR E 169 ARG 0.003 0.000 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 636) hydrogen bonds : angle 3.81399 ( 1878) covalent geometry : bond 0.00287 (10067) covalent geometry : angle 0.48589 (13675) *********************** 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 156 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.214 Fit side-chains REVERT: A 75 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7396 (pt0) REVERT: A 79 GLU cc_start: 0.7641 (tt0) cc_final: 0.7216 (mt-10) REVERT: A 212 GLU cc_start: 0.7606 (tt0) cc_final: 0.6690 (pm20) REVERT: B 112 GLN cc_start: 0.6529 (mm-40) cc_final: 0.5932 (tp40) REVERT: B 165 VAL cc_start: 0.8311 (t) cc_final: 0.7926 (m) REVERT: B 170 LYS cc_start: 0.8361 (tttm) cc_final: 0.8067 (tptt) REVERT: B 192 GLN cc_start: 0.7730 (mt0) cc_final: 0.7358 (mm110) REVERT: C 39 MET cc_start: 0.8389 (tpt) cc_final: 0.8052 (tpt) REVERT: C 50 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: C 118 MET cc_start: 0.8652 (mtp) cc_final: 0.8389 (mtm) REVERT: C 154 ARG cc_start: 0.7684 (mtt-85) cc_final: 0.7452 (mtp-110) REVERT: C 170 LYS cc_start: 0.8787 (tttm) cc_final: 0.8346 (tptp) REVERT: C 192 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: D 21 ASN cc_start: 0.8163 (m-40) cc_final: 0.7837 (m110) REVERT: D 140 LYS cc_start: 0.8755 (mttt) cc_final: 0.8414 (mttm) REVERT: D 170 LYS cc_start: 0.8628 (tttm) cc_final: 0.7786 (ttpp) REVERT: D 212 GLU cc_start: 0.7542 (tt0) cc_final: 0.6904 (pt0) REVERT: E 144 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7515 (ttm) REVERT: F 55 MET cc_start: 0.8607 (mtp) cc_final: 0.8277 (mtp) REVERT: F 75 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7164 (pt0) REVERT: F 144 MET cc_start: 0.8458 (ttm) cc_final: 0.8042 (mtt) REVERT: F 151 LEU cc_start: 0.8864 (mt) cc_final: 0.8579 (mp) outliers start: 18 outliers final: 7 residues processed: 145 average time/residue: 1.6554 time to fit residues: 253.1394 Evaluate side-chains 139 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 96 MET 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 120 optimal weight: 0.0070 chunk 18 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.200347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.166061 restraints weight = 9382.510| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.04 r_work: 0.3716 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10067 Z= 0.147 Angle : 0.510 6.637 13675 Z= 0.255 Chirality : 0.042 0.150 1545 Planarity : 0.005 0.043 1769 Dihedral : 4.164 28.806 1337 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.16 % Allowed : 10.42 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.23), residues: 1241 helix: 1.51 (0.17), residues: 883 sheet: -0.93 (0.84), residues: 27 loop : 0.88 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 184 HIS 0.003 0.001 HIS C 12 PHE 0.013 0.002 PHE C 32 TYR 0.015 0.001 TYR E 169 ARG 0.002 0.000 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 636) hydrogen bonds : angle 3.87399 ( 1878) covalent geometry : bond 0.00372 (10067) covalent geometry : angle 0.51039 (13675) *********************** 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 152 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.007 Fit side-chains REVERT: A 75 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7292 (pt0) REVERT: A 79 GLU cc_start: 0.7582 (tt0) cc_final: 0.7166 (mt-10) REVERT: A 170 LYS cc_start: 0.8508 (tttp) cc_final: 0.8271 (tptp) REVERT: A 212 GLU cc_start: 0.7635 (tt0) cc_final: 0.6792 (pm20) REVERT: B 112 GLN cc_start: 0.6594 (mm-40) cc_final: 0.6009 (tp40) REVERT: B 170 LYS cc_start: 0.8349 (tttm) cc_final: 0.8093 (tptt) REVERT: B 192 GLN cc_start: 0.7808 (mt0) cc_final: 0.7438 (mm110) REVERT: C 39 MET cc_start: 0.8394 (tpt) cc_final: 0.8012 (tpt) REVERT: C 50 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: C 118 MET cc_start: 0.8671 (mtp) cc_final: 0.8336 (mtm) REVERT: C 170 LYS cc_start: 0.8833 (tttm) cc_final: 0.8399 (tptp) REVERT: D 21 ASN cc_start: 0.8183 (m-40) cc_final: 0.7869 (m110) REVERT: D 103 ASP cc_start: 0.8700 (m-30) cc_final: 0.8463 (m-30) REVERT: D 140 LYS cc_start: 0.8765 (mttt) cc_final: 0.8548 (mttm) REVERT: D 170 LYS cc_start: 0.8658 (tttm) cc_final: 0.7827 (ttpp) REVERT: D 212 GLU cc_start: 0.7555 (tt0) cc_final: 0.6970 (pt0) REVERT: E 10 MET cc_start: 0.3489 (mmp) cc_final: 0.2858 (pp-130) REVERT: E 144 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7471 (ttm) REVERT: F 55 MET cc_start: 0.8650 (mtp) cc_final: 0.8326 (mtp) outliers start: 23 outliers final: 7 residues processed: 136 average time/residue: 1.6292 time to fit residues: 234.4942 Evaluate side-chains 137 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 29 GLU 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 102 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 32 optimal weight: 0.0060 chunk 90 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 = 0.4286 r_free = 0.4286 target = 0.201090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.166389 restraints weight = 9401.427| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.05 r_work: 0.3720 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2823 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= 0.138 Angle : 0.501 6.505 13675 Z= 0.252 Chirality : 0.042 0.142 1545 Planarity : 0.005 0.043 1769 Dihedral : 4.143 28.643 1337 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.78 % Allowed : 11.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.23), residues: 1241 helix: 1.51 (0.17), residues: 887 sheet: -0.75 (0.84), residues: 27 loop : 0.87 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 184 HIS 0.002 0.001 HIS D 12 PHE 0.013 0.002 PHE C 32 TYR 0.013 0.001 TYR E 169 ARG 0.004 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 636) hydrogen bonds : angle 3.86777 ( 1878) covalent geometry : bond 0.00346 (10067) covalent geometry : angle 0.50147 (13675) *********************** 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 149 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.516 Fit side-chains REVERT: A 45 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6966 (mt-10) REVERT: A 75 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7293 (pt0) REVERT: A 79 GLU cc_start: 0.7557 (tt0) cc_final: 0.7131 (mt-10) REVERT: A 170 LYS cc_start: 0.8534 (tttp) cc_final: 0.8284 (tptp) REVERT: A 212 GLU cc_start: 0.7600 (tt0) cc_final: 0.6750 (pm20) REVERT: B 112 GLN cc_start: 0.6576 (mm-40) cc_final: 0.5986 (tp40) REVERT: B 170 LYS cc_start: 0.8336 (tttm) cc_final: 0.8066 (tptt) REVERT: B 192 GLN cc_start: 0.7808 (mt0) cc_final: 0.7436 (mm110) REVERT: C 50 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: C 118 MET cc_start: 0.8660 (mtp) cc_final: 0.8207 (mtp) REVERT: C 170 LYS cc_start: 0.8797 (tttm) cc_final: 0.8360 (tptp) REVERT: D 21 ASN cc_start: 0.8187 (m-40) cc_final: 0.7869 (m110) REVERT: D 140 LYS cc_start: 0.8759 (mttt) cc_final: 0.8511 (mttm) REVERT: D 170 LYS cc_start: 0.8640 (tttm) cc_final: 0.7793 (ttpp) REVERT: D 212 GLU cc_start: 0.7528 (tt0) cc_final: 0.6971 (pt0) REVERT: E 10 MET cc_start: 0.3754 (mmp) cc_final: 0.2992 (pp-130) REVERT: E 144 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7455 (ttm) REVERT: F 55 MET cc_start: 0.8656 (mtp) cc_final: 0.8329 (mtp) REVERT: F 75 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7154 (pt0) outliers start: 19 outliers final: 6 residues processed: 138 average time/residue: 1.6537 time to fit residues: 241.1087 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 : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 29 GLU 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 E residue 144 MET Chi-restraints excluded: chain F residue 75 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 0.0030 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.200986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.166341 restraints weight = 9440.920| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.08 r_work: 0.3675 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10067 Z= 0.129 Angle : 0.499 7.143 13675 Z= 0.250 Chirality : 0.041 0.143 1545 Planarity : 0.005 0.043 1769 Dihedral : 4.086 28.223 1337 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.60 % Allowed : 11.