Starting phenix.real_space_refine on Thu Jul 31 02:28:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6o_29776/07_2025/8g6o_29776.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6o_29776/07_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_29776/07_2025/8g6o_29776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6o_29776/07_2025/8g6o_29776.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6o_29776/07_2025/8g6o_29776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6o_29776/07_2025/8g6o_29776.cif" } resolution = 3.1 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= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.87, per 1000 atoms: 0.60 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: 3.65 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.07 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: 4.71 Time building geometry restraints manager: 4.41 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: 3.490 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: 0.250 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.590 Find NCS groups from input model: 0.670 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.760 ------------------------------------------------------------------------------- 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 (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 (0.29), 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 TRP 0.005 0.001 TRP A 80 HIS 0.003 0.001 HIS A 84 PHE 0.009 0.001 PHE D 32 TYR 0.010 0.001 TYR D 169 ARG 0.006 0.000 ARG C 154 Details of bonding type rmsd hydrogen bonds : bond 0.09952 ( 433) hydrogen bonds : angle 4.31552 ( 1281) covalent geometry : bond 0.00423 ( 6754) covalent geometry : angle 0.69310 ( 9174) *********************** 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 : 1.129 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: 0.5475 time to fit residues: 77.7056 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 : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.0470 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.0050 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.3892 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.145811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117692 restraints weight = 28631.892| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.33 r_work: 0.3250 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.0571 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= 0.101 Angle : 0.490 4.702 9174 Z= 0.243 Chirality : 0.036 0.147 1029 Planarity : 0.004 0.039 1189 Dihedral : 3.715 16.001 892 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.42 % Allowed : 14.39 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 2.36 (0.30), residues: 826 helix: 2.07 (0.22), residues: 599 sheet: -2.79 (0.85), residues: 9 loop : 0.45 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 117 HIS 0.002 0.000 HIS D 84 PHE 0.007 0.001 PHE D 32 TYR 0.010 0.001 TYR A 169 ARG 0.002 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 433) hydrogen bonds : angle 3.87219 ( 1281) covalent geometry : bond 0.00223 ( 6754) covalent geometry : angle 0.49023 ( 9174) *********************** 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 124 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 TYR cc_start: 0.7233 (t80) cc_final: 0.7030 (t80) outliers start: 3 outliers final: 3 residues processed: 123 average time/residue: 0.5211 time to fit residues: 80.9957 Evaluate side-chains 118 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 38 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.145335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111208 restraints weight = 28894.683| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.03 r_work: 0.3249 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.0809 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= 0.104 Angle : 0.474 4.432 9174 Z= 0.235 Chirality : 0.037 0.147 1029 Planarity : 0.004 0.038 1189 Dihedral : 3.612 16.115 892 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.56 % Allowed : 14.25 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 2.45 (0.30), residues: 826 helix: 2.15 (0.22), residues: 600 sheet: -2.92 (0.89), residues: 9 loop : 0.46 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 184 HIS 0.003 0.000 HIS A 84 PHE 0.008 0.001 PHE D 32 TYR 0.009 0.001 TYR A 169 ARG 0.004 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 433) hydrogen bonds : angle 3.77472 ( 1281) covalent geometry : bond 0.00238 ( 6754) covalent geometry : angle 0.47377 ( 9174) *********************** 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 120 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.8380 (mmm) cc_final: 0.6239 (tpt) REVERT: C 10 MET cc_start: 0.6847 (mmm) cc_final: 0.6589 (mmm) REVERT: C 144 MET cc_start: 0.8651 (ttp) cc_final: 0.8321 (ttp) REVERT: E 28 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7677 (mm-30) outliers start: 4 outliers final: 3 residues processed: 119 average time/residue: 0.4746 time to fit residues: 72.0166 Evaluate side-chains 112 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 146 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 74 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN B 155 GLN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.144907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116715 restraints weight = 28762.601| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.39 r_work: 0.3168 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0943 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= 0.112 Angle : 0.476 4.189 9174 Z= 0.238 Chirality : 0.037 0.146 1029 Planarity : 0.004 0.039 1189 Dihedral : 3.592 16.320 892 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.98 % Allowed : 14.66 % 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 (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: 2.49 (0.30), residues: 