Starting phenix.real_space_refine on Sat Dec 28 13:24:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eit_28164/12_2024/8eit_28164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eit_28164/12_2024/8eit_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_28164/12_2024/8eit_28164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eit_28164/12_2024/8eit_28164.map" model { file = "/net/cci-nas-00/data/ceres_data/8eit_28164/12_2024/8eit_28164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eit_28164/12_2024/8eit_28164.cif" } resolution = 2.8 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= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'GLU:plan': 2, 'ASP: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: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP: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, 'ARG:plan': 1, 'ASP: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: {'GLU:plan': 1, 'ARG:plan': 4} 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-5': 1, 'HXA:plan-4': 1, 'HXA:plan-7': 1, 'HXA:plan-6': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 5.32, per 1000 atoms: 0.62 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: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.07 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: 2.79 Time building geometry restraints manager: 2.76 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.310 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- 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 8765 Z= 0.214 Angle : 0.685 12.870 11906 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 (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: 1.13 (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 TRP 0.014 0.001 TRP B 339 HIS 0.009 0.001 HIS R 86 PHE 0.021 0.002 PHE R 82 TYR 0.024 0.001 TYR E 190 ARG 0.015 0.000 ARG C 13 *********************** 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 : 1.037 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: 1.2514 time to fit residues: 250.0837 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 : 1.029 ------------------------------------------------------------------------------- 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 92 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.0770 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 215 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 75 GLN B 155 ASN R 272 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8765 Z= 0.252 Angle : 0.597 10.017 11906 Z= 0.308 Chirality : 0.044 0.281 1349 Planarity : 0.005 0.067 1523 Dihedral : 5.347 77.722 1220 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.00 % Allowed : 13.41 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.26), residues: 1101 helix: 2.24 (0.27), residues: 384 sheet: 0.90 (0.32), residues: 262 loop : 0.07 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 131 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.002 PHE B 234 TYR 0.022 0.002 TYR E 190 ARG 0.007 0.000 ARG E 160 *********************** 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 178 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.175 Fit side-chains REVERT: C 32 LYS cc_start: 0.8616 (tppt) cc_final: 0.7937 (tppt) REVERT: E 87 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7168 (mmt90) REVERT: E 223 ASP cc_start: 0.7658 (m-30) cc_final: 0.7227 (m-30) REVERT: R 6 GLN cc_start: 0.8080 (mp10) cc_final: 0.7742 (mt0) REVERT: R 52 ASP cc_start: 0.7646 (t70) cc_final: 0.7397 (t70) REVERT: R 137 HIS cc_start: 0.7390 (m-70) cc_final: 0.6688 (m-70) REVERT: R 188 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8816 (mp) REVERT: R 259 LYS cc_start: 0.8937 (mtpt) cc_final: 0.8633 (mtpp) outliers start: 18 outliers final: 8 residues processed: 170 average time/residue: 1.2772 time to fit residues: 231.1758 Evaluate side-chains 156 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 98 ARG 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 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 111 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 155 ASN R 23 ASN R 244 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 8765 Z= 0.380 Angle : 0.648 6.874 11906 Z= 0.341 Chirality : 0.046 0.198 1349 Planarity : 0.005 0.060 1523 Dihedral : 5.226 54.520 1218 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.33 % Allowed : 16.63 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.33 (0.26), residues: 1101 helix: 2.10 (0.27), residues: 385 sheet: 0.72 (0.31), residues: 272 loop : -0.03 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 131 HIS 0.006 0.001 HIS E 35 PHE 0.017 0.002 PHE B 234 TYR 0.029 0.002 TYR E 190 ARG 0.010 0.001 ARG E 191 *********************** 