Starting phenix.real_space_refine on Fri Feb 14 18:59:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cqd_16796/02_2025/8cqd_16796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cqd_16796/02_2025/8cqd_16796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cqd_16796/02_2025/8cqd_16796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cqd_16796/02_2025/8cqd_16796.map" model { file = "/net/cci-nas-00/data/ceres_data/8cqd_16796/02_2025/8cqd_16796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cqd_16796/02_2025/8cqd_16796.cif" } resolution = 3.54 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= 0.030 sd= 0.168 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 68 5.16 5 C 7306 2.51 5 N 1612 2.21 5 O 1842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10828 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1884 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 1 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1735 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain breaks: 1 Chain: "C" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1735 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain breaks: 1 Chain: "E" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1735 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain breaks: 1 Chain: "F" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1735 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain breaks: 1 Chain: "D" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1884 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.96, per 1000 atoms: 0.64 Number of scatterers: 10828 At special positions: 0 Unit cell: (111.769, 104.234, 67.815, 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 68 16.00 O 1842 8.00 N 1612 7.00 C 7306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.4 seconds 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2504 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 88.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 28 through 51 removed outlier: 4.398A pdb=" N VAL A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 56 through 59 Processing helix chain 'A' and resid 60 through 87 removed outlier: 3.945A pdb=" N THR A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 118 Proline residue: A 104 - end of helix removed outlier: 4.094A pdb=" N PHE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 144 Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.752A pdb=" N SER A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 197 Processing helix chain 'A' and resid 199 through 209 removed outlier: 3.619A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 248 removed outlier: 4.910A pdb=" N PHE A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 61 through 87 removed outlier: 3.905A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 118 removed outlier: 3.611A pdb=" N ARG B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Proline residue: B 104 - end of helix removed outlier: 4.155A pdb=" N PHE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 144 removed outlier: 3.643A pdb=" N LYS B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 169 Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.758A pdb=" N THR B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 197 Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 220 through 248 removed outlier: 4.804A pdb=" N PHE B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 51 removed outlier: 4.378A pdb=" N VAL C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 61 through 87 Processing helix chain 'C' and resid 91 through 118 removed outlier: 3.527A pdb=" N ARG C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Proline residue: C 104 - end of helix removed outlier: 4.253A pdb=" N PHE C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 145 Processing helix chain 'C' and resid 148 through 169 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.839A pdb=" N THR C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 197 Processing helix chain 'C' and resid 199 through 209 Processing helix chain 'C' and resid 220 through 250 removed outlier: 4.498A pdb=" N PHE C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY C 236 " --> pdb=" O LYS C 232 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 51 removed outlier: 3.574A pdb=" N SER E 33 " --> pdb=" O TYR E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 61 through 87 removed outlier: 3.905A pdb=" N SER E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 118 removed outlier: 3.595A pdb=" N ARG E 95 " --> pdb=" O PRO E 91 " (cutoff:3.500A) Proline residue: E 104 - end of helix removed outlier: 4.152A pdb=" N PHE E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 144 removed outlier: 3.626A pdb=" N LYS E 126 " --> pdb=" O GLY E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 169 Processing helix chain 'E' and resid 170 through 178 removed outlier: 