826 helix: 2.20 (0.22), residues: 594 sheet: -3.10 (0.88), residues: 9 loop : 0.46 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 80 HIS 0.003 0.000 HIS A 84 PHE 0.009 0.001 PHE D 32 TYR 0.009 0.001 TYR A 169 ARG 0.002 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 433) hydrogen bonds : angle 3.75646 ( 1281) covalent geometry : bond 0.00258 ( 6754) covalent geometry : angle 0.47624 ( 9174) *********************** 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 118 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.8438 (mmm) cc_final: 0.6252 (tpt) REVERT: C 10 MET cc_start: 0.6857 (mmm) cc_final: 0.6609 (mmm) REVERT: C 144 MET cc_start: 0.8753 (ttp) cc_final: 0.8203 (ttp) REVERT: E 28 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7648 (mm-30) outliers start: 7 outliers final: 4 residues processed: 116 average time/residue: 0.4758 time to fit residues: 70.3978 Evaluate side-chains 112 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 2 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.144464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110394 restraints weight = 29057.446| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.02 r_work: 0.3231 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: 0.7947 moved from start: 0.1040 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= 0.109 Angle : 0.468 4.201 9174 Z= 0.233 Chirality : 0.037 0.145 1029 Planarity : 0.004 0.039 1189 Dihedral : 3.560 16.167 892 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.84 % Allowed : 15.08 % 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 (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: 2.55 (0.30), residues: 826 helix: 2.25 (0.22), residues: 594 sheet: -3.02 (0.95), residues: 9 loop : 0.46 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 80 HIS 0.003 0.000 HIS A 84 PHE 0.009 0.001 PHE D 32 TYR 0.010 0.001 TYR A 169 ARG 0.001 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 433) hydrogen bonds : angle 3.72169 ( 1281) covalent geometry : bond 0.00253 ( 6754) covalent geometry : angle 0.46842 ( 9174) *********************** 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: 6 poor density : 116 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 MET cc_start: 0.6817 (mmm) cc_final: 0.6566 (mmm) REVERT: C 144 MET cc_start: 0.8722 (ttp) cc_final: 0.8280 (ttp) REVERT: E 28 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7643 (mm-30) outliers start: 6 outliers final: 6 residues processed: 121 average time/residue: 0.4866 time to fit residues: 75.0922 Evaluate side-chains 116 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.143870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109717 restraints weight = 29149.163| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.03 r_work: 0.3213 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1127 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= 0.123 Angle : 0.477 4.191 9174 Z= 0.239 Chirality : 0.037 0.143 1029 Planarity : 0.004 0.039 1189 Dihedral : 3.591 16.746 892 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.26 % Allowed : 14.25 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 2.53 (0.30), residues: 826 helix: 2.24 (0.22), residues: 594 sheet: -3.06 (0.94), residues: 9 loop : 0.45 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 80 HIS 0.003 0.001 HIS A 84 PHE 0.011 0.001 PHE D 32 TYR 0.011 0.001 TYR A 169 ARG 0.001 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 433) hydrogen bonds : angle 3.74660 ( 1281) covalent geometry : bond 0.00290 ( 6754) covalent geometry : angle 0.47738 ( 9174) *********************** 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 126 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 MET cc_start: 0.6860 (mmm) cc_final: 0.6586 (mmm) REVERT: E 28 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7550 (mm-30) outliers start: 9 outliers final: 8 residues processed: 123 average time/residue: 0.5084 time to fit residues: 80.9164 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 : 1.059 ------------------------------------------------------------------------------- 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 197 ASP 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 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.0070 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.144548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110439 restraints weight = 28913.938| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.03 r_work: 0.3226 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1185 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= 0.101 Angle : 0.468 4.139 9174 Z= 0.233 Chirality : 0.036 0.143 1029 Planarity : 0.004 0.041 1189 Dihedral : 3.530 16.424 892 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.70 % Allowed : 15.22 % 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 (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: 2.59 (0.30), residues: 826 helix: 2.28 (0.22), residues: 594 sheet: -2.94 (0.98), residues: 9 loop : 0.47 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 80 HIS 0.002 0.000 HIS A 84 PHE 0.008 0.001 PHE D 32 TYR 0.010 0.001 TYR A 169 ARG 0.001 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 433) hydrogen bonds : angle 3.68248 ( 1281) covalent geometry : bond 0.00233 ( 6754) covalent geometry : angle 0.46769 ( 9174) *********************** 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 122 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.8371 (mmm) cc_final: 0.6325 (tpt) REVERT: C 10 MET cc_start: 0.6884 (mmm) cc_final: 0.6640 (mmm) REVERT: E 28 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7570 (mm-30) outliers start: 5 outliers final: 5 residues processed: 121 average time/residue: 0.5418 time to fit residues: 83.4779 Evaluate side-chains 119 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 175 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.143728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109545 