Starting phenix.real_space_refine on Sat Aug 23 15:33:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6o_29776/08_2025/8g6o_29776.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6o_29776/08_2025/8g6o_29776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g6o_29776/08_2025/8g6o_29776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6o_29776/08_2025/8g6o_29776.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6o_29776/08_2025/8g6o_29776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6o_29776/08_2025/8g6o_29776.cif" } resolution = 3.1 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 4170 2.51 5 N 1152 2.21 5 O 1240 1.98 5 H 6522 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13132 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3106 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2707 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3290 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3096 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 933 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.15, per 1000 atoms: 0.16 Number of scatterers: 13132 At special positions: 0 Unit cell: (114.4, 107.9, 122.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 1240 8.00 N 1152 7.00 C 4170 6.00 H 6522 1.00 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: 1.06 Conformation dependent library (CDL) restraints added in 484.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 1 sheets defined 76.8% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 removed outlier: 3.791A pdb=" N LEU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.769A pdb=" N MET A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) 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 120 Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.616A pdb=" N TRP A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 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 removed outlier: 3.571A pdb=" N MET B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) 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 106 Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 174 removed outlier: 3.703A pdb=" N ALA B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.357A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 31 removed outlier: 4.128A pdb=" N ALA C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 60 removed outlier: 3.857A pdb=" N THR C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.618A pdb=" N ALA C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.275A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 4.146A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 31 removed outlier: 3.767A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 removed outlier: 3.675A pdb=" N MET D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) 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 116 Processing helix chain 'D' and resid 125 through 146 Processing helix chain 'D' and resid 160 through 174 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.373A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.672A pdb=" N THR D 200 " --> pdb=" O PRO D 196 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) 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 removed outlier: 3.682A pdb=" N MET E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 59 removed outlier: 3.674A pdb=" N VAL E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 73 Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 433 hydrogen bonds defined for protein. 1281 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: 2.53 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6516 1.03 - 1.23: 27 1.23 - 1.42: 2683 1.42 - 1.62: 3960 1.62 - 1.81: 90 Bond restraints: 13276 Sorted by residual: bond pdb=" CB GLU B 28 " pdb=" CG GLU B 28 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.02e+00 bond pdb=" CB LYS B 25 " pdb=" CG LYS B 25 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CB ILE B 104 " pdb=" CG2 ILE B 104 " ideal model delta sigma weight residual 1.521 1.564 -0.043 3.30e-02 9.18e+02 1.68e+00 bond pdb=" CG LYS B 25 " pdb=" CD LYS B 25 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CB ILE D 104 " pdb=" CG2 ILE D 104 " ideal model delta sigma weight residual 1.521 1.563 -0.042 3.30e-02 9.18e+02 1.63e+00 ... (remaining 13271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 22712 1.34 - 2.68: 1126 2.68 - 4.02: 147 4.02 - 5.36: 50 5.36 - 6.70: 14 Bond angle restraints: 24049 Sorted by residual: angle pdb=" CA PRO D 207 " pdb=" N PRO D 207 " pdb=" CD PRO D 207 " ideal model delta sigma weight residual 112.00 107.49 4.51 1.40e+00 5.10e-01 1.04e+01 angle pdb=" CA GLU B 28 " pdb=" CB GLU B 28 " pdb=" CG GLU B 28 " ideal model delta sigma weight residual 114.10 119.69 -5.59 2.00e+00 2.50e-01 7.81e+00 angle pdb=" CB LYS B 25 " pdb=" CG LYS B 25 " pdb=" CD LYS B 25 " ideal model delta sigma weight residual 111.30 117.51 -6.21 2.30e+00 1.89e-01 7.28e+00 angle pdb=" N PRO D 207 " pdb=" CD PRO D 207 " pdb=" CG PRO D 207 " ideal model delta sigma weight residual 103.20 99.29 3.91 1.50e+00 4.44e-01 6.81e+00 angle pdb=" CA GLU E 29 " pdb=" CB GLU E 29 " pdb=" CG GLU E 29 " ideal model delta sigma weight residual 114.10 119.26 -5.16 