3.752A pdb=" N THR E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 197 Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 220 through 248 removed outlier: 4.806A pdb=" N PHE E 235 " --> pdb=" O ASN E 231 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 51 removed outlier: 4.361A pdb=" N VAL F 32 " --> pdb=" O ASP F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 87 removed outlier: 3.701A pdb=" N LEU F 63 " --> pdb=" O TRP F 59 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER F 66 " --> pdb=" O SER F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 118 removed outlier: 3.531A pdb=" N ARG F 95 " --> pdb=" O PRO F 91 " (cutoff:3.500A) Proline residue: F 104 - end of helix removed outlier: 4.267A pdb=" N PHE F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR F 111 " --> pdb=" O ILE F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 145 Processing helix chain 'F' and resid 148 through 169 Processing helix chain 'F' and resid 170 through 178 removed outlier: 3.839A pdb=" N THR F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 197 Processing helix chain 'F' and resid 199 through 209 Processing helix chain 'F' and resid 220 through 249 removed outlier: 4.484A pdb=" N PHE F 235 " --> pdb=" O ASN F 231 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY F 236 " --> pdb=" O LYS F 232 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN F 249 " --> pdb=" O LYS F 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 18 Proline residue: D 15 - end of helix removed outlier: 3.977A pdb=" N LEU D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 51 removed outlier: 4.376A pdb=" N VAL D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 60 through 87 removed outlier: 3.981A pdb=" N THR D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 118 Proline residue: D 104 - end of helix removed outlier: 4.092A pdb=" N PHE D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 144 Processing helix chain 'D' and resid 148 through 170 Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.728A pdb=" N SER D 174 " --> pdb=" O GLY D 170 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 197 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.643A pdb=" N VAL D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 248 removed outlier: 4.912A pdb=" N PHE D 235 " --> pdb=" O ASN D 231 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY D 236 " --> pdb=" O LYS D 232 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2649 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: 3.34 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1629 1.32 - 1.44: 3379 1.44 - 1.56: 6018 1.56 - 1.69: 0 1.69 - 1.81: 118 Bond restraints: 11144 Sorted by residual: bond pdb=" C MET C 135 " pdb=" N LEU C 136 " ideal model delta sigma weight residual 1.334 1.235 0.100 1.27e-02 6.20e+03 6.16e+01 bond pdb=" C GLY A 139 " pdb=" N TYR A 140 " ideal model delta sigma weight residual 1.335 1.248 0.087 1.36e-02 5.41e+03 4.12e+01 bond pdb=" C GLY D 67 " pdb=" N LEU D 68 " ideal model delta sigma weight residual 1.335 1.248 0.086 1.36e-02 5.41e+03 4.04e+01 bond pdb=" C LEU D 68 " pdb=" N VAL D 69 " ideal model delta sigma weight residual 1.335 1.403 -0.068 1.19e-02 7.06e+03 3.22e+01 bond pdb=" C VAL E 46 " pdb=" N PHE E 47 " ideal model delta sigma weight residual 1.334 1.406 -0.072 1.27e-02 6.20e+03 3.20e+01 ... (remaining 11139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 14747 1.36 - 2.73: 290 2.73 - 4.09: 104 4.09 - 5.45: 54 5.45 - 6.82: 21 Bond angle restraints: 15216 Sorted by residual: angle pdb=" O VAL E 46 " pdb=" C VAL E 46 " pdb=" N PHE E 47 " ideal model delta sigma weight residual 121.87 126.86 -4.99 9.70e-01 1.06e+00 2.64e+01 angle pdb=" O VAL B 46 " pdb=" C VAL B 46 " pdb=" N PHE B 47 " ideal model delta sigma weight residual 121.87 126.83 -4.96 9.70e-01 1.06e+00 2.61e+01 angle pdb=" O MET C 135 " pdb=" C MET C 135 " pdb=" N LEU C 136 " ideal model delta sigma weight residual 122.07 116.87 5.20 1.03e+00 9.43e-01 2.55e+01 angle pdb=" N PHE A 17 " pdb=" CA PHE A 17 " pdb=" C PHE A 17 " ideal model delta sigma weight residual 111.28 105.79 5.49 1.09e+00 8.42e-01 2.54e+01 angle pdb=" O GLY A 139 " pdb=" C GLY A 139 " pdb=" N TYR A 140 " ideal model delta sigma weight residual 122.19 117.37 4.82 9.60e-01 1.09e+00 2.52e+01 ... (remaining 15211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 5923 17.01 - 34.02: 240 34.02 - 51.03: 27 51.03 - 68.04: 0 68.04 - 85.05: 2 Dihedral angle restraints: 6192 sinusoidal: 2252 harmonic: 3940 Sorted by residual: dihedral pdb=" CB GLU D 51 " pdb=" CG GLU D 51 " pdb=" CD GLU D 51 " pdb=" OE1 GLU D 51 " ideal model delta sinusoidal sigma weight residual 0.00 85.05 -85.05 1 3.00e+01 1.11e-03 9.75e+00 dihedral pdb=" CB GLU A 51 " pdb=" CG GLU A 51 " pdb=" CD GLU A 51 " pdb=" OE1 GLU A 51 " ideal model delta sinusoidal sigma weight residual 0.00 84.84 -84.84 1 3.00e+01 1.11e-03 9.71e+00 dihedral