Starting phenix.real_space_refine on Wed Feb 14 04:05:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eit_28164/02_2024/8eit_28164_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eit_28164/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eit_28164/02_2024/8eit_28164.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eit_28164/02_2024/8eit_28164.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eit_28164/02_2024/8eit_28164_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eit_28164/02_2024/8eit_28164_updated.pdb" } 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 Residue "A ASP 20": "OD1" <-> "OD2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "R ASP 52": "OD1" <-> "OD2" Residue "R PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 175": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8578 Number of models: 1 Model: "" Number of chains: 5 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: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 1970 Unusual residues: {'HXA': 1} Classifications: {'peptide': 268, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 247, None: 1} Not linked: pdbres="LEU R 279 " pdbres="HXA R 401 " Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 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, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 5.14, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.7 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... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 34.2% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 Processing helix chain 'A' and resid 85 through 92 removed outlier: 3.504A pdb=" N ILE A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N CYS A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 92' Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 138 through 147 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 176 through 195 removed outlier: 3.687A pdb=" N PHE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.018A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 25 Processing helix chain 'C' and resid 30 through 41 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'R' and resid 5 through 36 Proline residue: R 21 - end of helix removed outlier: 4.000A pdb=" N LEU R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 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 76 through 86 Proline residue: R 80 - end of helix removed outlier: 4.478A pdb=" N VAL R 84 " --> pdb=" O VAL R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 106 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 111 through 116 Processing helix chain 'R' and resid 120 through 144 removed outlier: 3.856A pdb=" N LEU R 144 " --> pdb=" O LEU R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 190 Proline residue: R 181 - end of helix Processing helix chain 'R' and resid 192 through 211 Processing helix chain 'R' and resid 216 through 235 removed outlier: 3.874A pdb=" N GLY R 228 " --> pdb=" O TRP R 224 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA R 229 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU R 230 " --> pdb=" O ALA R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 249 Processing helix chain 'R' and resid 256 through 272 Processing sheet with id= A, first strand: chain 'A' and resid 203 through 208 removed outlier: 7.279A pdb=" N VAL A 131 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N HIS A 206 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU A 133 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR A 208 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU A 135 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 97 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL A 78 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, 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: 3.693A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, 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= D, first strand: chain 'B' and resid 166 through 170 Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.938A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (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= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.693A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) 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= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.589A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (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= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.692A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.721A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 149 removed outlier: 6.786A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL E 149 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU E 246 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'R' and resid 160 through 162 removed outlier: 3.586A pdb=" N VAL R 169 " --> pdb=" O ASN R 161 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1140 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: 2.56 Time building geometry restraints manager: 3.55 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: 100.14 - 106.95: 244 106.95 - 113.75: 4790 113.75 - 120.56: 3478 120.56 - 127.37: 3292 127.37 - 134.17: 102 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: 