2.00e+00 2.50e-01 6.67e+00 ... (remaining 24044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5438 17.96 - 35.93: 582 35.93 - 53.89: 194 53.89 - 71.86: 46 71.86 - 89.82: 18 Dihedral angle restraints: 6278 sinusoidal: 3497 harmonic: 2781 Sorted by residual: dihedral pdb=" CA ILE D 115 " pdb=" C ILE D 115 " pdb=" N GLY D 116 " pdb=" CA GLY D 116 " ideal model delta harmonic sigma weight residual 180.00 161.94 18.06 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CB GLU E 29 " pdb=" CG GLU E 29 " pdb=" CD GLU E 29 " pdb=" OE1 GLU E 29 " ideal model delta sinusoidal sigma weight residual 0.00 -89.78 89.78 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 159 " pdb=" CG GLU B 159 " pdb=" CD GLU B 159 " pdb=" OE1 GLU B 159 " ideal model delta sinusoidal sigma weight residual 0.00 -89.45 89.45 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 670 0.031 - 0.063: 235 0.063 - 0.094: 76 0.094 - 0.125: 44 0.125 - 0.157: 4 Chirality restraints: 1029 Sorted by residual: chirality pdb=" CA ILE B 124 " pdb=" N ILE B 124 " pdb=" C ILE B 124 " pdb=" CB ILE B 124 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 1026 not shown) Planarity restraints: 1962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 206 " -0.050 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO D 207 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 207 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 207 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 37 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO C 38 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 38 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 38 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 154 " 0.114 9.50e-02 1.11e+02 3.82e-02 1.73e+00 pdb=" NE ARG C 154 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG C 154 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 154 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C 154 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 154 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG C 154 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG C 154 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 154 " 0.001 2.00e-02 2.50e+03 ... (remaining 1959 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 2820 2.31 - 2.88: 29390 2.88 - 3.45: 34729 3.45 - 4.03: 44427 4.03 - 4.60: 68822 Nonbonded interactions: 180188 Sorted by model distance: nonbonded pdb=" O HIS D 84 " pdb="HH12 ARG D 100 " model vdw 1.737 2.450 nonbonded pdb=" OE1 GLN B 179 " pdb=" H GLN B 179 " model vdw 1.738 2.450 nonbonded pdb=" OE1 GLN D 112 " pdb=" H GLN D 112 " model vdw 1.743 2.450 nonbonded pdb=" O ILE C 115 " pdb=" HG1 THR C 119 " model vdw 1.746 2.450 nonbonded pdb=" OD1 ASN C 53 " pdb=" HH TYR C 130 " model vdw 1.747 2.450 ... (remaining 180183 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 12 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or (resid 66 and (name N or name CA or name C or name \ O or name CB or name CG or name SD or name CE )) or resid 67 through 85 or (resi \ d 96 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 97 through 117 or (resid 118 and (name N or name CA or name C or nam \ e O or name CB or name CG or name SD or name CE )) or resid 119 or (resid 120 an \ d (name N or name CA or name C or name O or name CB or name CG or name ND1 or na \ me CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or n \ ame HD1 or name HD2 or name HE1)) or resid 121 through 174 or (resid 175 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD or name OE1 \ or name OE2 or name H or name HA )) or resid 176 through 181 or (resid 182 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 183 through 193)) selection = (chain 'B' and ((resid 12 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 13 throug \ h 85 or (resid 96 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 97 through 117 or (resid 118 and (name N or name CA or \ name C or name O or name CB or name CG or name SD or name CE )) or resid 119 or \ (resid 120 and (name N or name CA or name C or name O or name CB or name CG or n \ ame ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or \ name HB3 or name HD1 or name HD2 or name HE1)) or resid 121 through 174 or (resi \ d 175 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name OE1 or name OE2 or name H or name HA )) or resid 176 through 193)) selection = (chain 'C' and (resid 12 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or (resid 66 and (name N or name CA or name C or name \ O or name CB or name CG or name SD or name CE )) or resid 67 through 85 or (resi \ d 96 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 97 through 117 or (resid 118 and (name N or name CA or name C or nam \ e O or name CB or name CG or name SD or name CE )) or resid 119 through 174 or ( \ resid 175 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1 or name OE2 or name H or name HA )) or resid 176 through 181 o \ r (resid 182 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 183 through 186 or (resid 187 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 188 through 193)) selection = (chain 'D' and ((resid 12 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 13 throug \ h 61 or (resid 62 and (name