Starting phenix.real_space_refine on Fri Aug 22 23:31:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eit_28164/08_2025/8eit_28164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eit_28164/08_2025/8eit_28164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eit_28164/08_2025/8eit_28164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eit_28164/08_2025/8eit_28164.map" model { file = "/net/cci-nas-00/data/ceres_data/8eit_28164/08_2025/8eit_28164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eit_28164/08_2025/8eit_28164.cif" } resolution = 2.8 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= 0.003 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: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 5453 2.51 5 N 1480 2.21 5 O 1596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s 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: 8578 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1821 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2565 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 422 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 1961 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 247} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'HXA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'HXA:plan-3': 1, 'HXA:plan-4': 1, 'HXA:plan-5': 1, 'HXA:plan-6': 1, 'HXA:plan-7': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 2.23, per 1000 atoms: 0.26 Number of scatterers: 8578 At special positions: 0 Unit cell: (100.44, 119.88, 125.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1596 8.00 N 1480 7.00 C 5453 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 447.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 38.4% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 4.111A pdb=" N THR A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 removed outlier: 4.403A pdb=" N TRP A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 89' Processing helix chain 'A' and resid 90 through 93 removed outlier: 3.829A pdb=" N ASN A 93 " --> pdb=" O GLN A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 93' Processing helix chain 'A' and resid 109 through 122 Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 156 through 162 Processing helix chain 'A' and resid 175 through 196 removed outlier: 3.687A pdb=" N PHE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 235 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.534A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 26 Processing helix chain 'C' and resid 29 through 42 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.209A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.564A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.569A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 220 through 224 removed outlier: 4.030A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 37 Proline residue: R 21 - end of helix removed outlier: 4.000A pdb=" N LEU R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG R 37 " --> pdb=" O HIS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 68 Proline residue: R 60 - end of helix removed outlier: 3.585A pdb=" N ALA R 68 " --> pdb=" O VAL R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 77 No H-bonds generated for 'chain 'R' and resid 75 through 77' Processing helix chain 'R' and resid 78 through 87 removed outlier: 3.534A pdb=" N PHE R 82 " --> pdb=" O LEU R 78 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 107 removed outlier: 5.270A pdb=" N GLY R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY R 95 " --> pdb=" O TYR R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 117 Processing helix chain 'R' and resid 119 through 143 removed outlier: 3.511A pdb=" N SER R 123 " --> pdb=" O ARG R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 191 Proline residue: R 181 - end of helix Processing helix chain 'R' and resid 191 through 212 Processing helix chain 'R' and resid 215 through 226 Processing helix chain 'R' and resid 226 through 236 removed outlier: 4.667A pdb=" N LEU R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 250 removed outlier: 4.192A pdb=" N TYR R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 272 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68 removed outlier: 4.686A pdb=" N VAL A 78 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 97 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.266A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.908A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.024A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.565A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.509A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.382A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.668A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.737A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.000A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 149 removed outlier: 