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 178 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.088 Fit side-chains REVERT: C 32 LYS cc_start: 0.8439 (tppt) cc_final: 0.8130 (tppt) REVERT: E 87 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7223 (mmt90) REVERT: R 135 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8290 (mm) REVERT: R 137 HIS cc_start: 0.7485 (m-70) cc_final: 0.6778 (m-70) REVERT: R 188 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8740 (mp) REVERT: R 259 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8688 (mtpp) outliers start: 30 outliers final: 12 residues processed: 167 average time/residue: 1.2768 time to fit residues: 226.5944 Evaluate side-chains 157 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 98 ARG 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 50 CYS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 118 ARG Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 260 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.0470 chunk 74 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 0.0770 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 220 GLN R 23 ASN R 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8765 Z= 0.148 Angle : 0.529 7.662 11906 Z= 0.276 Chirality : 0.041 0.164 1349 Planarity : 0.004 0.055 1523 Dihedral : 4.427 47.338 1218 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.99 % Allowed : 17.96 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.26), residues: 1101 helix: 2.47 (0.27), residues: 378 sheet: 0.97 (0.31), residues: 271 loop : 0.13 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 131 HIS 0.002 0.001 HIS B 183 PHE 0.025 0.001 PHE R 200 TYR 0.019 0.001 TYR E 190 ARG 0.011 0.000 ARG A 161 *********************** 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 183 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.011 Fit side-chains REVERT: C 19 LEU cc_start: 0.6589 (tp) cc_final: 0.6353 (tp) REVERT: C 32 LYS cc_start: 0.8279 (tppt) cc_final: 0.8059 (tppt) REVERT: E 163 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7885 (ttpt) REVERT: E 219 LEU cc_start: 0.8150 (mp) cc_final: 0.7541 (tt) REVERT: E 223 ASP cc_start: 0.7480 (m-30) cc_final: 0.6887 (m-30) REVERT: R 6 GLN cc_start: 0.8173 (mp10) cc_final: 0.7962 (mt0) REVERT: R 137 HIS cc_start: 0.7376 (m-70) cc_final: 0.6695 (m-70) REVERT: R 259 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8617 (mtpp) outliers start: 27 outliers final: 8 residues processed: 170 average time/residue: 1.2489 time to fit residues: 225.8589 Evaluate side-chains 150 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 133 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.0170 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 155 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8765 Z= 0.147 Angle : 0.520 7.619 11906 Z= 0.270 Chirality : 0.041 0.157 1349 Planarity : 0.004 0.056 1523 Dihedral : 4.171 40.540 1218 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.10 % Allowed : 18.74 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.78 (0.26), residues: 1101 helix: 2.53 (0.27), residues: 378 sheet: 1.00 (0.31), residues: 264 loop : 0.20 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 131 HIS 0.003 0.001 HIS B 183 PHE 0.016 0.001 PHE R 200 TYR 0.013 0.001 TYR E 190 ARG 0.012 0.000 ARG A 161 *********************** 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 179 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.051 Fit side-chains REVERT: A 222 ASP cc_start: 0.8188 (m-30) cc_final: 0.7984 (m-30) REVERT: C 19 LEU cc_start: 0.6452 (tp) cc_final: 0.6212 (tp) REVERT: C 32 LYS cc_start: 0.8290 (tppt) cc_final: 0.8061 (tppt) REVERT: E 46 GLU cc_start: 0.7835 (tt0) cc_final: 0.7623 (pt0) REVERT: E 87 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7135 (mmt90) REVERT: E 219 LEU cc_start: 0.8206 (mp) cc_final: 0.7607 (tt) REVERT: R 23 ASN cc_start: 0.8406 (m-40) cc_final: 0.7678 (m110) REVERT: R 52 ASP cc_start: 0.7586 (t70) cc_final: 0.7372 (t70) REVERT: R 53 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8555 (tp) REVERT: R 135 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8094 (mm) REVERT: R 137 HIS cc_start: 0.7483 (m-70) cc_final: 0.6744 (m-70) REVERT: R 218 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7658 (mtt90) REVERT: R 259 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8613 (mtpp) outliers start: 28 outliers final: 9 residues processed: 165 average time/residue: 1.2587 time to fit residues: 221.0745 Evaluate side-chains 156 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 118 THR 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 133 LEU Chi-restraints excluded: chain R residue 135 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 