Starting phenix.real_space_refine on Mon Jul 28 16:56:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cqd_16796/07_2025/8cqd_16796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cqd_16796/07_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_16796/07_2025/8cqd_16796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cqd_16796/07_2025/8cqd_16796.map" model { file = "/net/cci-nas-00/data/ceres_data/8cqd_16796/07_2025/8cqd_16796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cqd_16796/07_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-5711/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: 7.17, per 1000 atoms: 0.66 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: 2.95 Conformation dependent library (CDL) restraints added in 1.5 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: 0.90 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: 3.05 Time building geometry restraints manager: 3.41 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: 0.160 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.680 Find NCS groups from input model: 0.580 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- 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 : 0.006 0.124 11150 Z= 0.404 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 Details of bonding type rmsd hydrogen bonds : bond 0.10097 ( 884) hydrogen bonds : angle 4.79136 ( 2649) covalent geometry : bond 0.00517 (11144) covalent geometry : angle 0.60680 (15216) Misc. bond : bond 0.10149 ( 6) *********************** 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 : 1.198 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: 112.3191 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 : 1.077 ------------------------------------------------------------------------------- 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 = 0.146045 restraints weight = 12309.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.144627 restraints weight = 12241.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146323 restraints weight = 10720.506| |-----------------------------------------------------------------------------| 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 11150 Z= 0.244 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 Details of bonding type rmsd hydrogen bonds : bond 0.04677 ( 884) hydrogen bonds : angle 3.98032 ( 2649) covalent geometry : bond 0.00588 (11144) covalent geometry : angle 0.62169 (15216) Misc. bond : bond 0.00145 ( 6) *********************** 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 : 1.098 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7062 (tp30) cc_final: 0.6783 (tp30) REVERT: A 191 MET cc_start: 0.8494 (tmm) cc_final: 0.8162 (tmm) REVERT: A 246 GLU cc_start: 0.7989 (tp30) cc_final: 0.7683 (mm-30) REVERT: B 77 TYR cc_start: 0.8708 (m-80) cc_final: 0.8442 (m-80) REVERT: B 80 MET cc_start: 0.6955 (mtm) cc_final: 0.6572 (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: 0.8125 (mt0) REVERT: C 100 LEU cc_start: 0.8754 (tp) cc_final: 0.8469 (mt) REVERT: C 135 MET cc_start: 0.7751 (ptp) cc_final: 0.7405 (ptp) REVERT: C 184 GLN cc_start: 0.8154 (mt0) cc_final: 0.7772 (mm-40) REVERT: C 185 SER cc_start: 0.8226 (m) cc_final: 0.7782 (t) REVERT: E 77 TYR cc_start: 0.8722 (m-80) cc_final: 0.8382 (m-80) REVERT: E 80 MET cc_start: 0.7179 (mtm) cc_final: 0.6748 (mtt) REVERT: E 127 LYS cc_start: 0.6469 (ptpt) cc_final: 0.6050 (ptpt) REVERT: E 184 GLN cc_start: 0.8406 (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: 0.7393 (ptp) REVERT: F 184 GLN cc_start: 0.8156 (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: 0.8117 (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: 0.2320 time to fit residues: 101.2351 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 : 1.689 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.9980 chunk 22 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4376 r_free = 0.4376 target = 0.206680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.150436 restraints weight = 12383.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.150159 restraints weight = 10828.