pdb=" CA ASP A 98 " pdb=" CB ASP A 98 " pdb=" CG ASP A 98 " pdb=" OD1 ASP A 98 " ideal model delta sinusoidal sigma weight residual -30.00 -80.16 50.16 1 2.00e+01 2.50e-03 8.62e+00 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1326 0.042 - 0.083: 317 0.083 - 0.125: 68 0.125 - 0.166: 8 0.166 - 0.208: 3 Chirality restraints: 1722 Sorted by residual: chirality pdb=" CA TYR A 77 " pdb=" N TYR A 77 " pdb=" C TYR A 77 " pdb=" CB TYR A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ASN D 231 " pdb=" N ASN D 231 " pdb=" C ASN D 231 " pdb=" CB ASN D 231 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA ASN A 231 " pdb=" N ASN A 231 " pdb=" C ASN A 231 " pdb=" CB ASN A 231 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 1719 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 246 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C GLU A 246 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU A 246 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 247 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 246 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C GLU D 246 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU D 246 " 0.012 2.00e-02 2.50e+03 pdb=" N SER D 247 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 76 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C HIS A 76 " -0.029 2.00e-02 2.50e+03 pdb=" O HIS A 76 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 77 " 0.010 2.00e-02 2.50e+03 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1925 2.76 - 3.29: 11079 3.29 - 3.83: 19080 3.83 - 4.36: 20582 4.36 - 4.90: 37276 Nonbonded interactions: 89942 Sorted by model distance: nonbonded pdb=" OG1 THR E 61 " pdb=" OE2 GLU D 51 " model vdw 2.223 3.040 nonbonded pdb=" OE2 GLU A 51 " pdb=" OG1 THR B 61 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR D 201 " pdb=" OD1 ASP D 228 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR A 201 " pdb=" OD1 ASP A 228 " model vdw 2.231 3.040 nonbonded pdb=" O ALA D 13 " pdb=" OG1 THR D 16 " model vdw 2.299 3.040 ... (remaining 89937 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 250 or resid 301)) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 23 through 250 or resid 301)) selection = chain 'E' selection = chain 'F' } 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 group one per residue 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: 0.190 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.240 Find NCS groups from input model: 0.500 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 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 : 0.005 0.100 11144 Z= 0.347 Angle : 0.607 6.815 15216 Z= 0.364 Chirality : 0.038 0.208 1722 Planarity : 0.004 0.040 1812 Dihedral : 9.169 85.053 3688 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % 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: 2.57 (0.23), residues: 1340 helix: 2.30 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -2.00 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 75 HIS 0.001 0.000 HIS A 76 PHE 0.010 0.001 PHE A 229 TYR 0.009 0.001 TYR A 96 ARG 0.001 0.000 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 TYR cc_start: 0.7180 (m-80) cc_final: 0.6969 (m-10) REVERT: A 191 MET cc_start: 0.8540 (tmm) cc_final: 0.8117 (tmm) REVERT: A 195 ILE cc_start: 0.8861 (mt) cc_final: 0.8654 (mt) REVERT: B 77 TYR cc_start: 0.8567 (m-80) cc_final: 0.8315 (m-80) REVERT: B 80 MET cc_start: 0.7067 (mtm) cc_final: 0.6763 (mtt) REVERT: B 107 ILE cc_start: 0.8431 (tp) cc_final: 0.7969 (tp) REVERT: B 125 PHE cc_start: 0.7691 (t80) cc_final: 0.7471 (t80) REVERT: B 184 GLN cc_start: 0.8412 (mt0) cc_final: 0.8069 (mt0) REVERT: B 185 SER cc_start: 0.8879 (m) cc_final: 0.8487 (p) REVERT: C 100 LEU cc_start: 0.8887 (tp) cc_final: 0.8580 (mt) REVERT: E 77 TYR cc_start: 0.8563 (m-80) cc_final: 0.8314 (m-80) REVERT: E 80 MET cc_start: 0.7158 (mtm) cc_final: 0.6842 (mtt) REVERT: E 125 PHE cc_start: 0.7702 (t80) cc_final: 0.7476 (t80) REVERT: E 161 VAL cc_start: 0.8702 (t) cc_final: 0.8496 (m) REVERT: E 184 GLN cc_start: 0.8420 (mt0) cc_final: 0.8082 (mt0) REVERT: E 185 SER cc_start: 0.8877 (m) cc_final: 0.8490 (p) REVERT: F 100 LEU cc_start: 0.8888 (tp) cc_final: 0.8565 (mt) REVERT: F 133 LEU cc_start: 0.7580 (mt) cc_final: 0.7284 (mt) REVERT: D 29 TYR cc_start: 0.7136 (m-80) cc_final: 0.6905 (m-10) REVERT: D 98 ASP cc_start: 0.7799 (t70) cc_final: 0.7534 (t0) REVERT: D 191 MET cc_start: 0.8483 (tmm) cc_final: 0.8075 (tmm) REVERT: D 195 ILE cc_start: 0.8809 (mt) cc_final: 0.8600 (mt) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.2097 time to fit residues: 112.5222 Evaluate side-chains 283 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.201411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.146046 restraints weight = 12309.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.144640 restraints weight = 12241.