94 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 155 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8765 Z= 0.167 Angle : 0.536 7.731 11906 Z= 0.277 Chirality : 0.042 0.235 1349 Planarity : 0.004 0.057 1523 Dihedral : 4.145 35.142 1218 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.99 % Allowed : 19.40 % 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 (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: 1.81 (0.26), residues: 1101 helix: 2.60 (0.27), residues: 379 sheet: 0.91 (0.32), residues: 262 loop : 0.24 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 131 HIS 0.003 0.001 HIS B 183 PHE 0.012 0.001 PHE R 200 TYR 0.016 0.001 TYR E 190 ARG 0.015 0.001 ARG A 161 *********************** 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 181 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.030 Fit side-chains REVERT: A 222 ASP cc_start: 0.8195 (m-30) cc_final: 0.7967 (m-30) REVERT: C 32 LYS cc_start: 0.8362 (tppt) cc_final: 0.8156 (tppt) REVERT: E 46 GLU cc_start: 0.7858 (tt0) cc_final: 0.7654 (pt0) REVERT: E 87 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7188 (mmt90) REVERT: E 219 LEU cc_start: 0.8183 (mp) cc_final: 0.7521 (tt) REVERT: R 6 GLN cc_start: 0.8299 (mp10) cc_final: 0.8064 (mt0) REVERT: R 53 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8558 (tp) REVERT: R 135 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8126 (mm) REVERT: R 137 HIS cc_start: 0.7478 (m-70) cc_final: 0.6745 (m-70) REVERT: R 259 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8619 (mtpp) outliers start: 27 outliers final: 12 residues processed: 171 average time/residue: 1.2712 time to fit residues: 232.7703 Evaluate side-chains 161 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP 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 98 ARG Chi-restraints excluded: chain E residue 118 THR 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 133 LEU Chi-restraints excluded: chain R residue 135 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 0.0770 chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 overall best weight: 0.4856 ------------------------------------------------------------------------------- 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 155 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8765 Z= 0.148 Angle : 0.548 8.921 11906 Z= 0.278 Chirality : 0.042 0.185 1349 Planarity : 0.004 0.061 1523 Dihedral : 3.968 27.776 1218 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.88 % Allowed : 20.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.26), residues: 1101 helix: 2.56 (0.27), residues: 377 sheet: 1.03 (0.31), residues: 263 loop : 0.26 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 131 HIS 0.002 0.000 HIS B 183 PHE 0.012 0.001 PHE R 200 TYR 0.013 0.001 TYR E 190 ARG 0.016 0.001 ARG A 161 *********************** 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 181 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8178 (m-30) cc_final: 0.7975 (m-30) REVERT: E 87 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7143 (mmt90) REVERT: R 6 GLN cc_start: 0.8187 (mp10) cc_final: 0.7925 (mt0) REVERT: R 53 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8473 (tp) REVERT: R 59 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9173 (mm) REVERT: R 135 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8100 (mm) REVERT: R 137 HIS cc_start: 0.7476 (m-70) cc_final: 0.6694 (m-70) REVERT: R 259 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8606 (mtpp) outliers start: 26 outliers final: 11 residues processed: 171 average time/residue: 1.2295 time to fit residues: 224.4845 Evaluate side-chains 161 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 118 THR 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 59 LEU Chi-restraints excluded: chain R residue 79 CYS Chi-restraints excluded: chain R residue 135 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 155 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8765 Z= 0.279 Angle : 0.633 8.011 11906 Z= 0.324 Chirality : 0.045 0.198 1349 Planarity : 0.004 0.059 1523 Dihedral : 4.578 45.178 1218 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.77 % Allowed : 21.29 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.26), residues: 1101 helix: 2.46 (0.27), residues: 378 sheet: 0.83 (0.31), residues: 268 loop : 0.23 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 131 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.002 PHE B 253 TYR 0.026 0.002 TYR E 190 ARG 0.013 0.001 ARG E 160 *********************** 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 169 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.059 Fit side-chains REVERT: C 11 GLN cc_start: 0.7678 (pm20) cc_final: 