Starting phenix.real_space_refine on Wed Sep 25 14:36:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqd_16796/09_2024/8cqd_16796.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqd_16796/09_2024/8cqd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqd_16796/09_2024/8cqd_16796.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqd_16796/09_2024/8cqd_16796.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqd_16796/09_2024/8cqd_16796.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqd_16796/09_2024/8cqd_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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.39, per 1000 atoms: 0.68 Number of scatterers: 10828 At special positions: 0 Unit cell: (111.769, 104.234, 67.815, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1842 8.00 N 1612 7.00 C 7306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.28 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: 0.94 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: 2.99 Time building geometry restraints manager: 3.68 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: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 0.150 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.560 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 11144 Z= 0.347 Angle : 0.607 6.815 15216 Z= 0.364 Chirality : 0.038 0.208 1722 Planarity : 0.004 0.040 1812 Dihedral : 9.169 85.053 3688 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.23), residues: 1340 helix: 2.30 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -2.00 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 75 HIS 0.001 0.000 HIS A 76 PHE 0.010 0.001 PHE A 229 TYR 0.009 0.001 TYR A 96 ARG 0.001 0.000 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 1.077 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: 0.2037 time to fit residues: 109.3864 Evaluate side-chains 283 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11144 Z= 0.376 Angle : 0.622 8.284 15216 Z= 0.318 Chirality : 0.043 0.252 1722 Planarity : 0.004 0.051 1812 Dihedral : 3.825 25.069 1520 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.54 % Allowed : 13.86 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.23), residues: 1340 helix: 1.90 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.38 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 75 HIS 0.003 0.001 HIS A 76 PHE 0.018 0.002 PHE E 47 TYR 0.013 0.001 TYR F 77 ARG 0.013 0.001 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 291 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7096 (tp30) cc_final: 0.6810 (tp30) REVERT: A 191 MET cc_start: 0.8519 (tmm) cc_final: 0.8149 (tmm) REVERT: A 246 GLU cc_start: 0.7960 (tp30) cc_final: 0.7655 (mm-30) REVERT: B 77 TYR cc_start: 0.8674 (m-80) cc_final: 0.8390 (m-80) REVERT: B 80 MET cc_start: 0.6996 (mtm) cc_final: 0.6609 (mtt) REVERT: B 127 LYS cc_start: 0.6478 (ptpt) cc_final: 0.6039 (ptpt) REVERT: B 184 GLN cc_start: 0.8404 (mt0) cc_final: 0.8111 (mt0) REVERT: C 100 LEU cc_start: 0.8746 (tp) cc_final: 0.8472 (mt) REVERT: C 135 MET cc_start: 0.7746 (ptp) cc_final: 0.7386 (ptp) REVERT: C 184 GLN cc_start: 0.8082 (mt0) cc_final: 0.7683 (mm-40) REVERT: C 185 SER cc_start: 0.8220 (m) cc_final: 0.7778 (t) REVERT: E 77 TYR cc_start: 0.8678 (m-80) cc_final: 0.8319 (m-80) REVERT: E 80 MET cc_start: 0.7272 (mtm) cc_final: 0.6832 (mtt) REVERT: E 127 LYS cc_start: 0.6478 (ptpt) cc_final: 0.6021 (ptpt) REVERT: E 184 GLN cc_start: 0.8404 (mt0) cc_final: 0.8117 (mt0) REVERT: F 100 LEU cc_start: 0.8744 (tp) cc_final: 0.8473 (mt) REVERT: F 135 MET cc_start: 0.7715 (ptp) cc_final: 0.7386 (ptp) REVERT: F 184 GLN cc_start: 0.8087 (mt0) cc_final: 0.7723 (mm-40) REVERT: D 166 GLU cc_start: 0.7226 (tp30) cc_final: 0.6896 (tp30) REVERT: D 191 MET cc_start: 0.8465 (tmm) cc_final: 0.8115 (tmm) REVERT: D 246 GLU cc_start: 0.7900 (tp30) cc_final: 0.7584 (mm-30) outliers start: 28 outliers final: 17 residues processed: 304 average time/residue: 0.2093 time to fit residues: 90.7743 Evaluate side-chains 299 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 282 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 68 optimal weight: 0.0970 chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11144 Z= 0.168 Angle : 0.514 5.726 15216 Z= 0.263 Chirality : 0.037 0.217 1722 Planarity : 0.004 0.042 1812 Dihedral : 3.799 24.983 1520 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: 2.31 (0.23), residues: 1340 helix: 2.07 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.04 (0.41), residues: 188 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 0.026 0.001 TYR C 96 ARG 0.008 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 297 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8523 (tmm) cc_final: 0.8167 (tmm) REVERT: B 77 TYR cc_start: 0.8531 (m-80) cc_final: 0.8330 (m-80) REVERT: B 80 MET cc_start: 0.6887 (mtm) cc_final: 0.6534 (mtt) REVERT: B 140 TYR cc_start: 0.7794 (t80) cc_final: 0.7396 (t80) REVERT: B 162 TYR cc_start: 0.8127 (t80) cc_final: 0.7891 (t80) REVERT: B 184 GLN cc_start: 0.8395 (mt0) cc_final: 0.8047 (mt0) REVERT: C 100 LEU cc_start: 0.8797 (tp) cc_final: 0.8491 (mt) REVERT: C 140 TYR cc_start: 0.7857 (t80) cc_final: 0.7505 (t80) REVERT: C 184 GLN cc_start: 0.8108 (mt0) cc_final: 0.7699 (mm-40) REVERT: C 185 SER cc_start: 0.8204 (m) cc_final: 0.7753 (t) REVERT: C 246 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7756 (mm-30) REVERT: E 77 TYR cc_start: 0.8535 (m-80) cc_final: 0.8329 (m-80) REVERT: E 80 MET cc_start: 0.6942 (mtm) cc_final: 0.6338 (mtt) REVERT: E 140 TYR cc_start: 0.7795 (t80) cc_final: 0.7402 (t80) REVERT: E 162 TYR cc_start: 0.8120 (t80) cc_final: 0.7853 (t80) REVERT: E 166 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6348 (mt-10) REVERT: E 167 LEU cc_start: 0.8127 (mt) cc_final: 0.7902 (tt) REVERT: E 184 GLN cc_start: 0.8396 (mt0) cc_final: 0.8053 (mt0) REVERT: F 100 LEU cc_start: 0.8808 (tp) cc_final: 0.8500 (mt) REVERT: F 140 TYR cc_start: 0.7590 (t80) cc_final: 0.7290 (t80) REVERT: F 184 GLN cc_start: 0.8094 (mt0) cc_final: 0.7732 (mm-40) REVERT: D 166 GLU cc_start: 0.7277 (tp30) cc_final: 0.6927 (tp30) REVERT: D 191 MET cc_start: 0.8369 (tmm) cc_final: 0.8051 (tmm) outliers start: 27 outliers final: 17 residues processed: 309 average time/residue: 0.2042 time to fit residues: 90.6198 Evaluate side-chains 279 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 262 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 117 optimal weight: 0.1980 chunk 35 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11144 Z= 0.192 Angle : 0.513 5.593 15216 Z= 0.263 Chirality : 0.038 0.193 1722 Planarity : 0.004 0.042 1812 Dihedral : 3.821 30.700 1520 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.17 % Allowed : 17.39 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.23), residues: 1340 helix: 2.05 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -2.04 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 160 HIS 0.001 0.001 HIS F 76 PHE 0.026 0.002 PHE F 153 TYR 0.018 0.001 TYR E 205 ARG 0.004 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 292 