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151728 restraints weight = 10567.284| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11150 Z= 0.122 Angle : 0.513 5.744 15216 Z= 0.263 Chirality : 0.038 0.214 1722 Planarity : 0.004 0.042 1812 Dihedral : 3.817 25.607 1520 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.45 % Allowed : 15.31 % Favored : 82.25 % 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 : -2.07 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 75 HIS 0.001 0.000 HIS C 76 PHE 0.024 0.002 PHE C 153 TYR 0.024 0.001 TYR C 96 ARG 0.007 0.001 ARG F 81 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 884) hydrogen bonds : angle 3.66785 ( 2649) covalent geometry : bond 0.00268 (11144) covalent geometry : angle 0.51336 (15216) Misc. bond : bond 0.00054 ( 6) *********************** 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 323 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 296 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.6747 (ttp) cc_final: 0.6451 (ttt) REVERT: A 191 MET cc_start: 0.8511 (tmm) cc_final: 0.8196 (tmm) REVERT: B 80 MET cc_start: 0.6844 (mtm) cc_final: 0.6490 (mtt) REVERT: B 140 TYR cc_start: 0.7801 (t80) cc_final: 0.7425 (t80) REVERT: B 162 TYR cc_start: 0.8206 (t80) cc_final: 0.7967 (t80) REVERT: B 184 GLN cc_start: 0.8400 (mt0) cc_final: 0.8057 (mt0) REVERT: B 191 MET cc_start: 0.7571 (ttp) cc_final: 0.7269 (tmm) REVERT: C 100 LEU cc_start: 0.8796 (tp) cc_final: 0.8480 (mt) REVERT: C 140 TYR cc_start: 0.7868 (t80) cc_final: 0.7526 (t80) REVERT: C 184 GLN cc_start: 0.8179 (mt0) cc_final: 0.7777 (mm-40) REVERT: C 185 SER cc_start: 0.8246 (m) cc_final: 0.7783 (t) REVERT: C 246 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7775 (mm-30) REVERT: E 80 MET cc_start: 0.6877 (mtm) cc_final: 0.6263 (mtt) REVERT: E 140 TYR cc_start: 0.7788 (t80) cc_final: 0.7362 (t80) REVERT: E 162 TYR cc_start: 0.8214 (t80) cc_final: 0.7935 (t80) REVERT: E 166 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6365 (mt-10) REVERT: E 184 GLN cc_start: 0.8398 (mt0) cc_final: 0.8047 (mt0) REVERT: F 100 LEU cc_start: 0.8686 (tp) cc_final: 0.8472 (mt) REVERT: F 140 TYR cc_start: 0.7613 (t80) cc_final: 0.7334 (t80) REVERT: F 184 GLN cc_start: 0.8181 (mt0) cc_final: 0.7796 (mm-40) REVERT: D 166 GLU cc_start: 0.7237 (tp30) cc_final: 0.6900 (tp30) REVERT: D 191 MET cc_start: 0.8340 (tmm) cc_final: 0.8061 (tmm) outliers start: 27 outliers final: 18 residues processed: 308 average time/residue: 0.2698 time to fit residues: 119.3166 Evaluate side-chains 279 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 261 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 F residue 167 LEU 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: 0.9980 chunk 123 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 27 optimal weight: 0.0070 chunk 9 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.5802 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.203809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.148509 restraints weight = 12111.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.147655 restraints weight = 10874.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.149160 restraints weight = 10661.126| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11150 Z= 0.142 Angle : 0.530 6.973 15216 Z= 0.269 Chirality : 0.038 0.194 1722 Planarity : 0.004 0.041 1812 Dihedral : 3.850 30.452 1520 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.72 % Allowed : 16.94 % Favored : 80.34 % 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: 2.21 (0.23), residues: 1340 helix: 2.02 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -2.05 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 160 HIS 0.001 0.001 HIS D 76 PHE 0.026 0.002 PHE F 153 TYR 0.015 0.001 TYR A 165 ARG 0.004 0.000 ARG F 81 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 884) hydrogen bonds : angle 3.68821 ( 2649) covalent geometry : bond 0.00330 (11144) covalent geometry : angle 0.52971 (15216) Misc. bond : bond 0.00072 ( 6) *********************** 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 319 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 289 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8453 (tmm) cc_final: 0.8128 (tmm) REVERT: B 80 MET cc_start: 0.6866 (mtm) cc_final: 0.6501 (mtt) REVERT: B 140 TYR cc_start: 0.7742 (t80) cc_final: 