1367 2.76 - 3.30: 7976 3.30 - 3.83: 14513 3.83 - 4.37: 16870 4.37 - 4.90: 29327 Nonbonded interactions: 70053 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.230 2.440 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.240 2.440 nonbonded pdb=" OH TYR R 240 " pdb=" O1 HXA R 401 " model vdw 2.292 2.440 nonbonded pdb=" OG SER E 161 " pdb=" O LYS E 163 " model vdw 2.311 2.440 nonbonded pdb=" OG SER R 268 " pdb=" OD1 ASN R 272 " model vdw 2.319 2.440 ... (remaining 70048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.400 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: 2.290 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 26.780 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.840 ------------------------------------------------------------------------------- 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= 0.261 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 fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 1.016 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: 1.2391 time to fit residues: 247.9622 Evaluate side-chains 143 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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: 5.9990 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 33 optimal weight: 0.0870 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 272 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8765 Z= 0.142 Angle : 0.519 9.957 11906 Z= 0.260 Chirality : 0.041 0.264 1349 Planarity : 0.004 0.057 1523 Dihedral : 4.808 71.483 1220 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.77 % Allowed : 12.75 % Favored : 85.48 % 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: 1.60 (0.26), residues: 1101 helix: 2.32 (0.27), residues: 379 sheet: 0.96 (0.32), residues: 260 loop : 0.12 (0.31), residues: 462 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 0.010 0.001 PHE B 199 TYR 0.016 0.001 TYR E 190 ARG 0.008 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 174 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 1.060 Fit side-chains REVERT: C 19 LEU cc_start: 0.6543 (tp) cc_final: 0.6311 (tp) REVERT: R 137 HIS cc_start: 0.7491 (m-70) cc_final: 0.6704 (m-70) REVERT: R 188 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8795 (mp) outliers start: 16 outliers final: 5 residues processed: 166 average time/residue: 1.1751 time to fit residues: 208.1807 Evaluate side-chains 156 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 56 THR 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: 0.8980 chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 0.0770 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 155 ASN B 220 GLN ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8765 Z= 0.182 Angle : 0.525 6.880 11906 Z= 0.268 Chirality : 0.041 0.178 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.355 47.464 1218 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.44 % Allowed : 14.63 % Favored : 82.93 % 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: 1.74 (0.26), residues: 1101 helix: 2.51 (0.27), residues: 379 sheet: 0.99 (0.32), residues: 260 loop : 0.17 (0.31), residues: 462 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 R 82 TYR 0.019 0.001 TYR E 190 ARG 0.009 0.000 ARG E 160 *********************** 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 fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.114 Fit side-chains REVERT: C 19 LEU cc_start: 0.6588 (tp) cc_final: 0.6380 (tp) REVERT: R 137 HIS cc_start: 0.7542 (m-70) cc_final: 0.6725 (m-70) REVERT: R 188 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8766 (mp) REVERT: R 218 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7791 (mtt90) outliers start: 22 outliers final: 7 residues processed: 160 average time/residue: 1.3080 time to fit residues: 222.8039 Evaluate side-chains 153 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain E residue 39 GLN 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 56 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.0970 chunk 74 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 0.0070 chunk 99 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8765 Z= 0.128 Angle : 0.492 7.123 11906 Z= 0.251 Chirality : 0.040 0.133 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.125 48.200 1218 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.88 % Allowed : 15.52 % Favored : 81.60 % 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: 1.82 (0.26), residues: 1101 helix: 2.55 (0.27), residues: 379 sheet: 1.11 (0.31), residues: 256 loop : 0.19 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 131 HIS 0.002 0.000 HIS E 35 PHE 0.023 0.001 PHE R 200 TYR 0.015 0.001 TYR E 190 ARG 0.009 0.000 ARG E 160 *********************** 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 178 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 1.003 Fit side-chains REVERT: C 32 LYS cc_start: 0.8337 (tppt) cc_final: 0.7456 (tppt) REVERT: R 137 HIS cc_start: 0.7515 (m-70) cc_final: 0.6665 (m-70) REVERT: R 188 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8766 (mp) outliers start: 26 outliers final: 11 residues processed: 162 average time/residue: 1.1621 time to fit residues: 201.1011 Evaluate side-chains 153 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 36 ASN 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 