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8473 (tmm) cc_final: 0.8102 (tmm) REVERT: B 80 MET cc_start: 0.6901 (mtm) cc_final: 0.6544 (mtt) REVERT: B 140 TYR cc_start: 0.7722 (t80) cc_final: 0.7304 (t80) REVERT: B 184 GLN cc_start: 0.8348 (mt0) cc_final: 0.8022 (mt0) REVERT: C 100 LEU cc_start: 0.8732 (tp) cc_final: 0.8499 (mt) REVERT: C 140 TYR cc_start: 0.7748 (t80) cc_final: 0.7460 (t80) REVERT: C 141 MET cc_start: 0.7770 (mmt) cc_final: 0.7539 (mmt) REVERT: C 184 GLN cc_start: 0.8094 (mt0) cc_final: 0.7705 (mm-40) REVERT: C 185 SER cc_start: 0.8284 (m) cc_final: 0.7800 (t) REVERT: E 80 MET cc_start: 0.6955 (mtm) cc_final: 0.6588 (mtt) REVERT: E 140 TYR cc_start: 0.7723 (t80) cc_final: 0.7308 (t80) REVERT: E 162 TYR cc_start: 0.8212 (t80) cc_final: 0.7899 (t80) REVERT: E 166 GLU cc_start: 0.6797 (mt-10) cc_final: 0.6340 (mt-10) REVERT: E 167 LEU cc_start: 0.8117 (mt) cc_final: 0.7905 (tt) REVERT: E 184 GLN cc_start: 0.8348 (mt0) cc_final: 0.8017 (mt0) REVERT: F 100 LEU cc_start: 0.8733 (tp) cc_final: 0.8476 (mt) REVERT: F 141 MET cc_start: 0.7771 (mmt) cc_final: 0.7274 (mmt) REVERT: F 143 GLU cc_start: 0.7759 (tp30) cc_final: 0.7333 (tp30) REVERT: F 184 GLN cc_start: 0.8039 (mt0) cc_final: 0.7691 (mm-40) REVERT: F 190 MET cc_start: 0.8355 (mtm) cc_final: 0.8154 (mtt) REVERT: D 166 GLU cc_start: 0.7302 (tp30) cc_final: 0.7002 (tp30) REVERT: D 191 MET cc_start: 0.8270 (tmm) cc_final: 0.7868 (tmm) REVERT: D 205 TYR cc_start: 0.5807 (t80) cc_final: 0.5601 (t80) outliers start: 24 outliers final: 16 residues processed: 302 average time/residue: 0.2091 time to fit residues: 90.4607 Evaluate side-chains 282 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 266 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 90 optimal weight: 0.0170 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 44 optimal weight: 5.9990 overall best weight: 0.5220 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11144 Z= 0.156 Angle : 0.503 7.234 15216 Z= 0.257 Chirality : 0.037 0.189 1722 Planarity : 0.004 0.054 1812 Dihedral : 3.781 28.897 1520 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.36 % Allowed : 19.38 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.23), residues: 1340 helix: 2.12 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -2.04 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 160 HIS 0.001 0.000 HIS C 76 PHE 0.027 0.001 PHE F 153 TYR 0.020 0.001 TYR A 205 ARG 0.002 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 289 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8841 (mtmm) cc_final: 0.8602 (tppt) REVERT: A 191 MET cc_start: 0.8419 (tmm) cc_final: 0.8029 (tmm) REVERT: B 80 MET cc_start: 0.6893 (mtm) cc_final: 0.6569 (mtt) REVERT: B 162 TYR cc_start: 0.8047 (t80) cc_final: 0.7789 (t80) REVERT: B 166 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6462 (mt-10) REVERT: B 184 GLN cc_start: 0.8347 (mt0) cc_final: 0.8005 (mt0) REVERT: B 191 MET cc_start: 0.7453 (ttp) cc_final: 0.7231 (tmm) REVERT: C 78 MET cc_start: 0.8221 (mmt) cc_final: 0.7836 (mmm) REVERT: C 100 LEU cc_start: 0.8730 (tp) cc_final: 0.8503 (mt) REVERT: C 140 TYR cc_start: 0.7757 (t80) cc_final: 0.7464 (t80) REVERT: C 184 GLN cc_start: 0.8154 (mt0) cc_final: 0.7769 (mm-40) REVERT: C 185 SER cc_start: 0.8296 (m) cc_final: 0.7806 (t) REVERT: E 80 MET cc_start: 0.6923 (mtm) cc_final: 0.6564 (mtt) REVERT: E 140 TYR cc_start: 0.7858 (t80) cc_final: 0.7145 (t80) REVERT: E 162 TYR cc_start: 0.8259 (t80) cc_final: 0.8047 (t80) REVERT: E 166 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6414 (mt-10) REVERT: E 184 GLN cc_start: 0.8376 (mt0) cc_final: 0.8173 (mt0) REVERT: F 78 MET cc_start: 0.8218 (mmt) cc_final: 0.7841 (mmm) REVERT: F 100 LEU cc_start: 0.8724 (tp) cc_final: 0.8480 (mt) REVERT: F 143 GLU cc_start: 0.7773 (tp30) cc_final: 0.7383 (tp30) REVERT: F 184 GLN cc_start: 0.8067 (mt0) cc_final: 0.7777 (mm-40) REVERT: D 191 MET cc_start: 0.8236 (tmm) cc_final: 0.7824 (tmm) outliers start: 15 outliers final: 9 residues processed: 298 average time/residue: 0.2069 time to fit residues: 88.2459 Evaluate side-chains 288 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 279 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 248 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 0.0020 chunk 10 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11144 Z= 0.156 Angle : 0.504 7.542 15216 Z= 0.256 Chirality : 0.038 0.263 1722 Planarity : 0.004 0.045 1812 Dihedral : 3.751 29.496 1520 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.18 % Allowed : 18.93 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.23), residues: 1340 helix: 2.15 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -2.05 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 160 HIS 0.001 0.000 HIS F 76 PHE 0.027 0.001 PHE F 153 TYR 0.016 0.001 TYR E 205 ARG 0.002 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 287 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8866 (mtmm) cc_final: 0.8650 (tppt) REVERT: A 75 TRP cc_start: 0.8007 (t60) cc_final: 0.6628 (t-100) REVERT: A 191 MET cc_start: 0.8259 (tmm) cc_final: 0.7872 (tmm) REVERT: B 80 MET cc_start: 0.6911 (mtm) cc_final: 0.6564 (mtt) REVERT: B 166 GLU cc_start: 0.6494 (mt-10) cc_final: 0.5971 (mt-10) REVERT: B 184 GLN cc_start: 0.8372 (mt0) cc_final: 0.8043 (mt0) REVERT: B 185 SER cc_start: 0.8854 (m) cc_final: 0.8626 (p) REVERT: B 191 MET cc_start: 0.7422 (ttp) cc_final: 0.7200 (tmm) REVERT: C 78 MET cc_start: 0.8293 (mmt) cc_final: 0.7923 (mmm) REVERT: C 96 TYR cc_start: 0.8090 (m-80) cc_final: 0.7818 (m-80) REVERT: C 100 LEU cc_start: 0.8719 (tp) cc_final: 0.8498 (mt) REVERT: C 140 TYR cc_start: 0.7726 (t80) cc_final: 0.7508 (t80) REVERT: C 143 GLU cc_start: 0.8078 (tp30) cc_final: 0.7639 (tp30) REVERT: C 184 GLN cc_start: 0.8083 (mt0) cc_final: 0.7781 (mm-40) REVERT: C 185 SER cc_start: 0.8283 (m) cc_final: 0.7807 (t) REVERT: E 80 MET cc_start: 0.6917 (mtm) cc_final: 0.6564 (mtt) REVERT: E 160 TRP cc_start: 0.7316 (t60) cc_final: 0.7086 (t60) REVERT: E 166 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6214 (mt-10) REVERT: E 185 SER cc_start: 0.8784 (m) cc_final: 0.8563 (p) REVERT: E 191 MET cc_start: 0.7517 (ttp) cc_final: 0.7275 (tmm) REVERT: F 78 MET cc_start: 0.8286 (mmt) cc_final: 0.7909 (mmm) REVERT: F 100 LEU cc_start: 0.8711 (tp) cc_final: 0.8481 (mt) REVERT: F 143 GLU cc_start: 0.7662 (tp30) cc_final: 0.7269 (tp30) REVERT: F 184 GLN cc_start: 0.8072 (mt0) cc_final: 0.7756 (mm-40) REVERT: F 185 SER cc_start: 0.8400 (m) cc_final: 0.7833 (t) REVERT: D 191 MET cc_start: 0.8206 (tmm) cc_final: 0.7762 (tmm) outliers start: 13 outliers final: 11 residues processed: 294 average time/residue: 0.2056 time to fit residues: 86.7321 Evaluate side-chains 283 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 272 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.0370 chunk 74 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.7264 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 0.048 11144 Z= 0.226 Angle : 0.538 7.772 15216 Z= 0.276 Chirality : 0.039 0.260 1722 Planarity : 0.004 0.041 1812 Dihedral : 3.801 