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.23), residues: 1241 helix: 1.57 (0.17), residues: 887 sheet: -0.59 (0.87), residues: 27 loop : 0.84 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 184 HIS 0.002 0.001 HIS D 12 PHE 0.011 0.002 PHE C 32 TYR 0.014 0.001 TYR E 169 ARG 0.003 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 636) hydrogen bonds : angle 3.83403 ( 1878) covalent geometry : bond 0.00324 (10067) covalent geometry : angle 0.49861 (13675) *********************** 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 144 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 1.128 Fit side-chains REVERT: A 45 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6944 (mt-10) REVERT: A 75 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: A 79 GLU cc_start: 0.7590 (tt0) cc_final: 0.7129 (mt-10) REVERT: A 212 GLU cc_start: 0.7620 (tt0) cc_final: 0.6674 (pm20) REVERT: B 112 GLN cc_start: 0.6569 (mm-40) cc_final: 0.5937 (tp40) REVERT: B 170 LYS cc_start: 0.8368 (tttm) cc_final: 0.8070 (tptt) REVERT: B 192 GLN cc_start: 0.7825 (mt0) cc_final: 0.7409 (mm110) REVERT: C 50 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: C 118 MET cc_start: 0.8642 (mtp) cc_final: 0.8371 (mtm) REVERT: C 170 LYS cc_start: 0.8795 (tttm) cc_final: 0.8347 (tptp) REVERT: C 192 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7864 (mm-40) REVERT: D 21 ASN cc_start: 0.8180 (m-40) cc_final: 0.7860 (m110) REVERT: D 140 LYS cc_start: 0.8790 (mttt) cc_final: 0.8546 (mttm) REVERT: D 170 LYS cc_start: 0.8660 (tttm) cc_final: 0.7807 (ttpp) REVERT: E 10 MET cc_start: 0.3822 (mmp) cc_final: 0.3063 (pp-130) REVERT: E 144 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7547 (ttm) REVERT: F 55 MET cc_start: 0.8647 (mtp) cc_final: 0.8310 (mtp) REVERT: F 75 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7232 (pt0) outliers start: 17 outliers final: 5 residues processed: 133 average time/residue: 1.7568 time to fit residues: 246.7531 Evaluate side-chains 134 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 144 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 99 optimal weight: 0.6980 chunk 47 optimal weight: 0.0970 chunk 112 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.200428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.165793 restraints weight = 9394.414| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.06 r_work: 0.3670 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10067 Z= 0.140 Angle : 0.504 6.936 13675 Z= 0.255 Chirality : 0.042 0.143 1545 Planarity : 0.005 0.043 1769 Dihedral : 4.111 28.197 1337 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.13 % Allowed : 12.49 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.23), residues: 1241 helix: 1.55 (0.17), residues: 884 sheet: -0.57 (0.87), residues: 27 loop : 0.81 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 184 HIS 0.002 0.001 HIS C 12 PHE 0.013 0.002 PHE C 32 TYR 0.014 0.001 TYR E 169 ARG 0.006 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 636) hydrogen bonds : angle 3.87038 ( 1878) covalent geometry : bond 0.00353 (10067) covalent geometry : angle 0.50386 (13675) *********************** 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 143 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 1.011 Fit side-chains REVERT: A 75 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7396 (pt0) REVERT: A 79 GLU cc_start: 0.7593 (tt0) cc_final: 0.7129 (mt-10) REVERT: A 212 GLU cc_start: 0.7609 (tt0) cc_final: 0.6674 (pm20) REVERT: B 112 GLN cc_start: 0.6582 (mm-40) cc_final: 0.5965 (tp40) REVERT: B 170 LYS cc_start: 0.8344 (tttm) cc_final: 0.8057 (tptt) REVERT: B 192 GLN cc_start: 0.7877 (mt0) cc_final: 0.7461 (mm110) REVERT: C 50 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: C 102 SER cc_start: 0.8760 (m) cc_final: 0.8293 (p) REVERT: C 118 MET cc_start: 0.8655 (mtp) cc_final: 0.8375 (mtm) REVERT: C 170 LYS cc_start: 0.8800 (tttm) cc_final: 0.8347 (tptp) REVERT: C 192 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7842 (mm-40) REVERT: D 21 ASN cc_start: 0.8184 (m-40) cc_final: 0.7863 (m110) REVERT: D 140 LYS cc_start: 0.8792 (mttt) cc_final: 0.8547 (mttm) REVERT: D 170 LYS cc_start: 0.8654 (tttm) cc_final: 0.7801 (ttpp) REVERT: D 212 GLU cc_start: 0.7526 (tt0) cc_final: 0.6922 (pt0) REVERT: E 10 MET cc_start: 0.3963 (mmp) cc_final: 0.3243 (pp-130) REVERT: E 144 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7478 (ttm) REVERT: F 55 MET cc_start: 0.8659 (mtp) cc_final: 0.8333 (mtp) outliers start: 12 outliers final: 4 residues processed: 136 