0.7363 (pm20) REVERT: E 87 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7218 (mmt90) REVERT: R 53 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8692 (tp) REVERT: R 135 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8199 (mm) REVERT: R 137 HIS cc_start: 0.7488 (m-70) cc_final: 0.6772 (m-70) outliers start: 25 outliers final: 11 residues processed: 159 average time/residue: 1.2015 time to fit residues: 203.9155 Evaluate side-chains 153 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 118 THR 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 79 CYS Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 135 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN R 47 ASN R 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8765 Z= 0.222 Angle : 0.614 8.647 11906 Z= 0.314 Chirality : 0.044 0.164 1349 Planarity : 0.004 0.057 1523 Dihedral : 4.494 45.883 1218 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.44 % Allowed : 22.17 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.67 (0.26), residues: 1101 helix: 2.41 (0.27), residues: 378 sheet: 0.82 (0.31), residues: 269 loop : 0.24 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 131 HIS 0.004 0.001 HIS E 35 PHE 0.011 0.001 PHE B 199 TYR 0.022 0.001 TYR E 190 ARG 0.016 0.001 ARG A 161 *********************** 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 164 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 87 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7161 (mmt90) REVERT: R 23 ASN cc_start: 0.8431 (m-40) cc_final: 0.7636 (m110) REVERT: R 53 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8583 (tp) REVERT: R 135 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8123 (mm) REVERT: R 137 HIS cc_start: 0.7475 (m-70) cc_final: 0.6752 (m-70) outliers start: 22 outliers final: 11 residues processed: 155 average time/residue: 1.2620 time to fit residues: 208.1534 Evaluate side-chains 157 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 118 THR 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 79 CYS Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 221 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 ASN R 47 ASN R 244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8765 Z= 0.222 Angle : 0.627 8.350 11906 Z= 0.320 Chirality : 0.044 0.160 1349 Planarity : 0.004 0.057 1523 Dihedral : 4.521 47.753 1218 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.55 % Allowed : 21.95 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.62 (0.26), residues: 1101 helix: 2.35 (0.27), residues: 377 sheet: 0.82 (0.31), residues: 269 loop : 0.24 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 131 HIS 0.004 0.001 HIS E 35 PHE 0.012 0.001 PHE B 199 TYR 0.022 0.001 TYR E 190 ARG 0.014 0.001 ARG E 160 ********************** 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 167 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: C 11 GLN cc_start: 0.7812 (pm20) cc_final: 0.7576 (pm20) REVERT: C 17 GLU cc_start: 0.7979 (tt0) cc_final: 0.7766 (tt0) REVERT: E 87 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7192 (mmt90) REVERT: R 6 GLN cc_start: 0.8307 (mp10) cc_final: 0.8018 (mt0) REVERT: R 135 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8120 (mm) REVERT: R 137 HIS cc_start: 0.7531 (m-70) cc_final: 0.6818 (m-70) outliers start: 23 outliers final: 14 residues processed: 156 average time/residue: 1.2267 time to fit residues: 203.8484 Evaluate side-chains 160 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 146 LEU 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 98 ARG Chi-restraints excluded: chain E residue 118 THR 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 64 VAL 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 221 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN R 23 ASN R 47 ASN R 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.134020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.098808 restraints weight = 13204.254| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.50 r_work: 0.3160 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8765 Z= 0.193 Angle : 0.620 8.377 11906 Z= 0.315 Chirality : 0.043 0.158 1349 Planarity : 0.004 0.057 1523 Dihedral : 4.398 46.053 1218 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.55 % Allowed : 22.51 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.26), residues: 1101 helix: 2.35 (0.27), residues: 377 sheet: 0.82 (0.31), residues: 269 loop : 0.25 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 131 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE B 199 TYR 0.019 0.001 TYR E 190 ARG 0.010 0.000 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3910.38 seconds wall clock time: 70 minutes 37.96 seconds (4237.96 seconds total)