32.981 1520 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.26 % Allowed : 18.93 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.23), residues: 1340 helix: 2.01 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -2.07 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 160 HIS 0.001 0.001 HIS D 76 PHE 0.028 0.002 PHE F 153 TYR 0.017 0.001 TYR E 205 ARG 0.002 0.000 ARG C 81 *********************** 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 298 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 273 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 TRP cc_start: 0.8127 (t60) cc_final: 0.6701 (t-100) REVERT: A 80 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6665 (mpp) REVERT: A 191 MET cc_start: 0.8384 (tmm) cc_final: 0.7985 (tmm) REVERT: B 80 MET cc_start: 0.6863 (mtm) cc_final: 0.6650 (mtt) REVERT: B 184 GLN cc_start: 0.8375 (mt0) cc_final: 0.8051 (mt0) REVERT: B 191 MET cc_start: 0.7438 (ttp) cc_final: 0.7204 (tmm) REVERT: C 96 TYR cc_start: 0.8076 (m-80) cc_final: 0.7799 (m-80) REVERT: C 100 LEU cc_start: 0.8756 (tp) cc_final: 0.8490 (mt) REVERT: C 143 GLU cc_start: 0.8096 (tp30) cc_final: 0.7827 (tp30) REVERT: C 184 GLN cc_start: 0.8121 (mt0) cc_final: 0.7757 (mm-40) REVERT: C 185 SER cc_start: 0.8384 (m) cc_final: 0.7845 (t) REVERT: C 246 GLU cc_start: 0.7671 (tp30) cc_final: 0.7121 (tm-30) REVERT: E 80 MET cc_start: 0.6859 (mtm) cc_final: 0.6468 (mtt) REVERT: E 162 TYR cc_start: 0.8194 (t80) cc_final: 0.7989 (t80) REVERT: E 166 GLU cc_start: 0.6481 (mt-10) cc_final: 0.6182 (mt-10) REVERT: E 191 MET cc_start: 0.7631 (ttp) cc_final: 0.7371 (tmm) REVERT: F 100 LEU cc_start: 0.8821 (tp) cc_final: 0.8474 (mt) REVERT: F 143 GLU cc_start: 0.7720 (tp30) cc_final: 0.7300 (tp30) REVERT: F 184 GLN cc_start: 0.8023 (mt0) cc_final: 0.7694 (mm-40) REVERT: F 185 SER cc_start: 0.8412 (m) cc_final: 0.7842 (t) REVERT: D 191 MET cc_start: 0.8209 (tmm) cc_final: 0.7811 (tmm) REVERT: D 246 GLU cc_start: 0.7888 (tp30) cc_final: 0.7484 (mm-30) outliers start: 25 outliers final: 19 residues processed: 286 average time/residue: 0.2079 time to fit residues: 85.2020 Evaluate side-chains 273 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 253 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 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 E residue 114 LEU Chi-restraints excluded: chain E residue 132 SER 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 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 78 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11144 Z= 0.278 Angle : 0.586 8.600 15216 Z= 0.295 Chirality : 0.041 0.266 1722 Planarity : 0.004 0.038 1812 Dihedral : 3.882 35.883 1520 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.26 % Allowed : 19.38 % Favored : 78.35 % 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: 1.99 (0.23), residues: 1340 helix: 1.86 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -2.14 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 160 HIS 0.001 0.001 HIS A 76 PHE 0.030 0.002 PHE F 153 TYR 0.016 0.001 TYR E 205 ARG 0.002 0.000 ARG C 54 *********************** 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 284 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.6827 (mpp) REVERT: A 176 CYS cc_start: 0.7779 (p) cc_final: 0.7558 (p) REVERT: A 191 MET cc_start: 0.8260 (tmm) cc_final: 0.7910 (tmm) REVERT: B 80 MET cc_start: 0.6855 (mtm) cc_final: 0.6522 (mtt) REVERT: B 163 MET cc_start: 0.8209 (mmm) cc_final: 0.7618 (mtt) REVERT: B 184 GLN cc_start: 0.8362 (mt0) cc_final: 0.8036 (mt0) REVERT: C 100 LEU cc_start: 0.8777 (tp) cc_final: 0.8495 (mt) REVERT: C 143 GLU cc_start: 0.7941 (tp30) cc_final: 0.7630 (tp30) REVERT: C 184 GLN cc_start: 0.8044 (mt0) cc_final: 0.7662 (mm-40) REVERT: C 185 SER cc_start: 0.8434 (m) cc_final: 0.7896 (t) REVERT: C 246 GLU cc_start: 0.7772 (tp30) cc_final: 0.7237 (tm-30) REVERT: E 80 MET cc_start: 0.6866 (mtm) cc_final: 0.6644 (mtt) REVERT: E 160 TRP cc_start: 0.7404 (t60) cc_final: 0.7182 (t60) REVERT: E 166 GLU cc_start: 0.6454 (mt-10) cc_final: 0.6236 (mt-10) REVERT: E 184 GLN cc_start: 0.8246 (mt0) cc_final: 0.7762 (mp10) REVERT: E 191 MET cc_start: 0.7650 (ttp) cc_final: 0.7383 (tmm) REVERT: F 100 LEU cc_start: 0.8738 (tp) cc_final: 0.8427 (mt) REVERT: F 143 GLU cc_start: 0.7726 (tp30) cc_final: 0.7345 (tp30) REVERT: F 153 PHE cc_start: 0.7634 (t80) cc_final: 0.7401 (t80) REVERT: F 184 GLN cc_start: 0.8030 (mt0) cc_final: 0.7660 (mm-40) REVERT: F 185 SER cc_start: 0.8366 (m) cc_final: 0.7788 (t) REVERT: D 150 TRP cc_start: 0.7671 (m100) cc_final: 0.7287 (m100) REVERT: D 191 MET cc_start: 0.8212 (tmm) cc_final: 0.7856 (tmm) outliers start: 25 outliers final: 23 residues processed: 277 average time/residue: 0.2058 time to fit residues: 82.2323 Evaluate side-chains 276 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 252 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain 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 114 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 244 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11144 Z= 0.202 Angle : 0.545 8.254 15216 Z= 0.276 Chirality : 0.039 0.249 1722 Planarity : 0.004 0.039 1812 Dihedral : 3.837 33.935 1520 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.99 % Allowed : 19.93 % 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: 2.09 (0.23), residues: 1340 helix: 1.92 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.05 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 160 HIS 0.001 0.000 HIS C 76 PHE 0.029 0.002 PHE F 153 TYR 0.017 0.001 TYR E 205 ARG 0.002 0.000 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 257 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6801 (mpp) REVERT: A 191 MET cc_start: 0.8204 (tmm) cc_final: 0.7877 (tmm) REVERT: B 80 MET cc_start: 0.6822 (mtm) cc_final: 0.6419 (mtt) REVERT: B 163 MET cc_start: 0.8182 (mmm) cc_final: 0.7753 (mtm) REVERT: B 184 GLN cc_start: 0.8351 (mt0) cc_final: 0.8056 (mt0) REVERT: B 191 MET cc_start: 0.7435 (ttp) cc_final: 0.7196 (tmm) REVERT: C 100 LEU cc_start: 0.8782 (tp) cc_final: 0.8538 (mt) REVERT: C 143 GLU cc_start: 0.7896 (tp30) cc_final: 0.7631 (tp30) REVERT: C 184 GLN cc_start: 0.8039 (mt0) cc_final: 0.7672 (mm-40) REVERT: C 185 SER cc_start: 0.8429 (m) cc_final: 0.7886 (t) REVERT: C 246 GLU cc_start: 0.7697 (tp30) cc_final: 0.7178 (tm-30) REVERT: E 80 MET cc_start: 0.6835 (mtm) cc_final: 0.6486 (mtt) REVERT: E 163 MET cc_start: 0.8359 (tpp) cc_final: 0.7704 (mtt) REVERT: E 184 GLN cc_start: 0.8177 (mt0) cc_final: 0.7680 (mp10) REVERT: E 191 MET cc_start: 0.7556 (ttp) cc_final: 0.7333 (tmm) REVERT: F 100 LEU cc_start: 0.8777 (tp) cc_final: 0.8534 (mt) REVERT: F 143 GLU cc_start: 0.7694 (tp30) cc_final: 0.7333 (tp30) REVERT: F 153 PHE cc_start: 0.7633 (t80) cc_final: 0.7417 (t80) REVERT: F 184 GLN cc_start: 0.8018 (mt0) cc_final: 0.7659 (mm-40) REVERT: F 185 SER cc_start: 0.8443 (m) cc_final: 0.7887 (t) REVERT: D 143 GLU cc_start: 0.8018 (tp30) cc_final: 0.7614 (tp30) REVERT: D 150 TRP cc_start: 0.7629 (m100) cc_final: 0.7246 (m100) REVERT: D 191 MET cc_start: 0.8145 (tmm) cc_final: 