0.7344 (t80) REVERT: B 162 TYR cc_start: 0.8206 (t80) cc_final: 0.7877 (t80) REVERT: B 184 GLN cc_start: 0.8355 (mt0) cc_final: 0.8055 (mt0) REVERT: C 100 LEU cc_start: 0.8740 (tp) cc_final: 0.8496 (mt) REVERT: C 140 TYR cc_start: 0.7775 (t80) cc_final: 0.7494 (t80) REVERT: C 184 GLN cc_start: 0.8173 (mt0) cc_final: 0.7787 (mm-40) REVERT: C 185 SER cc_start: 0.8334 (m) cc_final: 0.7837 (t) REVERT: E 80 MET cc_start: 0.6773 (mtm) cc_final: 0.6359 (mtt) REVERT: E 162 TYR cc_start: 0.8276 (t80) cc_final: 0.7807 (t80) REVERT: E 166 GLU cc_start: 0.6741 (mt-10) cc_final: 0.6193 (mt-10) REVERT: E 184 GLN cc_start: 0.8363 (mt0) cc_final: 0.8053 (mt0) REVERT: F 143 GLU cc_start: 0.7846 (tp30) cc_final: 0.7514 (tp30) REVERT: F 184 GLN cc_start: 0.8158 (mt0) cc_final: 0.7792 (mm-40) REVERT: D 166 GLU cc_start: 0.7260 (tp30) cc_final: 0.6973 (tp30) REVERT: D 191 MET cc_start: 0.8265 (tmm) cc_final: 0.7899 (tmm) REVERT: D 205 TYR cc_start: 0.5723 (t80) cc_final: 0.5484 (t80) outliers start: 30 outliers final: 20 residues processed: 304 average time/residue: 0.3414 time to fit residues: 148.2861 Evaluate side-chains 281 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 261 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 171 GLU 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 167 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 171 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 30.0000 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.204277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.148873 restraints weight = 12110.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147125 restraints weight = 11063.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.148680 restraints weight = 10653.693| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11150 Z= 0.139 Angle : 0.527 6.921 15216 Z= 0.271 Chirality : 0.038 0.194 1722 Planarity : 0.004 0.054 1812 Dihedral : 3.825 31.383 1520 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.17 % Allowed : 18.21 % Favored : 79.62 % 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: 2.07 (0.23), residues: 1340 helix: 1.92 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -2.11 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 160 HIS 0.001 0.001 HIS F 76 PHE 0.027 0.002 PHE F 153 TYR 0.021 0.001 TYR D 205 ARG 0.002 0.000 ARG F 81 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 884) hydrogen bonds : angle 3.69329 ( 2649) covalent geometry : bond 0.00326 (11144) covalent geometry : angle 0.52744 (15216) Misc. bond : bond 0.00064 ( 6) *********************** 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 290 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8445 (tmm) cc_final: 0.8094 (tmm) REVERT: B 80 MET cc_start: 0.6752 (mtm) cc_final: 0.6540 (mtt) REVERT: B 162 TYR cc_start: 0.8198 (t80) cc_final: 0.7978 (t80) REVERT: B 184 GLN cc_start: 0.8355 (mt0) cc_final: 0.8027 (mt0) REVERT: C 140 TYR cc_start: 0.7723 (t80) cc_final: 0.7433 (t80) REVERT: C 184 GLN cc_start: 0.8177 (mt0) cc_final: 0.7775 (mm-40) REVERT: C 185 SER cc_start: 0.8352 (m) cc_final: 0.7851 (t) REVERT: E 80 MET cc_start: 0.6801 (mtm) cc_final: 0.6380 (mtt) REVERT: E 166 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6251 (mt-10) REVERT: E 184 GLN cc_start: 0.8360 (mt0) cc_final: 0.8045 (mt0) REVERT: E 191 MET cc_start: 0.7530 (ttp) cc_final: 0.7288 (tmm) REVERT: F 141 MET cc_start: 0.7819 (mmt) cc_final: 0.7483 (mmt) REVERT: F 143 GLU cc_start: 0.7777 (tp30) cc_final: 0.7441 (tp30) REVERT: F 184 GLN cc_start: 0.8095 (mt0) cc_final: 0.7719 (mm-40) REVERT: F 185 SER cc_start: 0.8339 (m) cc_final: 0.7846 (t) REVERT: F 246 GLU cc_start: 0.7776 (tp30) cc_final: 0.7565 (tm-30) REVERT: D 166 GLU cc_start: 0.7436 (tp30) cc_final: 0.7162 (tp30) REVERT: D 191 MET cc_start: 0.8253 (tmm) cc_final: 0.7866 (tmm) outliers start: 24 outliers final: 19 residues processed: 282 average time/residue: 0.3310 time to fit residues: 138.3925 Evaluate side-chains 275 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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 A residue 244 VAL 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 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 F residue 244 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 244 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** E 76 HIS ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.206859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.150951 restraints weight = 12174.