N or name CA or name C or name O or name CB or name \ CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name \ HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 63 through 64 or \ (resid 65 and (name N or name CA or name C or name O or name CB )) or (resid 66 \ and (name N or name CA or name C or name O or name CB or name CG or name SD or n \ ame CE )) or resid 67 through 83 or (resid 84 and (name N or name CA or name C o \ r name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 o \ r name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1) \ ) or resid 85 through 119 or (resid 120 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or r \ esid 121 through 181 or (resid 182 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 183 through 186 or (resid 187 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 1 \ 88 through 193)) } 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: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.450 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6754 Z= 0.168 Angle : 0.693 6.701 9174 Z= 0.331 Chirality : 0.040 0.157 1029 Planarity : 0.005 0.074 1189 Dihedral : 17.304 89.825 2539 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 14.39 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: 1.88 (0.29), residues: 826 helix: 1.71 (0.21), residues: 598 sheet: -2.93 (0.89), residues: 9 loop : 0.29 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 154 TYR 0.010 0.001 TYR D 169 PHE 0.009 0.001 PHE D 32 TRP 0.005 0.001 TRP A 80 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 6754) covalent geometry : angle 0.69310 ( 9174) hydrogen bonds : bond 0.09952 ( 433) hydrogen bonds : angle 4.31552 ( 1281) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 MET cc_start: 0.8615 (ptp) cc_final: 0.8398 (ptp) REVERT: C 144 MET cc_start: 0.8428 (ttp) cc_final: 0.8214 (ttm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2353 time to fit residues: 32.7445 Evaluate side-chains 110 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN D 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.144675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116353 restraints weight = 28925.769| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.33 r_work: 0.3196 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6754 Z= 0.127 Angle : 0.502 4.975 9174 Z= 0.250 Chirality : 0.037 0.146 1029 Planarity : 0.004 0.038 1189 Dihedral : 3.769 16.513 892 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.56 % Allowed : 14.39 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: 2.27 (0.30), residues: 826 helix: 2.02 (0.22), residues: 599 sheet: -2.88 (0.84), residues: 9 loop : 0.38 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 143 TYR 0.011 0.001 TYR A 169 PHE 0.010 0.001 PHE D 32 TRP 0.005 0.001 TRP C 184 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6754) covalent geometry : angle 0.50223 ( 9174) hydrogen bonds : bond 0.03999 ( 433) hydrogen bonds : angle 3.92265 ( 1281) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.8397 (mmm) cc_final: 0.6335 (tpt) outliers start: 4 outliers final: 4 residues processed: 121 average time/residue: 0.2363 time to fit residues: 35.8524 Evaluate side-chains 115 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 197 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 78 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 0.0060 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.144705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116427 restraints weight = 29139.145| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.41 r_work: 0.3226 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6754 Z= 0.112 Angle : 0.482 4.502 9174 Z= 0.239 Chirality : 0.037 0.147 1029 Planarity : 0.004 0.038 1189 Dihedral : 3.673 16.397 892 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.42 % Allowed : 14.94 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: 2.38 (0.30), residues: 826 helix: 2.11 (0.22), residues: 599 sheet: -3.07 (0.90), residues: 9 loop : 0.39 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 143 TYR 0.009 0.001 TYR D 169 PHE 0.009 0.001 PHE D 32 TRP 0.004 0.001 TRP B 184 HIS 0.003 0.000 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6754) covalent geometry : angle 0.48248 ( 9174) hydrogen bonds : bond 0.03744 ( 433) hydrogen bonds : angle 3.81738 ( 1281) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: B 66 MET cc_start: 0.8449 (mmm) cc_final: 0.6336 (tpt) REVERT: C 10 MET cc_start: 0.6790 (mmm) cc_final: 0.6535 (mmm) outliers start: 3 outliers final: 3 residues processed: 116 average time/residue: 0.2069 time to fit residues: 30.2795 Evaluate side-chains 111 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 197 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN B 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109004 restraints weight = 29003.455| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.00 r_work: 0.3194 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6754 Z= 0.147 Angle : 0.503 4.570 9174 Z= 0.254 Chirality : 0.038 0.145 1029 Planarity : 0.004 0.038 1189 Dihedral : 3.723 16.776 892 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.68 % Allowed : 14.25 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: 