0.7788 (tmm) outliers start: 22 outliers final: 21 residues processed: 272 average time/residue: 0.2075 time to fit residues: 80.7534 Evaluate side-chains 267 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11144 Z= 0.250 Angle : 0.577 8.483 15216 Z= 0.293 Chirality : 0.040 0.244 1722 Planarity : 0.004 0.038 1812 Dihedral : 3.899 36.156 1520 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.81 % Allowed : 20.11 % 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: 1.98 (0.23), residues: 1340 helix: 1.85 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -2.09 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 160 HIS 0.001 0.001 HIS C 76 PHE 0.028 0.002 PHE F 153 TYR 0.016 0.001 TYR E 205 ARG 0.002 0.000 ARG C 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2680 Ramachandran restraints generated. 1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 240 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6868 (mpp) REVERT: A 191 MET cc_start: 0.8335 (tmm) cc_final: 0.7975 (tmm) REVERT: B 80 MET cc_start: 0.6846 (mtm) cc_final: 0.6620 (mtt) REVERT: B 163 MET cc_start: 0.8140 (mmm) cc_final: 0.7750 (mtm) REVERT: B 184 GLN cc_start: 0.8383 (mt0) cc_final: 0.8059 (mt0) REVERT: C 100 LEU cc_start: 0.8808 (tp) cc_final: 0.8532 (mt) REVERT: C 143 GLU cc_start: 0.7937 (tp30) cc_final: 0.7650 (tp30) REVERT: C 184 GLN cc_start: 0.8032 (mt0) cc_final: 0.7637 (mm-40) REVERT: C 185 SER cc_start: 0.8395 (m) cc_final: 0.7839 (t) REVERT: C 246 GLU cc_start: 0.7784 (tp30) cc_final: 0.7274 (tm-30) REVERT: E 163 MET cc_start: 0.8330 (tpp) cc_final: 0.7648 (mtt) REVERT: E 184 GLN cc_start: 0.8135 (mt0) cc_final: 0.7714 (mp10) REVERT: E 191 MET cc_start: 0.7575 (ttp) cc_final: 0.7334 (tmm) REVERT: F 100 LEU cc_start: 0.8763 (tp) cc_final: 0.8466 (mt) REVERT: F 143 GLU cc_start: 0.7745 (tp30) cc_final: 0.7371 (tp30) REVERT: F 184 GLN cc_start: 0.8013 (mt0) cc_final: 0.7625 (mm-40) REVERT: F 185 SER cc_start: 0.8412 (m) cc_final: 0.7839 (t) REVERT: D 143 GLU cc_start: 0.7909 (tp30) cc_final: 0.7552 (tp30) REVERT: D 191 MET cc_start: 0.8177 (tmm) cc_final: 0.7806 (tmm) outliers start: 20 outliers final: 18 residues processed: 253 average time/residue: 0.2042 time to fit residues: 74.1105 Evaluate side-chains 259 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 240 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain 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 244 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 124 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4366 r_free = 0.4366 target = 0.204496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.147145 restraints weight = 12123.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.145126 restraints weight = 11562.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.147137 restraints weight = 10722.870| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11144 Z= 0.247 Angle : 0.581 8.605 15216 Z= 0.297 Chirality : 0.040 0.240 1722 Planarity : 0.004 0.038 1812 Dihedral : 3.906 36.202 1520 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.08 % Allowed : 19.84 % 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: 1.96 (0.23), residues: 1340 helix: 1.85 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -2.18 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 160 HIS 0.001 0.001 HIS A 76 PHE 0.022 0.002 PHE C 153 TYR 0.016 0.001 TYR E 205 ARG 0.002 0.000 ARG C 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2250.17 seconds wall clock time: 40 minutes 58.71 seconds (2458.71 seconds total)