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146324 restraints weight = 10732.262| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11144 Z= 0.376 Angle : 0.622 8.284 15216 Z= 0.318 Chirality : 0.043 0.252 1722 Planarity : 0.004 0.051 1812 Dihedral : 3.825 25.069 1520 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.54 % Allowed : 13.86 % Favored : 83.61 % 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: 2.00 (0.23), residues: 1340 helix: 1.90 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.38 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 75 HIS 0.003 0.001 HIS A 76 PHE 0.018 0.002 PHE E 47 TYR 0.013 0.001 TYR F 77 ARG 0.013 0.001 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 291 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7061 (tp30) cc_final: 0.6783 (tp30) REVERT: A 191 MET cc_start: 0.8494 (tmm) cc_final: 0.8161 (tmm) REVERT: A 246 GLU cc_start: 0.7990 (tp30) cc_final: 0.7684 (mm-30) REVERT: B 77 TYR cc_start: 0.8709 (m-80) cc_final: 0.8443 (m-80) REVERT: B 80 MET cc_start: 0.6955 (mtm) cc_final: 0.6571 (mtt) REVERT: B 127 LYS cc_start: 0.6464 (ptpt) cc_final: 0.6035 (ptpt) REVERT: B 184 GLN cc_start: 0.8399 (mt0) cc_final: 0.8126 (mt0) REVERT: C 100 LEU cc_start: 0.8754 (tp) cc_final: 0.8468 (mt) REVERT: C 135 MET cc_start: 0.7751 (ptp) cc_final: 0.7404 (ptp) REVERT: C 184 GLN cc_start: 0.8154 (mt0) cc_final: 0.7772 (mm-40) REVERT: C 185 SER cc_start: 0.8225 (m) cc_final: 0.7782 (t) REVERT: E 77 TYR cc_start: 0.8723 (m-80) cc_final: 0.8382 (m-80) REVERT: E 80 MET cc_start: 0.7179 (mtm) cc_final: 0.6749 (mtt) REVERT: E 127 LYS cc_start: 0.6470 (ptpt) cc_final: 0.6051 (ptpt) REVERT: E 184 GLN cc_start: 0.8407 (mt0) cc_final: 0.8133 (mt0) REVERT: F 100 LEU cc_start: 0.8749 (tp) cc_final: 0.8473 (mt) REVERT: F 135 MET cc_start: 0.7707 (ptp) cc_final: 0.7392 (ptp) REVERT: F 184 GLN cc_start: 0.8155 (mt0) cc_final: 0.7808 (mm-40) REVERT: D 166 GLU cc_start: 0.7180 (tp30) cc_final: 0.6857 (tp30) REVERT: D 191 MET cc_start: 0.8437 (tmm) cc_final: 0.8118 (tmm) REVERT: D 246 GLU cc_start: 0.7946 (tp30) cc_final: 0.7626 (mm-30) outliers start: 28 outliers final: 17 residues processed: 304 average time/residue: 0.2123 time to fit residues: 92.5387 Evaluate side-chains 299 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 282 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 71 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 124 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 90 optimal weight: 0.0770 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.207067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.150691 restraints weight = 12346.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.150626 restraints weight = 10741.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.152174 restraints weight = 10437.979| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11144 Z= 0.163 Angle : 0.513 5.871 15216 Z= 0.263 Chirality : 0.037 0.217 1722 Planarity : 0.004 0.042 1812 Dihedral : 3.795 24.587 1520 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.45 % Allowed : 15.13 % Favored : 82.43 % 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: 2.34 (0.23), residues: 1340 helix: 2.11 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -2.05 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 35 HIS 0.001 0.000 HIS C 76 PHE 0.024 0.001 PHE C 153 TYR 0.026 0.001 TYR C 96 ARG 0.008 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 294 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8523 (tmm) cc_final: 0.8193 (tmm) REVERT: B 80 MET cc_start: 0.6848 (mtm) cc_final: 0.6495 (mtt) REVERT: B 140 TYR cc_start: 0.7792 (t80) cc_final: 0.7400 (t80) REVERT: B 162 TYR cc_start: 0.8192 (t80) cc_final: 0.7939 (t80) REVERT: B 166 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6424 (mt-10) REVERT: B 184 GLN cc_start: 0.8395 (mt0) cc_final: 0.8034 (mt0) REVERT: C 100 LEU cc_start: 0.8791 (tp) cc_final: 0.8480 (mt) REVERT: C 140 TYR cc_start: 0.7867 (t80) cc_final: 0.7528 (t80) REVERT: C 184 GLN cc_start: 0.8170 (mt0) cc_final: 0.7764 (mm-40) REVERT: C 185 SER cc_start: 0.8245 (m) cc_final: 0.7789 (t) REVERT: C 246 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7779 (mm-30) REVERT: E 80 MET cc_start: 0.6881 (mtm) cc_final: 0.6265 (mtt) REVERT: E 140 TYR cc_start: 0.7773 (t80) cc_final: 0.7387 (t80) REVERT: E 162 TYR cc_start: 0.8200 (t80) cc_final: 0.7938 (t80) REVERT: E 166 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6417 (mt-10) REVERT: E 167 LEU cc_start: 0.8110 (mt) cc_final: 0.7898 (tt) REVERT: E 184 GLN cc_start: 0.8393 (mt0) cc_final: 0.8037 (mt0) REVERT: F 100 LEU cc_start: 0.8803 (tp) cc_final: 0.8499 (mt) REVERT: F 140 TYR cc_start: 0.7608 (t80) cc_final: 0.7317 (t80) REVERT: F 184 GLN cc_start: 0.8172 (mt0) cc_final: 0.7776 (mm-40) REVERT: D 166 GLU cc_start: 0.7251 (tp30) cc_final: 0.6911 (tp30) REVERT: D 191 MET cc_start: 0.8349 (tmm) cc_final: 0.8055 (tmm) outliers start: 27 outliers final: 17 residues processed: 306 average time/residue: 0.2180 time to fit residues: 95.8920 Evaluate side-chains 278 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 261 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 24 optimal weight: 0.2980 chunk 123 optimal weight: 3.9990 chunk 74 optimal weight: 30.0000 chunk 46 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 27 optimal weight: 0.0270 chunk 9 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 overall best weight: 1.