118 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 188 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8765 Z= 0.232 Angle : 0.540 7.147 11906 Z= 0.280 Chirality : 0.042 0.170 1349 Planarity : 0.004 0.059 1523 Dihedral : 4.416 37.610 1218 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.99 % Allowed : 16.85 % Favored : 80.16 % 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: 1.79 (0.26), residues: 1101 helix: 2.50 (0.27), residues: 382 sheet: 0.88 (0.31), residues: 274 loop : 0.29 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 131 HIS 0.004 0.001 HIS E 35 PHE 0.014 0.002 PHE R 200 TYR 0.022 0.001 TYR E 190 ARG 0.010 0.000 ARG E 160 *********************** 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 fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 0.919 Fit side-chains REVERT: B 262 MET cc_start: 0.7522 (tpp) cc_final: 0.7244 (ttm) REVERT: C 32 LYS cc_start: 0.8309 (tppt) cc_final: 0.7993 (tppt) REVERT: E 87 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7180 (mmt90) REVERT: R 135 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8141 (mm) REVERT: R 137 HIS cc_start: 0.7557 (m-70) cc_final: 0.6761 (m-70) REVERT: R 188 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8772 (mp) outliers start: 27 outliers final: 13 residues processed: 166 average time/residue: 1.1334 time to fit residues: 201.1611 Evaluate side-chains 155 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 228 ASP 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 137 ASP Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 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: 0.1707 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= 0.146 Angle : 0.505 7.611 11906 Z= 0.259 Chirality : 0.041 0.151 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.116 31.795 1218 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.44 % Allowed : 18.74 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.53 (0.27), residues: 382 sheet: 0.95 (0.31), residues: 270 loop : 0.31 (0.32), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 131 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE R 200 TYR 0.016 0.001 TYR E 190 ARG 0.011 0.000 ARG E 160 *********************** 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 168 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 0.905 Fit side-chains REVERT: B 262 MET cc_start: 0.7486 (tpp) cc_final: 0.7197 (ttm) REVERT: C 32 LYS cc_start: 0.8282 (tppt) cc_final: 0.8028 (tppt) REVERT: E 87 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7146 (mmt90) REVERT: R 135 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8050 (mm) REVERT: R 137 HIS cc_start: 0.7532 (m-70) cc_final: 0.6744 (m-70) outliers start: 22 outliers final: 12 residues processed: 159 average time/residue: 1.1455 time to fit residues: 194.1236 Evaluate side-chains 153 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 36 ASN 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 56 THR 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: 3.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 47 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 8765 Z= 0.323 Angle : 0.601 7.914 11906 Z= 0.314 Chirality : 0.044 0.189 1349 Planarity : 0.004 0.060 1523 Dihedral : 4.719 38.964 1218 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.66 % Allowed : 19.51 % Favored : 77.83 % 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: 2.39 (0.27), residues: 383 sheet: 0.80 (0.30), residues: 278 loop : 0.31 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 131 HIS 0.005 0.001 HIS B 183 PHE 0.013 0.002 PHE B 234 TYR 0.026 0.002 TYR E 190 ARG 0.013 0.001 ARG E 160 *********************** 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 163 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 1.043 Fit side-chains REVERT: B 262 MET cc_start: 0.7553 (tpp) cc_final: 0.7288 (ttm) REVERT: C 17 GLU cc_start: 0.8016 (tt0) cc_final: 0.7807 (tt0) REVERT: E 87 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7244 (mmt90) REVERT: E 140 MET cc_start: 0.8690 (mmm) cc_final: 0.8180 (tpt) REVERT: E 223 ASP cc_start: 0.7975 (m-30) cc_final: 0.7592 (m-30) REVERT: R 6 GLN cc_start: 0.8349 (mp10) cc_final: 0.7935 (mt0) REVERT: R 135 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8195 (mm) REVERT: R 137 HIS cc_start: 0.7478 (m-70) cc_final: 0.6742 (m-70) outliers start: 24 outliers final: 15 residues processed: 154 average time/residue: 1.2524 time to fit residues: 205.2281 Evaluate side-chains 151 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain B residue 228 ASP 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 137 ASP Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 56 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 95 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN R 244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8765 Z= 0.183 Angle : 0.543 8.138 11906 Z= 0.280 Chirality : 0.042 0.143 1349 Planarity : 0.004 0.079 1523 Dihedral : 4.376 39.537 1218 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.44 % Allowed : 20.73 % Favored : 76.83 % 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: 1.77 (0.26), residues: 1101 helix: 2.46 (0.26), residues: 383 sheet: 0.91 (0.30), residues: 270 loop : 0.29 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 131 