average time/residue: 1.5253 time to fit residues: 219.5228 Evaluate side-chains 135 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 83 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 22 optimal weight: 0.0070 chunk 51 optimal weight: 0.0870 chunk 57 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 30 optimal weight: 0.0010 chunk 98 optimal weight: 0.0270 chunk 55 optimal weight: 0.7980 overall best weight: 0.1440 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.205252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.171374 restraints weight = 9343.969| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.03 r_work: 0.3725 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10067 Z= 0.099 Angle : 0.474 7.899 13675 Z= 0.240 Chirality : 0.040 0.142 1545 Planarity : 0.005 0.042 1769 Dihedral : 3.860 27.297 1337 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.31 % Allowed : 12.39 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.24), residues: 1241 helix: 1.82 (0.18), residues: 887 sheet: -0.30 (0.92), residues: 27 loop : 0.91 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 184 HIS 0.001 0.000 HIS C 62 PHE 0.011 0.001 PHE C 32 TYR 0.010 0.001 TYR C 169 ARG 0.006 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 636) hydrogen bonds : angle 3.72976 ( 1878) covalent geometry : bond 0.00229 (10067) covalent geometry : angle 0.47386 (13675) ********************** 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 143 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.974 Fit side-chains REVERT: A 75 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7499 (pt0) REVERT: A 79 GLU cc_start: 0.7602 (tt0) cc_final: 0.7153 (mt-10) REVERT: A 170 LYS cc_start: 0.8463 (tttp) cc_final: 0.8253 (tptp) REVERT: A 212 GLU cc_start: 0.7602 (tt0) cc_final: 0.6655 (pm20) REVERT: B 66 MET cc_start: 0.8281 (mmt) cc_final: 0.7982 (mmm) REVERT: B 112 GLN cc_start: 0.6444 (mm-40) cc_final: 0.5838 (tp40) REVERT: B 170 LYS cc_start: 0.8341 (tttm) cc_final: 0.8043 (tptt) REVERT: B 192 GLN cc_start: 0.7725 (mt0) cc_final: 0.7325 (mm110) REVERT: C 98 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: C 102 SER cc_start: 0.8641 (m) cc_final: 0.8249 (p) REVERT: C 118 MET cc_start: 0.8543 (mtp) cc_final: 0.8322 (mtm) REVERT: C 170 LYS cc_start: 0.8799 (tttm) cc_final: 0.8369 (tptp) REVERT: D 21 ASN cc_start: 0.8222 (m-40) cc_final: 0.7898 (m110) REVERT: D 140 LYS cc_start: 0.8758 (mttt) cc_final: 0.8438 (mttm) REVERT: D 170 LYS cc_start: 0.8670 (tttm) cc_final: 0.7812 (ttpp) REVERT: E 10 MET cc_start: 0.3825 (mmp) cc_final: 0.3053 (pp-130) REVERT: E 144 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7456 (ttm) REVERT: F 55 MET cc_start: 0.8574 (mtp) cc_final: 0.8174 (mtp) REVERT: F 75 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7237 (pt0) outliers start: 14 outliers final: 5 residues processed: 135 average time/residue: 1.6285 time to fit residues: 232.4292 Evaluate side-chains 135 residues out of total 1091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 144 MET 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 F residue 75 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.200680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.165991 restraints weight = 9394.225| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.04 r_work: 0.3665 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3013 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= 0.160 Angle : 0.516 7.585 13675 Z= 0.259 Chirality : 0.043 0.142 1545 Planarity : 0.005 0.044 1769 Dihedral : 4.057 27.511 1337 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.13 % Allowed : 12.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.23), residues: 1241 helix: 1.60 (0.17), residues: 887 sheet: -0.46 (0.88), residues: 27 loop : 0.90 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 80 HIS 0.003 0.001 HIS C 12 PHE 0.013 0.002 PHE C 32 TYR 0.014 0.002 TYR E 169 ARG 0.005 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 636) hydrogen bonds : angle 3.86466 ( 1878) covalent geometry : bond 0.00406 (10067) covalent geometry : angle 0.51638 (13675) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6779.16 seconds wall clock time: 118 minutes 32.98 seconds (7112.98 seconds total)