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.151500 restraints weight = 10525.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.152909 restraints weight = 10170.487| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11150 Z= 0.116 Angle : 0.519 7.550 15216 Z= 0.265 Chirality : 0.038 0.270 1722 Planarity : 0.004 0.044 1812 Dihedral : 3.799 30.510 1520 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.81 % Allowed : 19.66 % Favored : 78.53 % 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: 2.14 (0.23), residues: 1340 helix: 1.97 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -2.10 (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 F 76 PHE 0.028 0.002 PHE F 153 TYR 0.014 0.001 TYR D 205 ARG 0.002 0.000 ARG F 81 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 884) hydrogen bonds : angle 3.62941 ( 2649) covalent geometry : bond 0.00259 (11144) covalent geometry : angle 0.51854 (15216) Misc. bond : bond 0.00040 ( 6) *********************** 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 302 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 282 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 TRP cc_start: 0.7636 (m100) cc_final: 0.7306 (m100) REVERT: A 191 MET cc_start: 0.8250 (tmm) cc_final: 0.7907 (tmm) REVERT: B 80 MET cc_start: 0.6730 (mtm) cc_final: 0.6497 (mtt) REVERT: C 96 TYR cc_start: 0.8264 (m-80) cc_final: 0.7963 (m-80) REVERT: C 184 GLN cc_start: 0.8143 (mt0) cc_final: 0.7822 (mm-40) REVERT: C 185 SER cc_start: 0.8308 (m) cc_final: 0.7830 (t) REVERT: E 80 MET cc_start: 0.6708 (mtm) cc_final: 0.6459 (mtt) REVERT: E 162 TYR cc_start: 0.8295 (t80) cc_final: 0.7747 (t80) REVERT: E 166 GLU cc_start: 0.6655 (mt-10) cc_final: 0.6203 (mt-10) REVERT: E 191 MET cc_start: 0.7517 (ttp) cc_final: 0.7306 (tmm) REVERT: F 141 MET cc_start: 0.7868 (mmt) cc_final: 0.7527 (mmt) REVERT: F 143 GLU cc_start: 0.7659 (tp30) cc_final: 0.7386 (tp30) REVERT: F 184 GLN cc_start: 0.8176 (mt0) cc_final: 0.7828 (mm-40) REVERT: F 185 SER cc_start: 0.8323 (m) cc_final: 0.7836 (t) REVERT: F 246 GLU cc_start: 0.7800 (tp30) cc_final: 0.7587 (tm-30) REVERT: D 166 GLU cc_start: 0.7391 (tp30) cc_final: 0.7159 (tp30) REVERT: D 191 MET cc_start: 0.8221 (tmm) cc_final: 0.7847 (tmm) outliers start: 20 outliers final: 16 residues processed: 291 average time/residue: 0.2231 time to fit residues: 93.0691 Evaluate side-chains 284 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 268 time to evaluate : 1.800 ------------------------------------------------------------------------------- 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 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 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 F residue 107 ILE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 114 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 123 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 129 optimal weight: 40.0000 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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** E 76 HIS ** 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 = 0.4356 r_free = 0.4356 target = 0.203821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147111 restraints weight = 12174.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145894 restraints weight = 11400.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.147571 restraints weight = 9978.359| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11150 Z= 0.176 Angle : 0.575 7.903 15216 Z= 0.294 Chirality : 0.041 0.259 1722 Planarity : 0.004 0.040 1812 Dihedral : 3.873 34.134 1520 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.54 % Allowed : 19.75 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.23), residues: 1340 helix: 1.84 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -2.18 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 160 HIS 0.002 0.001 HIS A 76 PHE 0.028 0.002 PHE F 153 TYR 0.014 0.001 TYR A 205 ARG 0.002 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 