2.35 (0.30), residues: 826 helix: 2.12 (0.22), residues: 593 sheet: -3.18 (0.89), residues: 9 loop : 0.32 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 TYR 0.011 0.001 TYR A 169 PHE 0.012 0.001 PHE D 32 TRP 0.006 0.001 TRP A 80 HIS 0.006 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6754) covalent geometry : angle 0.50300 ( 9174) hydrogen bonds : bond 0.03888 ( 433) hydrogen bonds : angle 3.86140 ( 1281) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.8398 (mmm) cc_final: 0.6239 (tpt) REVERT: C 10 MET cc_start: 0.6822 (mmm) cc_final: 0.6565 (mmm) REVERT: C 202 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8106 (mm) outliers start: 12 outliers final: 6 residues processed: 121 average time/residue: 0.2201 time to fit residues: 33.5428 Evaluate side-chains 114 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain E residue 68 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 0.0060 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN B 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.143525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109476 restraints weight = 29053.496| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.02 r_work: 0.3225 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6754 Z= 0.114 Angle : 0.484 4.795 9174 Z= 0.240 Chirality : 0.037 0.145 1029 Planarity : 0.004 0.040 1189 Dihedral : 3.651 16.726 892 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.12 % Allowed : 14.53 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: 2.47 (0.30), residues: 826 helix: 2.21 (0.22), residues: 593 sheet: -3.07 (0.92), residues: 9 loop : 0.38 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 100 TYR 0.010 0.001 TYR A 169 PHE 0.010 0.001 PHE D 32 TRP 0.006 0.001 TRP A 80 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6754) covalent geometry : angle 0.48446 ( 9174) hydrogen bonds : bond 0.03625 ( 433) hydrogen bonds : angle 3.78524 ( 1281) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 10 MET cc_start: 0.6867 (mmm) cc_final: 0.6616 (mmm) REVERT: C 202 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8148 (mm) outliers start: 8 outliers final: 7 residues processed: 120 average time/residue: 0.2014 time to fit residues: 31.2233 Evaluate side-chains 117 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain E residue 68 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 0.0980 chunk 56 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 59 optimal weight: 0.0470 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 0.2878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110943 restraints weight = 29051.806| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.03 r_work: 0.3236 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6754 Z= 0.088 Angle : 0.456 4.067 9174 Z= 0.227 Chirality : 0.036 0.144 1029 Planarity : 0.004 0.042 1189 Dihedral : 3.487 16.184 892 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.70 % Allowed : 14.53 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: 2.69 (0.30), residues: 826 helix: 2.35 (0.22), residues: 593 sheet: -2.94 (0.98), residues: 9 loop : 0.53 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 100 TYR 0.009 0.001 TYR D 169 PHE 0.005 0.001 PHE D 32 TRP 0.004 0.000 TRP A 80 HIS 0.001 0.000 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00195 ( 6754) covalent geometry : angle 0.45644 ( 9174) hydrogen bonds : bond 0.03315 ( 433) hydrogen bonds : angle 3.64929 ( 1281) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLN cc_start: 0.7890 (mt0) cc_final: 0.7662 (mt0) REVERT: C 10 MET cc_start: 0.6865 (mmm) cc_final: 0.6596 (mmm) outliers start: 5 outliers final: 5 residues processed: 121 average time/residue: 0.2243 time to fit residues: 34.8507 Evaluate side-chains 118 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain E residue 68 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN B 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.143817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111848 restraints weight = 28900.495| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.06 r_work: 0.3207 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6754 Z= 0.117 Angle : 0.475 4.172 9174 Z= 0.237 Chirality : 0.037 0.141 1029 Planarity : 0.004 0.040 1189 Dihedral : 3.525 16.524 892 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.12 % Allowed : 14.53 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: 2.64 (0.30), residues: 826 helix: 2.33 (0.22), residues: 593 sheet: -3.01 (0.99), residues: 9 loop : 0.46 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 167 TYR 0.010 0.001 TYR A 169 PHE 0.010 0.001 PHE D 32 TRP 0.005 0.001 TRP A 80 HIS 0.004 0.000 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6754) covalent geometry : angle 0.47479 ( 9174) hydrogen bonds : bond 0.03476 ( 433) hydrogen bonds : angle 3.71605 ( 1281) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLN cc_start: 0.7974 (mt0) cc_final: 0.7707 (mt0) REVERT: C 10 MET cc_start: 0.6814 (mmm) cc_final: 0.6563 (mmm) outliers start: 8 outliers final: 7 residues processed: 121 average time/residue: 0.2298 time to fit residues: 35.6439 Evaluate side-chains 120 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain E residue 68 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.142763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108756 restraints weight = 28892.907| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.00 r_work: 0.3209 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6754 Z= 0.141 Angle : 0.493 4.231 9174 Z= 0.247 Chirality : 0.038 0.140 1029 Planarity : 0.004 0.039 1189 Dihedral : 3.610 16.951 892 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.26 % Allowed : 15.08 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: 2.56 (0.30), residues: 826 helix: 2.28 (0.22), residues: 593 sheet: -3.12 (1.03), residues: 9 loop : 0.38 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 167 TYR 0.011 0.001 TYR A 169 PHE 0.012 0.001 PHE D 32 TRP 0.006 0.001 TRP A 80 HIS 0.004 0.000 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6754) covalent geometry : angle 0.49268 ( 9174) hydrogen bonds : bond 0.03653 ( 433) hydrogen bonds : angle 3.78704 ( 1281) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 MET cc_start: 0.6863 (mmm) cc_final: 0.6616 (mmm) outliers start: 9 outliers final: 7 residues processed: 118 average time/residue: 0.2348 time to fit residues: 35.2756 Evaluate side-chains 119 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain E residue 68 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.143563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109541 restraints weight = 28953.953| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.00 r_work: 0.3229 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6754 Z= 0.109 Angle : 0.475 4.086 9174 Z= 0.237 Chirality : 0.037 0.140 1029 Planarity : 0.004 0.041 1189 Dihedral : 3.558 16.824 892 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.98 % Allowed : 15.22 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: 2.64 (0.30), residues: 826 helix: 2.33 (0.22), residues: 593 sheet: -3.03 (1.07), residues: 9 loop : 0.44 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 167 TYR 0.010 0.001 TYR A 169 PHE 0.009 0.001 PHE D 32 TRP 0.005 0.001 TRP A 80 HIS 0.003 0.000 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6754) covalent geometry : angle 0.47527 ( 9174) hydrogen bonds : bond 0.03488 ( 433) hydrogen bonds : angle 3.72325 ( 1281) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.8292 (mmm) cc_final: 0.6403 (tpt) REVERT: C 10 MET cc_start: 0.6868 (mmm) cc_final: 0.6581 (mmm) outliers start: 7 outliers final: 6 residues processed: 122 average time/residue: 0.2347 time to fit residues: 36.2913 Evaluate side-chains 118 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain E residue 68 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.144000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111921 restraints weight = 28983.337| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.08 r_work: 0.3206 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6754 Z= 0.101 Angle : 0.475 4.109 9174 Z= 0.235 Chirality : 0.036 0.140 1029 Planarity : 0.004 0.041 1189 Dihedral : 3.516 16.704 892 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.98 % Allowed : 15.78 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: 2.69 (0.30), residues: 826 helix: 2.37 (0.22), residues: 593 sheet: -3.00 (1.09), residues: 9 loop : 0.45 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 100 TYR 0.010 0.001 TYR D 169 PHE 0.008 0.001 PHE D 32 TRP 0.005 0.001 TRP A 80 HIS 0.002 0.000 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 6754) covalent geometry : angle 0.47489 ( 9174) hydrogen bonds : bond 0.03384 ( 433) hydrogen bonds : angle 3.68299 ( 1281) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1652 Ramachandran restraints generated. 826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.8290 (mmm) cc_final: 0.6386 (tpt) REVERT: C 10 MET cc_start: 0.6864 (mmm) cc_final: 0.6588 (mmm) REVERT: C 118 MET cc_start: 0.8499 (mtm) cc_final: 0.8094 (mtm) outliers start: 7 outliers final: 6 residues processed: 121 average time/residue: 0.1974 time to fit residues: 30.5770 Evaluate side-chains 120 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain E residue 68 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.142388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110177 restraints weight = 29042.550| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.99 r_work: 0.3205 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6754 Z= 0.149 Angle : 0.498 4.235 9174 Z= 0.250 Chirality : 0.038 0.140 1029 Planarity : 0.004 0.040 1189 Dihedral : 3.628 17.228 892 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.12 % Allowed : 15.78 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 aren not related in a simple way. whole: 2.52 (0.30), residues: 826 helix: 2.26 (0.22), residues: 593 sheet: -3.15 (1.07), residues: 9 loop : 0.33 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 167 TYR 0.012 0.001 TYR A 169 PHE 0.013 0.001 PHE D 32 TRP 0.006 0.001 TRP A 80 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6754) covalent geometry : angle 0.49771 ( 9174) hydrogen bonds : bond 0.03666 ( 433) hydrogen bonds : angle 3.79957 ( 1281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4068.91 seconds wall clock time: 69 minutes 35.99 seconds (4175.99 seconds total)