4.182A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL E 149 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 160 through 161 removed outlier: 3.586A pdb=" N VAL R 169 " --> pdb=" O ASN R 161 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2792 1.34 - 1.46: 2064 1.46 - 1.58: 3843 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 8765 Sorted by residual: bond pdb=" C4 HXA R 401 " pdb=" C5 HXA R 401 " ideal model delta sigma weight residual 1.332 1.531 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" C3 HXA R 401 " pdb=" C4 HXA R 401 " ideal model delta sigma weight residual 1.496 1.530 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C5 HXA R 401 " pdb=" C6 HXA R 401 " ideal model delta sigma weight residual 1.503 1.529 -0.026 2.00e-02 2.50e+03 1.70e+00 bond pdb=" C6 HXA R 401 " pdb=" C7 HXA R 401 " ideal model delta sigma weight residual 1.502 1.527 -0.025 2.00e-02 2.50e+03 1.57e+00 bond pdb=" CG1 ILE R 130 " pdb=" CD1 ILE R 130 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.40e+00 ... (remaining 8760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 11762 2.57 - 5.15: 117 5.15 - 7.72: 22 7.72 - 10.30: 3 10.30 - 12.87: 2 Bond angle restraints: 11906 Sorted by residual: angle pdb=" C3 HXA R 401 " pdb=" C4 HXA R 401 " pdb=" C5 HXA R 401 " ideal model delta sigma weight residual 128.39 115.52 12.87 3.00e+00 1.11e-01 1.84e+01 angle pdb=" C4 HXA R 401 " pdb=" C5 HXA R 401 " pdb=" C6 HXA R 401 " ideal model delta sigma weight residual 127.44 115.45 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" N ASP C 48 " pdb=" CA ASP C 48 " pdb=" C ASP C 48 " ideal model delta sigma weight residual 109.64 114.51 -4.87 1.27e+00 6.20e-01 1.47e+01 angle pdb=" N ARG C 13 " pdb=" CA ARG C 13 " pdb=" CB ARG C 13 " ideal model delta sigma weight residual 110.12 115.34 -5.22 1.47e+00 4.63e-01 1.26e+01 angle pdb=" C ALA C 10 " pdb=" N GLN C 11 " pdb=" CA GLN C 11 " ideal model delta sigma weight residual 121.18 114.98 6.20 1.98e+00 2.55e-01 9.82e+00 ... (remaining 11901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 4659 16.83 - 33.67: 400 33.67 - 50.50: 77 50.50 - 67.33: 9 67.33 - 84.17: 10 Dihedral angle restraints: 5155 sinusoidal: 1932 harmonic: 3223 Sorted by residual: dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta harmonic sigma weight residual 180.00 162.08 17.92 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA LEU R 59 " pdb=" C LEU R 59 " pdb=" N PRO R 60 " pdb=" CA PRO R 60 " ideal model delta harmonic sigma weight residual -180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA PHE R 82 " pdb=" C PHE R 82 " pdb=" N ALA R 83 " pdb=" CA ALA R 83 " ideal model delta harmonic sigma weight residual 180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1043 0.050 - 0.100: 235 0.100 - 0.150: 62 0.150 - 0.200: 6 0.200 - 0.250: 3 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CB THR A 169 " pdb=" CA THR A 169 " pdb=" OG1 THR A 169 " pdb=" CG2 THR A 169 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB THR E 91 " pdb=" CA THR E 91 " pdb=" OG1 THR E 91 " pdb=" CG2 THR E 91 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE C 9 " pdb=" CA ILE C 9 " pdb=" CG1 ILE C 9 " pdb=" CG2 ILE C 9 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1346 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.38e+00 pdb=" N PRO E 75 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.24e+00 pdb=" N PRO C 49 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 238 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.39e+00 pdb=" N PRO R 239 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO R 239 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 239 " -0.032 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1358 2.76 - 3.30: 7951 3.30 - 3.83: 14467 3.83 - 4.37: 16781 4.37 - 4.90: 29308 Nonbonded interactions: 69865 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.230 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR R 240 " pdb=" O1 HXA R 401 " model vdw 2.292 3.040 nonbonded pdb=" OG SER E 161 " pdb=" O LYS E 163 " model vdw 2.311 3.040 nonbonded pdb=" OG SER R 268 " pdb=" OD1 ASN R 272 " model vdw 2.319 3.040 ... (remaining 69860 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.810 Find NCS groups from input model: 0.040 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:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 0.199 8766 Z= 0.177 Angle : 0.685 12.870 11908 Z= 0.351 Chirality : 0.047 0.250 1349 Planarity : 0.005 0.063 1523 Dihedral : 13.351 84.169 3080 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.26), residues: 1101 helix: 1.64 (0.26), residues: 370 sheet: 1.01 (0.32), residues: 250 loop : -0.03 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 13 TYR 0.024 0.001 TYR E 190 PHE 0.021 0.002 PHE R 82 TRP 0.014 0.001 TRP B 339 HIS 0.009 0.001 HIS R 86 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8765) covalent geometry : angle 0.68458 (11906) SS BOND : bond 0.00513 ( 1) SS BOND : angle 1.10121 ( 2) hydrogen bonds : bond 0.12451 ( 450) hydrogen bonds : angle 5.82093 ( 1284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.386 Fit side-chains REVERT: R 137 HIS cc_start: 0.7464 (m-70) cc_final: 0.6614 (m-70) outliers start: 1 outliers final: 1 residues processed: 188 average time/residue: 0.6272 time to fit residues: 124.9773 Evaluate side-chains 143 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 108 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 155 ASN ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 272 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.138796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104071 restraints weight = 13471.172| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.53 r_work: 0.3240 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8766 Z= 0.110 Angle : 0.549 10.490 11908 Z= 0.279 Chirality : 0.042 0.311 1349 Planarity : 0.004 0.057 1523 Dihedral : 4.976 80.039 1220 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.55 % Allowed : 12.75 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.26), residues: 1101 helix: 2.30 (0.27), residues: 385 sheet: 0.98 (0.32), residues: 259 loop : 0.08 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 160 TYR 0.015 0.001 TYR E 190 PHE 0.011 0.001 PHE R 82 TRP 0.016 0.001 TRP R 131 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8765) covalent geometry : angle 0.54818 (11906) SS BOND : bond 0.01983 ( 1) SS BOND : angle 1.81146 ( 2) hydrogen bonds : bond 0.03547 ( 450) hydrogen bonds : angle 4.49506 ( 1284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.340 Fit side-chains REVERT: B 254 ASP cc_start: 0.8751 (t0) cc_final: 0.8497 (t0) REVERT: C 19 LEU cc_start: 0.6664 (tp) cc_final: 0.6445 (tp) REVERT: C 32 LYS cc_start: 0.8766 (tppt) cc_final: 0.8249 (tppt) REVERT: R 137 HIS cc_start: 0.7706 (m-70) cc_final: 0.6789 (m-70) REVERT: R 188 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8837 (mp) outliers start: 14 outliers final: 5 residues processed: 169 average time/residue: 0.5861 time to fit residues: 105.4478 Evaluate side-chains 150 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 188 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 97 optimal weight: 0.0050 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 75 GLN R 23 ASN R 272 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.138397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.103648 restraints weight = 13283.317| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.49 r_work: 0.3240 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8766 Z= 0.104 Angle : 0.533 7.789 11908 Z= 0.272 Chirality : 0.042 0.194 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.159 40.528 1218 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.00 % Allowed : 16.30 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.26), residues: 1101 helix: 2.47 (0.27), residues: 385 sheet: 0.99 (0.32), residues: 259 loop : 0.13 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 160 TYR 0.015 0.001 TYR E 190 PHE 0.010 0.001 PHE R 82 TRP 0.016 0.001 TRP R 131 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8765) covalent geometry : angle 0.53242 (11906) SS BOND : bond 0.00332 ( 1) SS BOND : angle 0.98540 ( 2) hydrogen bonds : bond 0.03345 ( 450) hydrogen bonds : angle 4.26589 ( 1284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: C 19 LEU cc_start: 0.6699 (tp) cc_final: 0.6492 (tp) REVERT: C 32 LYS cc_start: 0.8598 (tppt) cc_final: 0.8257 (tppt) REVERT: R 6 GLN cc_start: 0.8222 (mp10) cc_final: 0.7829 (mt0) REVERT: R 119 ARG cc_start: 0.8125 (mmm-85) cc_final: 0.7452 (mmm-85) REVERT: R 137 HIS cc_start: 0.7718 (m-70) cc_final: 0.6813 (m-70) REVERT: R 188 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8847 (mp) outliers start: 18 outliers final: 6 residues processed: 165 average time/residue: 0.5903 time to fit residues: 103.7647 Evaluate side-chains 152 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 188 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 60 optimal weight: 0.0980 chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.134576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.098924 restraints weight = 13525.901| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.54 r_work: 0.3165 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8766 Z= 0.148 Angle : 0.551 7.312 11908 Z= 0.287 Chirality : 0.043 0.170 1349 Planarity : 0.004 0.059 1523 Dihedral : 4.359 45.987 1218 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.44 % Allowed : 17.74 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.26), residues: 1101 helix: 2.57 (0.27), residues: 379 sheet: 0.95 (0.32), residues: 261 loop : 0.20 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 160 TYR 0.021 0.001 TYR E 190 PHE 0.025 0.002 PHE R 200 TRP 0.016 0.001 TRP R 131 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8765) covalent geometry : angle 0.55045 (11906) SS BOND : bond 