884) hydrogen bonds : angle 3.79429 ( 2649) covalent geometry : bond 0.00427 (11144) covalent geometry : angle 0.57528 (15216) Misc. bond : bond 0.00087 ( 6) *********************** 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 285 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 TRP cc_start: 0.7677 (m100) cc_final: 0.7305 (m100) REVERT: A 191 MET cc_start: 0.8447 (tmm) cc_final: 0.8100 (tmm) REVERT: B 80 MET cc_start: 0.6838 (mtm) cc_final: 0.6611 (mtt) REVERT: C 96 TYR cc_start: 0.8368 (m-80) cc_final: 0.7972 (m-80) REVERT: C 185 SER cc_start: 0.8408 (m) cc_final: 0.7873 (t) REVERT: C 246 GLU cc_start: 0.7784 (tp30) cc_final: 0.7213 (tm-30) REVERT: E 80 MET cc_start: 0.6793 (mtm) cc_final: 0.6456 (mtt) REVERT: E 166 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6302 (mt-10) REVERT: E 184 GLN cc_start: 0.8162 (mt0) cc_final: 0.7334 (mp10) REVERT: E 191 MET cc_start: 0.7580 (ttp) cc_final: 0.7298 (tmm) REVERT: F 141 MET cc_start: 0.7791 (mmt) cc_final: 0.7454 (mmt) REVERT: F 143 GLU cc_start: 0.7802 (tp30) cc_final: 0.7478 (tp30) REVERT: F 184 GLN cc_start: 0.8083 (mt0) cc_final: 0.7680 (mm-40) REVERT: F 185 SER cc_start: 0.8447 (m) cc_final: 0.7905 (t) REVERT: F 246 GLU cc_start: 0.7869 (tp30) cc_final: 0.7581 (tm-30) REVERT: D 1 MET cc_start: 0.2097 (tpt) cc_final: 0.1763 (tpt) REVERT: D 191 MET cc_start: 0.8277 (tmm) cc_final: 0.7867 (tmm) outliers start: 28 outliers final: 24 residues processed: 276 average time/residue: 0.2166 time to fit residues: 85.6762 Evaluate side-chains 280 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 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 124 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 107 ILE 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 78 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 114 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: 0.7980 chunk 134 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 71 optimal weight: 0.0870 chunk 122 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4391 r_free = 0.4391 target = 0.207534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.151730 restraints weight = 12060.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.151272 restraints weight = 10242.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.153595 restraints weight = 9971.001| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11150 Z= 0.115 Angle : 0.535 8.008 15216 Z= 0.270 Chirality : 0.038 0.260 1722 Planarity : 0.004 0.041 1812 Dihedral : 3.799 30.431 1520 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.90 % Allowed : 20.56 % Favored : 77.54 % 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: 2.17 (0.23), residues: 1340 helix: 1.97 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.02 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 160 HIS 0.002 0.000 HIS E 76 PHE 0.029 0.001 PHE F 153 TYR 0.017 0.001 TYR A 205 ARG 0.002 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 884) hydrogen bonds : angle 3.69001 ( 2649) covalent geometry : bond 0.00256 (11144) covalent geometry : angle 0.53532 (15216) Misc. bond : bond 0.00024 ( 6) *********************** 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 294 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 273 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 TRP cc_start: 0.7671 (m100) cc_final: 0.7270 (m100) REVERT: A 163 MET cc_start: 0.6845 (ptp) cc_final: 0.6312 (mtm) REVERT: A 176 CYS cc_start: 0.7749 (p) cc_final: 0.7503 (p) REVERT: A 191 MET cc_start: 0.8246 (tmm) cc_final: 0.7931 (tmm) REVERT: B 80 MET cc_start: 0.6769 (mtm) cc_final: 0.6528 (mtt) REVERT: B 163 MET cc_start: 0.8478 (mmm) cc_final: 0.7611 (mtt) REVERT: B 184 GLN cc_start: 0.8360 (mt0) cc_final: 0.7864 (mp10) REVERT: C 185 SER cc_start: 0.8467 (m) cc_final: 0.7881 (t) REVERT: C 246 GLU cc_start: 0.7727 (tp30) cc_final: 0.7156 (tm-30) REVERT: E 80 MET cc_start: 0.6701 (mtm) cc_final: 0.6313 (mtt) REVERT: E 160 TRP cc_start: 0.7481 (t60) cc_final: 0.7263 (t60) REVERT: E 166 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6396 (mt-10) REVERT: E 184 GLN cc_start: 0.8202 (mt0) cc_final: 0.7358 (mp10) REVERT: F 141 MET cc_start: 0.7820 (mmt) cc_final: 0.7492 (mmt) REVERT: F 143 GLU cc_start: 0.7656 (tp30) cc_final: 0.7384 (tp30) REVERT: F 184 GLN cc_start: 0.8125 (mt0) cc_final: 0.7758 (mm-40) REVERT: F 185 SER cc_start: 0.8420 (m) cc_final: 0.7845 (t) REVERT: F 246 GLU cc_start: 0.7834 (tp30) cc_final: 0.7586 (tm-30) REVERT: D 191 MET cc_start: 0.8166 (tmm) cc_final: 0.7825 (tmm) outliers start: 21 outliers final: 13 residues processed: 283 average time/residue: 0.3101 time to fit residues: 126.9333 Evaluate side-chains 271 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 258 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 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 248 SER Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 167 LEU 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: 2.9990 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4375 r_free = 0.4375 target = 0.205495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.148090 restraints weight = 12272.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.148446 restraints weight = 10374.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.150706 restraints weight = 9717.236| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11150 Z= 0.135 Angle : 0.553 8.152 15216 Z= 0.281 Chirality : 0.039 0.243 1722 Planarity : 0.004 0.040 1812 Dihedral : 3.836 33.666 1520 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.72 % Allowed : 20.20 % Favored : 78.08 % 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: 2.08 (0.23), residues: 1340 helix: 1.91 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.07 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 160 HIS 0.001 0.001 HIS E 76 PHE 0.030 0.002 PHE F 153 TYR 0.014 0.001 TYR D 165 ARG 0.002 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 884) hydrogen bonds : angle 3.74832 ( 2649) covalent geometry : bond 0.00314 (11144) covalent geometry : angle 0.55328 (15216) Misc. bond : bond 0.00053 ( 6) *********************** 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 280 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 261 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 TRP cc_start: 0.7772 (m100) cc_final: 0.7339 (m100) REVERT: A 176 CYS cc_start: 0.7530 (p) cc_final: 0.7304 (p) REVERT: A 191 MET cc_start: 0.8347 (tmm) cc_final: 0.8038 (tmm) REVERT: B 80 MET cc_start: 0.6729 (mtm) cc_final: 0.6497 (mtt) REVERT: B 163 MET cc_start: 0.8346 (mmm) cc_final: 0.7598 (mtt) REVERT: B 191 MET cc_start: 0.7455 (ttp) cc_final: 0.7255 (tmm) REVERT: C 96 TYR cc_start: 0.8258 (m-80) cc_final: 0.7862 (m-80) REVERT: C 185 SER cc_start: 0.8474 (m) cc_final: 0.7865 (t) REVERT: C 246 GLU cc_start: 0.7734 (tp30) cc_final: 0.7146 (tm-30) REVERT: E 80 MET cc_start: 0.6744 (mtm) cc_final: 0.6339 (mtt) REVERT: E 166 GLU cc_start: 0.6479 (mt-10) cc_final: 0.6247 (mt-10) REVERT: E 184 GLN cc_start: 0.8205 (mt0) cc_final: 0.7367 (mp10) REVERT: F 143 GLU cc_start: 0.7717 (tp30) cc_final: 0.7413 (tp30) REVERT: F 185 SER cc_start: 0.8425 (m) cc_final: 0.7850 (t) REVERT: F 246 GLU cc_start: 0.7854 (tp30) cc_final: 0.7576 (tm-30) REVERT: D 191 MET cc_start: 0.8193 (tmm) cc_final: 0.7844 (tmm) REVERT: D 246 GLU cc_start: 0.7996 (tp30) cc_final: 0.7625 (mm-30) outliers start: 19 outliers final: 19 residues processed: 276 average time/residue: 0.2983 time to fit residues: 118.9197 Evaluate side-chains 275 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 3.295 ------------------------------------------------------------------------------- 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 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 124 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 244 VAL 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 124 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 244 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 9 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 102 optimal weight: 0.3980 chunk 131 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 134 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN B 184 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.207932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.152351 restraints weight = 12158.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.152641 restraints weight = 10013.