restraints weight = 29032.461| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.01 r_work: 0.3221 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1230 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= 0.120 Angle : 0.480 4.196 9174 Z= 0.240 Chirality : 0.037 0.140 1029 Planarity : 0.004 0.040 1189 Dihedral : 3.550 16.773 892 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.12 % Allowed : 14.94 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 2.52 (0.30), residues: 826 helix: 2.23 (0.22), residues: 594 sheet: -2.90 (1.01), residues: 9 loop : 0.40 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 80 HIS 0.003 0.000 HIS A 84 PHE 0.010 0.001 PHE D 32 TYR 0.011 0.001 TYR A 169 ARG 0.001 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 433) hydrogen bonds : angle 3.72485 ( 1281) covalent geometry : bond 0.00283 ( 6754) covalent geometry : angle 0.47978 ( 9174) *********************** 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 123 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.8393 (mmm) cc_final: 0.6347 (tpt) REVERT: C 10 MET cc_start: 0.6908 (mmm) cc_final: 0.6629 (mmm) REVERT: E 28 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7598 (mm-30) outliers start: 8 outliers final: 7 residues processed: 120 average time/residue: 0.6157 time to fit residues: 94.8293 Evaluate side-chains 118 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 176 GLN 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 197 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.144237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110203 restraints weight = 28867.024| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.01 r_work: 0.3224 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1272 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= 0.106 Angle : 0.472 4.117 9174 Z= 0.235 Chirality : 0.037 0.140 1029 Planarity : 0.004 0.041 1189 Dihedral : 3.514 16.704 892 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.84 % Allowed : 15.50 % 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 (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: 2.59 (0.30), residues: 826 helix: 2.29 (0.22), residues: 594 sheet: -2.77 (1.06), residues: 9 loop : 0.43 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 184 HIS 0.004 0.001 HIS B 120 PHE 0.009 0.001 PHE D 32 TYR 0.010 0.001 TYR A 169 ARG 0.002 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 433) hydrogen bonds : angle 3.68004 ( 1281) covalent geometry : bond 0.00245 ( 6754) covalent geometry : angle 0.47162 ( 9174) *********************** 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 122 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.8411 (mmm) cc_final: 0.6397 (tpt) REVERT: C 10 MET cc_start: 0.6930 (mmm) cc_final: 0.6688 (mmm) REVERT: E 28 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7600 (mm-30) outliers start: 6 outliers final: 5 residues processed: 120 average time/residue: 0.4791 time to fit residues: 73.4334 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 : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 175 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.144824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110806 restraints weight = 28897.556| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.01 r_work: 0.3237 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6754 Z= 0.096 Angle : 0.462 4.087 9174 Z= 0.230 Chirality : 0.036 0.141 1029 Planarity : 0.004 0.041 1189 Dihedral : 3.451 16.523 892 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.70 % Allowed : 16.06 % 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 (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: 2.64 (0.30), residues: 826 helix: 2.32 (0.22), residues: 594 sheet: -2.76 (1.10), residues: 9 loop : 0.45 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 184 HIS 0.002 0.000 HIS B 120 PHE 0.007 0.001 PHE D 32 TYR 0.010 0.001 TYR D 169 ARG 0.001 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 433) hydrogen bonds : angle 3.63975 ( 1281) covalent geometry : bond 0.00223 ( 6754) covalent geometry : angle 0.46243 ( 9174) ********************** 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 121 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 MET cc_start: 0.8400 (mmm) cc_final: 0.6365 (tpt) REVERT: C 10 MET cc_start: 0.6925 (mmm) cc_final: 0.6651 (mmm) REVERT: C 118 MET cc_start: 0.8501 (mtm) cc_final: 0.8068 (mtm) REVERT: E 28 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7593 (mm-30) outliers start: 5 outliers final: 5 residues processed: 119 average time/residue: 0.6216 time to fit residues: 95.2861 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 : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 175 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 72 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.144543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113052 restraints weight = 28814.782| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.09 r_work: 0.3235 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6754 Z= 0.100 Angle : 0.481 6.000 9174 Z= 0.241 Chirality : 0.036 0.140 1029 Planarity : 0.004 0.041 1189 Dihedral : 3.454 16.445 892 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.84 % Allowed : 16.20 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 2.65 (0.30), residues: 826 helix: 2.33 (0.22), residues: 594 sheet: -2.88 (1.11), residues: 9 loop : 0.47 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.008 0.001 HIS B 120 PHE 0.007 0.001 PHE D 32 TYR 0.010 0.001 TYR D 169 ARG 0.001 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 433) hydrogen bonds : angle 3.62626 ( 1281) covalent geometry : bond 0.00233 ( 6754) covalent geometry : angle 0.48086 ( 9174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9115.27 seconds wall clock time: 160 minutes 12.82 seconds (9612.82 seconds total)