0.00510 ( 1) SS BOND : angle 1.36321 ( 2) hydrogen bonds : bond 0.03711 ( 450) hydrogen bonds : angle 4.26424 ( 1284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.334 Fit side-chains REVERT: B 254 ASP cc_start: 0.8686 (t0) cc_final: 0.8483 (t0) REVERT: B 260 GLU cc_start: 0.8527 (tt0) cc_final: 0.8303 (tt0) REVERT: C 32 LYS cc_start: 0.8543 (tppt) cc_final: 0.8271 (tppt) REVERT: E 87 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7194 (mmt90) REVERT: E 140 MET cc_start: 0.8855 (mmm) cc_final: 0.8646 (mmm) REVERT: E 223 ASP cc_start: 0.7277 (m-30) cc_final: 0.6675 (m-30) REVERT: R 23 ASN cc_start: 0.8388 (m-40) cc_final: 0.7817 (m110) REVERT: R 52 ASP cc_start: 0.8046 (t70) cc_final: 0.7718 (t70) REVERT: R 119 ARG cc_start: 0.8223 (mmm-85) cc_final: 0.7558 (mmm-85) REVERT: R 137 HIS cc_start: 0.7724 (m-70) cc_final: 0.6831 (m-70) REVERT: R 188 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8924 (mp) REVERT: R 218 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7884 (mtt90) REVERT: R 259 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8651 (mtpp) outliers start: 22 outliers final: 9 residues processed: 162 average time/residue: 0.5811 time to fit residues: 99.7037 Evaluate side-chains 155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 218 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 14 optimal weight: 0.0970 chunk 30 optimal weight: 0.0770 chunk 25 optimal weight: 0.0770 chunk 91 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.4294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.137442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.102545 restraints weight = 13449.781| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.51 r_work: 0.3223 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8766 Z= 0.099 Angle : 0.525 8.136 11908 Z= 0.269 Chirality : 0.042 0.176 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.014 39.996 1218 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.11 % Allowed : 19.18 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.26), residues: 1101 helix: 2.66 (0.27), residues: 378 sheet: 1.06 (0.32), residues: 257 loop : 0.17 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 160 TYR 0.015 0.001 TYR E 190 PHE 0.016 0.001 PHE R 200 TRP 0.016 0.001 TRP R 131 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 8765) covalent geometry : angle 0.52494 (11906) SS BOND : bond 0.00352 ( 1) SS BOND : angle 0.80300 ( 2) hydrogen bonds : bond 0.03190 ( 450) hydrogen bonds : angle 4.12306 ( 1284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.337 Fit side-chains REVERT: B 260 GLU cc_start: 0.8533 (tt0) cc_final: 0.8309 (tt0) REVERT: B 262 MET cc_start: 0.8487 (tpp) cc_final: 0.8190 (ttm) REVERT: C 32 LYS cc_start: 0.8511 (tppt) cc_final: 0.8177 (tppt) REVERT: E 46 GLU cc_start: 0.8470 (tt0) cc_final: 0.8257 (pt0) REVERT: E 87 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7158 (mmt90) REVERT: R 6 GLN cc_start: 0.8338 (mp10) cc_final: 0.8044 (mt0) REVERT: R 119 ARG cc_start: 0.8149 (mmm-85) cc_final: 0.7512 (mmm-85) REVERT: R 135 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8030 (mm) REVERT: R 137 HIS cc_start: 0.7719 (m-70) cc_final: 0.6846 (m-70) REVERT: R 188 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8883 (mp) REVERT: R 218 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7877 (mtt90) REVERT: R 259 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8641 (mtpp) outliers start: 19 outliers final: 8 residues processed: 167 average time/residue: 0.6160 time to fit residues: 109.1849 Evaluate side-chains 157 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 218 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 0.0980 chunk 99 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 103 optimal weight: 0.0010 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN R 115 GLN R 244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.136898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.101762 restraints weight = 13387.484| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.52 r_work: 0.3209 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8766 Z= 0.108 Angle : 0.543 7.811 11908 Z= 0.276 Chirality : 0.042 0.176 1349 Planarity : 0.004 0.058 1523 Dihedral : 3.962 34.039 1218 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.22 % Allowed : 19.40 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.26), residues: 1101 helix: 2.62 (0.27), residues: 379 sheet: 1.03 (0.31), residues: 264 loop : 0.24 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 161 TYR 0.015 0.001 TYR E 190 PHE 0.011 0.001 PHE R 200 TRP 0.015 0.001 TRP R 131 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8765) covalent geometry : angle 0.54264 (11906) SS BOND : bond 0.00370 ( 1) SS BOND : angle 0.82871 ( 2) hydrogen bonds : bond 0.03227 ( 450) hydrogen bonds : angle 4.10169 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.326 Fit side-chains REVERT: B 260 GLU cc_start: 