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.154900 restraints weight = 9635.154| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11150 Z= 0.116 Angle : 0.543 8.887 15216 Z= 0.276 Chirality : 0.038 0.243 1722 Planarity : 0.004 0.042 1812 Dihedral : 3.771 29.657 1520 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.27 % Allowed : 20.92 % Favored : 77.81 % 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: 2.01 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.02 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 160 HIS 0.002 0.000 HIS E 76 PHE 0.030 0.001 PHE F 153 TYR 0.013 0.001 TYR C 140 ARG 0.002 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 884) hydrogen bonds : angle 3.74482 ( 2649) covalent geometry : bond 0.00260 (11144) covalent geometry : angle 0.54265 (15216) Misc. bond : bond 0.00034 ( 6) ********************** 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 301 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 287 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 75 TRP cc_start: 0.8043 (t60) cc_final: 0.6780 (t-100) REVERT: A 143 GLU cc_start: 0.7940 (tp30) cc_final: 0.7735 (mm-30) REVERT: A 150 TRP cc_start: 0.7805 (m100) cc_final: 0.7288 (m100) REVERT: A 176 CYS cc_start: 0.7529 (p) cc_final: 0.7299 (p) REVERT: A 191 MET cc_start: 0.8134 (tmm) cc_final: 0.7835 (tmm) REVERT: B 80 MET cc_start: 0.6691 (mtm) cc_final: 0.6452 (mtt) REVERT: B 143 GLU cc_start: 0.6696 (tp30) cc_final: 0.5556 (tm-30) REVERT: B 163 MET cc_start: 0.8270 (mmm) cc_final: 0.7520 (mtt) REVERT: B 184 GLN cc_start: 0.8406 (mt0) cc_final: 0.7978 (mp10) REVERT: B 191 MET cc_start: 0.7452 (ttp) cc_final: 0.7241 (tmm) REVERT: C 96 TYR cc_start: 0.8194 (m-80) cc_final: 0.7783 (m-80) REVERT: C 127 LYS cc_start: 0.5862 (ptpt) cc_final: 0.5619 (ptpt) REVERT: C 185 SER cc_start: 0.8475 (m) cc_final: 0.7845 (t) REVERT: C 246 GLU cc_start: 0.7742 (tp30) cc_final: 0.7175 (tm-30) REVERT: E 80 MET cc_start: 0.6695 (mtm) cc_final: 0.6321 (mtt) REVERT: E 166 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6449 (mt-10) REVERT: E 184 GLN cc_start: 0.8287 (mt0) cc_final: 0.7866 (mt0) REVERT: F 143 GLU cc_start: 0.7672 (tp30) cc_final: 0.7366 (tp30) REVERT: F 153 PHE cc_start: 0.7714 (t80) cc_final: 0.7453 (t80) REVERT: F 185 SER cc_start: 0.8442 (m) cc_final: 0.7800 (t) REVERT: F 246 GLU cc_start: 0.7842 (tp30) cc_final: 0.7578 (tm-30) REVERT: D 75 TRP cc_start: 0.8044 (t60) cc_final: 0.6769 (t-100) REVERT: D 191 MET cc_start: 0.8102 (tmm) cc_final: 0.7812 (tmm) outliers start: 14 outliers final: 13 residues processed: 297 average time/residue: 0.2418 time to fit residues: 102.5952 Evaluate side-chains 288 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 275 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 A residue 244 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 114 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: 0.4980 chunk 101 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 128 optimal weight: 0.0170 chunk 20 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4408 r_free = 0.4408 target = 0.208721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.153131 restraints weight = 12057.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.153608 restraints weight = 10107.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.155150 restraints weight = 9734.362| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11150 Z= 0.117 Angle : 0.566 9.685 15216 Z= 0.287 Chirality : 0.038 0.239 1722 Planarity : 0.004 0.042 1812 Dihedral : 3.945 30.203 1520 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.45 % Allowed : 21.38 % Favored : 77.17 % 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: 2.19 (0.23), residues: 1340 helix: 1.99 (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 0.019 0.001 TRP B 160 HIS 0.002 0.000 HIS E 76 PHE 0.030 0.001 PHE F 153 TYR 0.029 0.001 TYR A 201 ARG 0.001 0.000 ARG C 81 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 884) hydrogen bonds : angle 3.76561 ( 2649) covalent geometry : bond 0.00259 (11144) covalent geometry : angle 0.56605 (15216) Misc. bond : bond 0.00031 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3957.12 seconds wall clock time: 74 minutes 42.19 seconds (4482.19 seconds total)