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.204672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.149251 restraints weight = 12079.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.148473 restraints weight = 10296.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.150089 restraints weight = 9997.949| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11144 Z= 0.189 Angle : 0.510 5.662 15216 Z= 0.262 Chirality : 0.038 0.194 1722 Planarity : 0.004 0.041 1812 Dihedral : 3.813 29.323 1520 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.08 % Allowed : 17.48 % Favored : 80.43 % 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: 2.23 (0.23), residues: 1340 helix: 2.03 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -2.04 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 160 HIS 0.001 0.000 HIS F 76 PHE 0.026 0.002 PHE F 153 TYR 0.015 0.001 TYR A 165 ARG 0.005 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 291 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8459 (tmm) cc_final: 0.8129 (tmm) REVERT: B 80 MET cc_start: 0.6840 (mtm) cc_final: 0.6499 (mtt) REVERT: B 162 TYR cc_start: 0.8290 (t80) cc_final: 0.7963 (t80) REVERT: B 166 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6425 (mt-10) REVERT: B 167 LEU cc_start: 0.8082 (mt) cc_final: 0.7795 (tt) REVERT: B 184 GLN cc_start: 0.8350 (mt0) cc_final: 0.8054 (mt0) REVERT: C 100 LEU cc_start: 0.8719 (tp) cc_final: 0.8492 (mt) REVERT: C 140 TYR cc_start: 0.7770 (t80) cc_final: 0.7472 (t80) REVERT: C 184 GLN cc_start: 0.8171 (mt0) cc_final: 0.7787 (mm-40) REVERT: C 185 SER cc_start: 0.8320 (m) cc_final: 0.7831 (t) REVERT: E 80 MET cc_start: 0.6885 (mtm) cc_final: 0.6527 (mtt) REVERT: E 162 TYR cc_start: 0.8262 (t80) cc_final: 0.7821 (t80) REVERT: E 166 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6234 (mt-10) REVERT: E 184 GLN cc_start: 0.8350 (mt0) cc_final: 0.8046 (mt0) REVERT: F 100 LEU cc_start: 0.8726 (tp) cc_final: 0.8476 (mt) REVERT: F 143 GLU cc_start: 0.7771 (tp30) cc_final: 0.7352 (tp30) REVERT: F 184 GLN cc_start: 0.8031 (mt0) cc_final: 0.7675 (mm-40) REVERT: D 166 GLU cc_start: 0.7253 (tp30) cc_final: 0.6966 (tp30) REVERT: D 191 MET cc_start: 0.8250 (tmm) cc_final: 0.7890 (tmm) REVERT: D 205 TYR cc_start: 0.6201 (t80) cc_final: 0.5862 (t80) outliers start: 23 outliers final: 15 residues processed: 301 average time/residue: 0.2196 time to fit residues: 94.7712 Evaluate side-chains 277 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 262 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 30 optimal weight: 30.0000 chunk 76 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.206245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.151522 restraints weight = 12106.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.150822 restraints weight = 10704.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.153606 restraints weight = 9991.681| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11144 Z= 0.171 Angle : 0.507 7.214 15216 Z= 0.258 Chirality : 0.038 0.191 1722 Planarity : 0.004 0.054 1812 Dihedral : 3.767 29.504 1520 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.45 % Allowed : 19.66 % Favored : 78.89 % 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: 2.25 (0.23), residues: 1340 helix: 2.04 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -2.08 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 160 HIS 0.001 0.000 HIS F 76 PHE 0.027 0.001 PHE F 153 TYR 0.020 0.001 TYR A 205 ARG 0.002 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 282 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8871 (mtmm) cc_final: 0.8615 (tppt) REVERT: A 191 MET cc_start: 0.8413 (tmm) cc_final: 0.8059 (tmm) REVERT: B 80 MET cc_start: 0.6874 (mtm) cc_final: 0.6555 (mtt) REVERT: B 162 TYR cc_start: 0.8325 (t80) cc_final: 0.8008 (t80) REVERT: B 166 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6283 (mt-10) REVERT: B 167 LEU cc_start: 0.8081 (mt) cc_final: 0.7785 (tt) REVERT: B 184 GLN cc_start: 0.8341 (mt0) cc_final: 0.8028 (mt0) REVERT: C 100 LEU cc_start: 0.8737 (tp) cc_final: 0.8493 (mt) REVERT: C 140 TYR cc_start: 0.7738 (t80) cc_final: 0.7473 (t80) REVERT: C 184 GLN cc_start: 0.8244 (mt0) cc_final: 0.7893 (mm-40) REVERT: C 185 SER cc_start: 0.8352 (m) cc_final: 0.7848 (t) REVERT: E 80 MET cc_start: 0.6876 (mtm) cc_final: 0.6494 (mtt) REVERT: E 166 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6521 (mt-10) REVERT: E 184 GLN cc_start: 0.8362 (mt0) cc_final: 0.8046 (mt0) REVERT: E 191 MET cc_start: 0.7540 (ttp) cc_final: 0.7313 (tmm) REVERT: F 100 LEU cc_start: 0.8736 (tp) cc_final: 0.8423 (mt) REVERT: F 143 GLU cc_start: 0.7796 (tp30) cc_final: 0.7409 (tp30) REVERT: F 184 GLN cc_start: 0.8231 (mt0) cc_final: 0.7863 (mm-40) REVERT: F 185 SER cc_start: 0.8352 (m) cc_final: 0.7863 (t) REVERT: F 246 GLU cc_start: 0.7792 (tp30) cc_final: 0.7590 (tm-30) REVERT: D 166 GLU cc_start: 0.7318 (tp30) cc_final: 0.7100 (tp30) REVERT: D 191 MET cc_start: 0.8221 (tmm) cc_final: 0.7848 (tmm) outliers start: 16 outliers final: 12 residues processed: 292 average time/residue: 0.2148 time to fit residues: 90.0819 Evaluate side-chains 281 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 269 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 7 optimal weight: 0.0970 chunk 64 optimal weight: 0.0470 chunk 115 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 chunk 88 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.209654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.155006 restraints weight = 12075.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.155093 restraints weight = 10138.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.157276 restraints weight = 10370.188| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11144 Z= 0.150 Angle : 0.498 7.620 15216 Z= 0.254 Chirality : 0.038 0.267 1722 Planarity : 0.004 0.045 1812 Dihedral : 3.724 28.562 1520 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.90 % Allowed : 18.84 % Favored : 79.26 % 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: 2.39 (0.23), residues: 1340 helix: 2.14 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -2.03 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 160 HIS 0.001 0.000 HIS C 76 PHE 0.028 0.001 PHE F 153 TYR 0.013 0.001 TYR C 205 ARG 0.002 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 290 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8877 (mtmm) cc_final: 0.8649 (tppt) REVERT: A 191 MET cc_start: 0.8237 (tmm) cc_final: 0.7912 (tmm) REVERT: B 80 MET cc_start: 0.6856 (mtm) cc_final: 0.6509 (mtt) REVERT: B 162 TYR cc_start: 0.8295 (t80) cc_final: 0.7971 (t80) REVERT: B 166 GLU cc_start: 0.6629 (mt-10) cc_final: 0.6174 (mt-10) REVERT: B 184 GLN cc_start: 0.8371 (mt0) cc_final: 0.8089 (mt0) REVERT: B 191 MET cc_start: 0.7351 (ttp) cc_final: 0.7149 (tmm) REVERT: C 100 LEU cc_start: 0.8709 (tp) cc_final: 0.8488 (mt) REVERT: C 140 TYR cc_start: 0.7767 (t80) cc_final: 0.7551 (t80) REVERT: C 184 GLN cc_start: 0.8156 (mt0) cc_final: 0.7866 (mm-40) REVERT: C 185 SER cc_start: 0.8318 (m) cc_final: 0.7832 (t) REVERT: E 80 MET cc_start: 0.6872 (mtm) cc_final: 0.6508 (mtt) REVERT: E 162 TYR cc_start: 0.8134 (t80) cc_final: 0.7658 (t80) REVERT: E 166 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6215 (mt-10) REVERT: F 78 MET cc_start: 0.8256 (mmt) cc_final: 0.7885 (mmm) REVERT: F 100 LEU cc_start: 0.8708 (tp) cc_final: 0.8474 (mt) REVERT: F 141 MET cc_start: 0.7757 (mmt) cc_final: 0.7439 (mmt) REVERT: F 143 GLU cc_start: 0.7644 (tp30) cc_final: 0.7281 (tp30) REVERT: F 184 GLN cc_start: 0.8190 (mt0) cc_final: 0.7868 (mm-40) REVERT: F 185 SER cc_start: 0.8337 (m) cc_final: 0.7836 (t) REVERT: F 246 GLU cc_start: 0.7793 (tp30) cc_final: 0.7549 (tm-30) REVERT: D 75 TRP cc_start: 0.8007 (t60) cc_final: 0.6734 (t-100) REVERT: D 191 MET cc_start: 0.8173 (tmm) cc_final: 0.7772 (tmm) outliers start: 21 outliers final: 15 residues processed: 301 average time/residue: 0.2235 time to fit residues: 96.4625 Evaluate side-chains 281 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 266 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain D residue 124 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 123 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 126 optimal weight: 30.0000 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.200811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.145288 restraints weight = 12363.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.144911 restraints weight = 10734.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147345 restraints weight = 9160.260| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11144 Z= 0.321 Angle : 0.589 7.468 15216 Z= 0.302 Chirality : 0.041 0.258 1722 Planarity : 0.004 0.041 1812 Dihedral : 3.982 34.374 1520 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.54 % Allowed : 18.75 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.94 (0.23), residues: 1340 helix: 1.83 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -2.16 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 160 HIS 0.002 0.001 HIS F 76 PHE 0.028 0.002 PHE F 153 TYR 0.020 0.001 TYR A 201 ARG 0.002 0.000 ARG F 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 262 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6788 (mpp) REVERT: A 191 MET cc_start: 0.8420 (tmm) cc_final: 0.8047 (tmm) REVERT: B 80 MET cc_start: 0.6866 (mtm) cc_final: 0.6502 (mtt) REVERT: B 167 LEU cc_start: 0.8081 (mt) cc_final: 0.7779 (tt) REVERT: B 184 GLN cc_start: 0.8355 (mt0) cc_final: 0.8047 (mt0) REVERT: C 96 TYR cc_start: 0.8209 (m-80) cc_final: 0.7916 (m-80) REVERT: C 100 LEU cc_start: 0.8722 (tp) cc_final: 0.8494 (mt) REVERT: C 185 SER cc_start: 0.8464 (m) cc_final: 0.7924 (t) REVERT: C 246 GLU cc_start: 0.7796 (tp30) cc_final: 0.7215 (tm-30) REVERT: E 184 GLN cc_start: 0.8179 (mt0) cc_final: 0.7390 (mp10) REVERT: F 100 LEU cc_start: 0.8737 (tp) cc_final: 0.8423 (mt) REVERT: F 141 MET cc_start: 0.7754 (mmt) cc_final: 0.7413 (mmt) REVERT: F 143 GLU cc_start: 0.7742 (tp30) cc_final: 0.7389 (tp30) REVERT: F 185 SER cc_start: 0.8368 (m) cc_final: 0.7822 (t) REVERT: F 246 GLU cc_start: 0.7887 (tp30) cc_final: 0.7587 (tm-30) REVERT: D 80 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6752 (mpp) REVERT: D 191 MET cc_start: 0.8237 (tmm) cc_final: 0.7877 (tmm) REVERT: D 246 GLU cc_start: 0.8007 (tp30) cc_final: 0.7580 (mm-30) outliers start: 28 outliers final: 22 residues processed: 279 average time/residue: 0.2203 time to fit residues: 88.3408 Evaluate side-chains 282 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 244 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.3980 chunk 134 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.205394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.149650 restraints weight = 12171.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.148238 restraints weight = 10527.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.149808 restraints weight = 10037.483| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11144 Z= 0.188 Angle : 0.536 7.862 15216 Z= 0.272 Chirality : 0.039 0.265 1722 Planarity : 0.004 0.039 1812 Dihedral : 3.925 31.729 1520 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.99 % Allowed : 19.75 % Favored : 78.26 % 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: 2.10 (0.23), residues: 1340 helix: 1.92 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.01 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 160 HIS 0.001 0.000 HIS C 76 PHE 0.030 0.002 PHE F 153 TYR 0.014 0.001 TYR A 201 ARG 0.002 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 268 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6757 (mpp) REVERT: A 163 MET cc_start: 0.6836 (ptp) cc_final: 0.6319 (mtm) REVERT: A 176 CYS cc_start: 0.7740 (p) cc_final: 0.7532 (p) REVERT: A 191 MET cc_start: 0.8269 (tmm) cc_final: 0.7932 (tmm) REVERT: B 80 MET cc_start: 0.6719 (mtm) cc_final: 0.6334 (mtt) REVERT: B 184 GLN cc_start: 0.8368 (mt0) cc_final: 0.8053 (mt0) REVERT: B 191 MET cc_start: 0.7445 (ttp) cc_final: 0.7214 (tmm) REVERT: C 96 TYR cc_start: 0.8082 (m-80) cc_final: 0.7797 (m-80) REVERT: C 100 LEU cc_start: 0.8756 (tp) cc_final: 0.8492 (mt) REVERT: C 127 LYS cc_start: 0.5923 (ptpt) cc_final: 0.5704 (ptpt) REVERT: C 185 SER cc_start: 0.8451 (m) cc_final: 0.7887 (t) REVERT: C 246 GLU cc_start: 0.7738 (tp30) cc_final: 0.7178 (tm-30) REVERT: E 184 GLN cc_start: 0.8160 (mt0) cc_final: 0.7343 (mp10) REVERT: F 100 LEU cc_start: 0.8728 (tp) cc_final: 0.8453 (mt) REVERT: F 141 MET cc_start: 0.7690 (mmt) cc_final: 0.7397 (mmt) REVERT: F 143 GLU cc_start: 0.7731 (tp30) cc_final: 0.7386 (tp30) REVERT: F 185 SER cc_start: 0.8438 (m) cc_final: 0.7861 (t) REVERT: F 246 GLU cc_start: 0.7866 (tp30) cc_final: 0.7601 (tm-30) REVERT: D 80 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6720 (mpp) REVERT: D 191 MET cc_start: 0.8207 (tmm) cc_final: 0.7852 (tmm) outliers start: 22 outliers final: 18 residues processed: 282 average time/residue: 0.2173 time to fit residues: 87.6554 Evaluate side-chains 275 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 124 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 63 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.206346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.150037 restraints weight = 12285.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.148895 restraints weight = 10603.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150284 restraints weight = 10159.213| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11144 Z= 0.184 Angle : 0.528 8.238 15216 Z= 0.270 Chirality : 0.039 0.253 1722 Planarity : 0.004 0.040 1812 Dihedral : 3.919 32.207 1520 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.17 % Allowed : 19.66 % Favored : 78.17 % 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: 2.20 (0.23), residues: 1340 helix: 2.00 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -2.00 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 160 HIS 0.001 0.000 HIS F 76 PHE 0.031 0.002 PHE F 153 TYR 0.016 0.001 TYR D 205 ARG 0.002 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.6764 (mpp) REVERT: A 138 PHE cc_start: 0.8101 (m-80) cc_final: 0.7834 (m-80) REVERT: A 147 MET cc_start: 0.5569 (ttt) cc_final: 0.4911 (tpp) REVERT: A 176 CYS cc_start: 0.7501 (p) cc_final: 0.7300 (p) REVERT: A 191 MET cc_start: 0.8328 (tmm) cc_final: 0.8018 (tmm) REVERT: B 80 MET cc_start: 0.6731 (mtm) cc_final: 0.6374 (mtt) REVERT: B 163 MET cc_start: 0.8365 (tpp) cc_final: 0.7593 (mtt) REVERT: B 184 GLN cc_start: 0.8360 (mt0) cc_final: 0.8066 (mt0) REVERT: C 96 TYR cc_start: 0.8021 (m-80) cc_final: 0.7745 (m-80) REVERT: C 100 LEU cc_start: 0.8732 (tp) cc_final: 0.8469 (mt) REVERT: C 185 SER cc_start: 0.8467 (m) cc_final: 0.7892 (t) REVERT: C 246 GLU cc_start: 0.7742 (tp30) cc_final: 0.7171 (tm-30) REVERT: E 184 GLN cc_start: 0.8248 (mt0) cc_final: 0.7425 (mp10) REVERT: F 100 LEU cc_start: 0.8736 (tp) cc_final: 0.8472 (mt) REVERT: F 141 MET cc_start: 0.7615 (mmt) cc_final: 0.7317 (mmt) REVERT: F 143 GLU cc_start: 0.7734 (tp30) cc_final: 0.7390 (tp30) REVERT: F 153 PHE cc_start: 0.7642 (t80) cc_final: 0.7406 (t80) REVERT: F 185 SER cc_start: 0.8449 (m) cc_final: 0.7862 (t) REVERT: F 246 GLU cc_start: 0.7877 (tp30) cc_final: 0.7604 (tm-30) REVERT: D 80 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.6740 (mpp) REVERT: D 191 MET cc_start: 0.8128 (tmm) cc_final: 0.7761 (tmm) outliers start: 24 outliers final: 20 residues processed: 287 average time/residue: 0.2338 time to fit residues: 96.5788 Evaluate side-chains 274 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 252 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 9 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.206028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.150123 restraints weight = 12232.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.147991 restraints weight = 11198.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.149272 restraints weight = 10686.441| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11144 Z= 0.193 Angle : 0.554 8.436 15216 Z= 0.283 Chirality : 0.039 0.247 1722 Planarity : 0.004 0.040 1812 Dihedral : 3.926 32.242 1520 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.26 % Allowed : 19.47 % Favored : 78.26 % 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: 2.15 (0.23), residues: 1340 helix: 1.96 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.03 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 160 HIS 0.001 0.000 HIS C 76 PHE 0.030 0.002 PHE F 153 TYR 0.018 0.001 TYR D 205 ARG 0.001 0.000 ARG C 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6759 (mpp) REVERT: A 191 MET cc_start: 0.8132 (tmm) cc_final: 0.7844 (tmm) REVERT: B 80 MET cc_start: 0.6742 (mtm) cc_final: 0.6386 (mtt) REVERT: B 184 GLN cc_start: 0.8371 (mt0) cc_final: 0.8066 (mt0) REVERT: C 96 TYR cc_start: 0.8005 (m-80) cc_final: 0.7726 (m-80) REVERT: C 100 LEU cc_start: 0.8727 (tp) cc_final: 0.8457 (mt) REVERT: C 185 SER cc_start: 0.8462 (m) cc_final: 0.7885 (t) REVERT: C 246 GLU cc_start: 0.7739 (tp30) cc_final: 0.7170 (tm-30) REVERT: E 184 GLN cc_start: 0.8261 (mt0) cc_final: 0.7864 (mt0) REVERT: F 100 LEU cc_start: 0.8744 (tp) cc_final: 0.8468 (mt) REVERT: F 141 MET cc_start: 0.7623 (mmt) cc_final: 0.7304 (mmt) REVERT: F 143 GLU cc_start: 0.7756 (tp30) cc_final: 0.7406 (tp30) REVERT: F 153 PHE cc_start: 0.7650 (t80) cc_final: 0.7414 (t80) REVERT: F 185 SER cc_start: 0.8449 (m) cc_final: 0.7864 (t) REVERT: F 246 GLU cc_start: 0.7849 (tp30) cc_final: 0.7602 (tm-30) REVERT: D 75 TRP cc_start: 0.8054 (t60) cc_final: 0.6770 (t-100) REVERT: D 80 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6726 (mpp) REVERT: D 163 MET cc_start: 0.6910 (ptp) cc_final: 0.6452 (mtm) REVERT: D 191 MET cc_start: 0.8154 (tmm) cc_final: 0.7767 (tmm) outliers start: 25 outliers final: 21 residues processed: 280 average time/residue: 0.2131 time to fit residues: 85.3343 Evaluate side-chains 285 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 262 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 11 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 HIS ** C 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.201131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.142770 restraints weight = 12218.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141455 restraints weight = 11870.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.143058 restraints weight = 10634.598| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11144 Z= 0.346 Angle : 0.648 9.774 15216 Z= 0.331 Chirality : 0.042 0.237 1722 Planarity : 0.004 0.037 1812 Dihedral : 4.093 36.103 1520 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.45 % Allowed : 19.38 % Favored : 78.17 % 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 (0.23), residues: 1340 helix: 1.66 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.19 (0.38), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 160 HIS 0.002 0.001 HIS A 76 PHE 0.029 0.002 PHE F 153 TYR 0.021 0.002 TYR D 209 ARG 0.002 0.000 ARG C 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3091.49 seconds wall clock time: 56 minutes 16.56 seconds (3376.56 seconds total)