0.8560 (tt0) cc_final: 0.8352 (tt0) REVERT: B 262 MET cc_start: 0.8503 (tpp) cc_final: 0.8291 (ttm) REVERT: C 19 LEU cc_start: 0.6304 (tp) cc_final: 0.6069 (tp) REVERT: C 32 LYS cc_start: 0.8444 (tppt) cc_final: 0.8153 (tppt) REVERT: E 87 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7168 (mmt90) REVERT: E 95 TYR cc_start: 0.8972 (m-80) cc_final: 0.8751 (m-80) REVERT: R 53 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8496 (tp) REVERT: R 119 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7530 (mmm-85) REVERT: R 135 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8015 (mm) REVERT: R 137 HIS cc_start: 0.7670 (m-70) cc_final: 0.6757 (m-70) REVERT: R 188 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8904 (mp) REVERT: R 259 LYS cc_start: 0.8944 (mtpt) cc_final: 0.8642 (mtpp) outliers start: 20 outliers final: 7 residues processed: 161 average time/residue: 0.6235 time to fit residues: 106.4875 Evaluate side-chains 151 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 0.0980 chunk 108 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN R 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099939 restraints weight = 13459.657| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.52 r_work: 0.3180 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8766 Z= 0.131 Angle : 0.568 8.053 11908 Z= 0.293 Chirality : 0.043 0.197 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.083 31.326 1218 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.55 % Allowed : 19.84 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.26), residues: 1101 helix: 2.58 (0.27), residues: 379 sheet: 1.00 (0.32), residues: 260 loop : 0.25 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 160 TYR 0.019 0.001 TYR E 190 PHE 0.010 0.001 PHE R 200 TRP 0.016 0.001 TRP R 131 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8765) covalent geometry : angle 0.56840 (11906) SS BOND : bond 0.00374 ( 1) SS BOND : angle 0.83776 ( 2) hydrogen bonds : bond 0.03410 ( 450) hydrogen bonds : angle 4.17994 ( 1284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: C 19 LEU cc_start: 0.6333 (tp) cc_final: 0.6097 (tp) REVERT: C 32 LYS cc_start: 0.8495 (tppt) cc_final: 0.8203 (tppt) REVERT: E 87 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7219 (mmt90) REVERT: R 6 GLN cc_start: 0.8448 (mp10) cc_final: 0.8007 (mt0) REVERT: R 53 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8435 (tp) REVERT: R 119 ARG cc_start: 0.8202 (mmm-85) cc_final: 0.7523 (mmm-85) REVERT: R 135 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8030 (mm) REVERT: R 137 HIS cc_start: 0.7695 (m-70) cc_final: 0.6844 (m-70) REVERT: R 188 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8909 (mp) outliers start: 23 outliers final: 12 residues processed: 160 average time/residue: 0.6191 time to fit residues: 105.3942 Evaluate side-chains 155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN R 23 ASN R 244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.135716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.100576 restraints weight = 13236.363| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.49 r_work: 0.3189 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8766 Z= 0.120 Angle : 0.577 8.613 11908 Z= 0.294 Chirality : 0.042 0.160 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.024 27.835 1218 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.55 % Allowed : 20.18 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.26), residues: 1101 helix: 2.60 (0.27), residues: 378 sheet: 0.98 (0.32), residues: 260 loop : 0.28 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 160 TYR 0.018 0.001 TYR E 190 PHE 0.010 0.001 PHE B 199 TRP 0.014 0.001 TRP R 131 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8765) covalent geometry : angle 0.57685 (11906) SS BOND : bond 0.00452 ( 1) SS BOND : angle 0.63463 ( 2) hydrogen bonds : bond 0.03311 ( 450) hydrogen bonds : angle 4.15728 ( 1284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.347 Fit side-chains REVERT: C 19 LEU cc_start: 0.6322 (tp) cc_final: 0.6081 (tp) REVERT: C 32 LYS cc_start: 0.8484 (tppt) cc_final: 0.8215 (tppt) REVERT: E 87 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7246 (mmt90) REVERT: R 6 GLN cc_start: 0.8471 (mp10) cc_final: 0.8046 (mt0) REVERT: R 53 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8626 (tp) REVERT: R 119 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7520 (mmm-85) REVERT: R 135 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8022 (mm) REVERT: R 137 HIS cc_start: 0.7676 (m-70) cc_final: 0.6795 (m-70) REVERT: R 188 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8915 (mp) REVERT: R 218 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7900 (mtt90) outliers start: 23 outliers final: 12 residues processed: 155 average time/residue: 0.6483 time to fit residues: 106.5239 Evaluate side-chains 155 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 218 