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 199 TYR 0.018 0.001 TYR E 190 ARG 0.015 0.001 ARG A 161 *********************** 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 fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: E 87 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7201 (mmt90) REVERT: E 160 ARG cc_start: 0.7512 (mtp-110) cc_final: 0.7275 (mtp85) REVERT: E 223 ASP cc_start: 0.7948 (m-30) cc_final: 0.7602 (m-30) REVERT: R 6 GLN cc_start: 0.8292 (mp10) cc_final: 0.7854 (mt0) REVERT: R 135 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8122 (mm) REVERT: R 137 HIS cc_start: 0.7541 (m-70) cc_final: 0.6751 (m-70) REVERT: R 188 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8746 (mp) outliers start: 22 outliers final: 15 residues processed: 160 average time/residue: 1.1717 time to fit residues: 199.9313 Evaluate side-chains 159 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 228 ASP 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 36 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 56 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 155 ASN ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 47 ASN R 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2050 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= 0.193 Angle : 0.562 8.194 11906 Z= 0.287 Chirality : 0.042 0.145 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.345 40.927 1218 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.44 % Allowed : 20.18 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.75 (0.26), residues: 1101 helix: 2.43 (0.27), residues: 383 sheet: 0.86 (0.30), residues: 272 loop : 0.32 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 131 HIS 0.004 0.001 HIS E 35 PHE 0.012 0.001 PHE B 199 TYR 0.019 0.001 TYR E 190 ARG 0.013 0.000 ARG E 160 *********************** 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 169 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: E 87 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7197 (mmt90) REVERT: E 223 ASP cc_start: 0.7943 (m-30) cc_final: 0.7535 (m-30) REVERT: R 6 GLN cc_start: 0.8331 (mp10) cc_final: 0.7904 (mt0) REVERT: R 135 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8140 (mm) REVERT: R 137 HIS cc_start: 0.7541 (m-70) cc_final: 0.6748 (m-70) REVERT: R 188 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8742 (mp) outliers start: 22 outliers final: 17 residues processed: 161 average time/residue: 1.1706 time to fit residues: 201.1141 Evaluate side-chains 159 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP 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 36 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 56 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 155 ASN ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN R 47 ASN R 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8765 Z= 0.280 Angle : 0.614 8.188 11906 Z= 0.315 Chirality : 0.044 0.171 1349 Planarity : 0.004 0.058 1523 Dihedral : 4.609 40.138 1218 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.55 % Allowed : 20.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.26), residues: 1101 helix: 2.38 (0.27), residues: 382 sheet: 0.85 (0.30), residues: 277 loop : 0.31 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 131 HIS 0.005 0.001 HIS E 35 PHE 0.012 0.002 PHE B 234 TYR 0.023 0.002 TYR E 190 ARG 0.016 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 164 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.141 Fit side-chains REVERT: E 87 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7263 (mmt90) REVERT: E 223 ASP cc_start: 0.7967 (m-30) cc_final: 0.7560 (m-30) REVERT: R 6 GLN cc_start: 0.8348 (mp10) cc_final: 0.7919 (mt0) REVERT: R 135 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8134 (mm) REVERT: R 137 HIS cc_start: 0.7471 (m-70) cc_final: 0.6732 (m-70) REVERT: R 188 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8724 (mp) REVERT: R 207 ARG cc_start: 0.7879 (ttp-170) cc_final: 0.7621 (ttp80) outliers start: 23 outliers final: 16 residues processed: 157 average time/residue: 1.3193 time to fit residues: 220.1617 Evaluate side-chains 158 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 228 ASP 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 36 LEU Chi-restraints excluded: chain R residue 50 CYS Chi-restraints excluded: chain R residue 56 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.0570 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 155 ASN ** C 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 142 GLN R 47 ASN R 244 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101561 restraints weight = 13250.454| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.48 r_work: 0.3203 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8765 Z= 0.153 Angle : 0.558 8.239 11906 Z= 0.281 Chirality : 0.042 0.146 1349 Planarity : 0.004 0.057 1523 Dihedral : 4.179 40.894 1218 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.88 % Allowed : 20.62 % Favored : 77.49 % 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: 2.45 (0.27), residues: 381 sheet: 0.92 (0.30), residues: 270 loop : 0.31 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE B 199 TYR 0.014 0.001 TYR E 190 ARG 0.005 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3980.92 seconds wall clock time: 71 minutes 28.83 seconds (4288.83 seconds total)