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 244 ASN 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 = 0.134480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099187 restraints weight = 13328.550| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.50 r_work: 0.3168 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8766 Z= 0.142 Angle : 0.601 8.196 11908 Z= 0.307 Chirality : 0.043 0.163 1349 Planarity : 0.004 0.059 1523 Dihedral : 4.162 28.182 1218 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.88 % Allowed : 21.06 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.26), residues: 1101 helix: 2.52 (0.27), residues: 378 sheet: 0.88 (0.31), residues: 268 loop : 0.29 (0.32), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 160 TYR 0.019 0.001 TYR E 190 PHE 0.010 0.001 PHE B 199 TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8765) covalent geometry : angle 0.60127 (11906) SS BOND : bond 0.00455 ( 1) SS BOND : angle 0.63485 ( 2) hydrogen bonds : bond 0.03500 ( 450) hydrogen bonds : angle 4.21735 ( 1284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: C 19 LEU cc_start: 0.6331 (tp) cc_final: 0.6090 (tp) REVERT: E 87 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7245 (mmt90) REVERT: R 6 GLN cc_start: 0.8550 (mp10) cc_final: 0.8175 (mt0) REVERT: R 53 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8639 (tp) REVERT: R 135 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8028 (mm) REVERT: R 137 HIS cc_start: 0.7733 (m-70) cc_final: 0.6880 (m-70) REVERT: R 188 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8855 (mp) REVERT: R 218 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7900 (mtt90) outliers start: 17 outliers final: 11 residues processed: 154 average time/residue: 0.6371 time to fit residues: 104.2709 Evaluate side-chains 156 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 218 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.098406 restraints weight = 13330.105| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.51 r_work: 0.3156 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8766 Z= 0.146 Angle : 0.613 8.263 11908 Z= 0.313 Chirality : 0.043 0.164 1349 Planarity : 0.004 0.059 1523 Dihedral : 4.274 29.688 1218 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.11 % Allowed : 21.18 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.26), residues: 1101 helix: 2.53 (0.27), residues: 378 sheet: 0.90 (0.31), residues: 267 loop : 0.28 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 160 TYR 0.021 0.001 TYR E 190 PHE 0.010 0.001 PHE B 199 TRP 0.015 0.001 TRP B 339 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8765) covalent geometry : angle 0.61302 (11906) SS BOND : bond 0.00469 ( 1) SS BOND : angle 0.54315 ( 2) hydrogen bonds : bond 0.03581 ( 450) hydrogen bonds : angle 4.26301 ( 1284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: C 19 LEU cc_start: 0.6331 (tp) cc_final: 0.6084 (tp) REVERT: E 87 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7226 (mmt90) REVERT: E 202 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7918 (ptt90) REVERT: R 6 GLN cc_start: 0.8511 (mp10) cc_final: 0.8184 (mt0) REVERT: R 53 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8582 (tp) REVERT: R 135 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8060 (mm) REVERT: R 137 HIS cc_start: 0.7696 (m-70) cc_final: 0.6840 (m-70) REVERT: R 188 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8883 (mp) REVERT: R 218 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7899 (mtt90) outliers start: 19 outliers final: 10 residues processed: 155 average time/residue: 0.6468 time to fit residues: 106.1699 Evaluate side-chains 158 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 218 ARG Chi-restraints excluded: chain R residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 57 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN R 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.098927 restraints weight = 13313.697| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.51 r_work: 0.3163 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8766 Z= 0.136 Angle : 0.624 8.343 11908 Z= 0.318 Chirality : 0.043 0.164 1349 Planarity : 0.004 0.059 1523 Dihedral : 4.268 29.963 1218 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.22 % Allowed : 21.18 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.26), residues: 1101 helix: 2.47 (0.27), residues: 378 sheet: 0.91 (0.32), residues: 260 loop : 0.29 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 161 TYR 0.020 0.001 TYR E 190 PHE 0.010 0.001 PHE B 199 TRP 0.013 0.001 TRP R 131 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8765) covalent geometry : angle 0.62375 (11906) SS BOND : bond 0.00441 ( 1) SS BOND : angle 0.43192 ( 2) hydrogen bonds : bond 0.03508 ( 450) hydrogen bonds : angle 4.25449 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4296.51 seconds wall clock time: 73 minutes 50.11 seconds (4430.11 seconds total)