Starting phenix.real_space_refine on Wed Mar 4 05:52:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zgj_11208/03_2026/6zgj_11208.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zgj_11208/03_2026/6zgj_11208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zgj_11208/03_2026/6zgj_11208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zgj_11208/03_2026/6zgj_11208.map" model { file = "/net/cci-nas-00/data/ceres_data/6zgj_11208/03_2026/6zgj_11208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zgj_11208/03_2026/6zgj_11208.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 20 5.16 5 C 7675 2.51 5 N 1885 2.21 5 O 1975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11555 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2311 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 18, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 4, 'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 123 Chain: "B" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2311 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 18, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 4, 'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 123 Chain: "C" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2311 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 18, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 4, 'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 123 Chain: "D" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2311 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 18, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 4, 'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 123 Chain: "E" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2311 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 18, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 4, 'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 123 Time building chain proxies: 2.66, per 1000 atoms: 0.23 Number of scatterers: 11555 At special positions: 0 Unit cell: (93.48, 91.84, 118.08, 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 20 16.00 O 1975 8.00 N 1885 7.00 C 7675 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=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 511.4 milliseconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3030 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 20 sheets defined 35.4% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 215 through 218 removed outlier: 3.783A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 218' Processing helix chain 'A' and resid 220 through 244 removed outlier: 3.737A pdb=" N THR A 244 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 282 removed outlier: 3.521A pdb=" N ILE A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 315 Proline residue: A 300 - end of helix Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 215 through 218 removed outlier: 3.783A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 215 through 218' Processing helix chain 'B' and resid 220 through 244 removed outlier: 3.736A pdb=" N THR B 244 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 282 removed outlier: 3.522A pdb=" N ILE B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 315 Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 215 through 218 removed outlier: 3.782A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 218' Processing helix chain 'C' and resid 220 through 244 removed outlier: 3.737A pdb=" N THR C 244 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 282 removed outlier: 3.521A pdb=" N ILE C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 315 Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 194 through 198 Processing helix chain 'D' and resid 202 through 214 Processing helix chain 'D' and resid 215 through 218 removed outlier: 3.783A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 215 through 218' Processing helix chain 'D' and resid 220 through 244 removed outlier: 3.736A pdb=" N THR D 244 " --> pdb=" O ILE D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 282 removed outlier: 3.521A pdb=" N ILE D 259 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 315 Proline residue: D 300 - end of helix Processing helix chain 'E' and resid 194 through 198 Processing helix chain 'E' and resid 202 through 214 Processing helix chain 'E' and resid 215 through 218 removed outlier: 3.783A pdb=" N SER E 218 " --> pdb=" O ALA E 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'E' and resid 220 through 244 removed outlier: 3.737A pdb=" N THR E 244 " --> pdb=" O ILE E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 282 removed outlier: 3.521A pdb=" N ILE E 259 " --> pdb=" O THR E 255 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 315 Proline residue: E 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 23 removed outlier: 6.045A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER A 107 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA A 87 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.620A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 23 Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 23 removed outlier: 6.045A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER B 107 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA B 87 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.620A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 19 through 23 Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 23 removed outlier: 6.045A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER C 107 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA C 87 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.620A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 23 removed outlier: 6.045A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER D 107 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA D 87 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.621A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AB8, first strand: chain 'E' and resid 19 through 23 Processing sheet with id=AB9, first strand: chain 'E' and resid 19 through 23 removed outlier: 6.045A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER E 107 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ALA E 87 " --> pdb=" O SER E 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.620A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 685 hydrogen bonds defined for protein. 1920 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: 1.52 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3575 1.34 - 1.46: 2823 1.46 - 1.58: 5442 1.58 - 1.70: 0 1.70 - 1.81: 35 Bond restraints: 11875 Sorted by residual: bond pdb=" CB THR E 231 " pdb=" CG2 THR E 231 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.67e+00 bond pdb=" CB THR D 231 " pdb=" CG2 THR D 231 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.66e+00 bond pdb=" CB THR A 231 " pdb=" CG2 THR A 231 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB THR C 231 " pdb=" CG2 THR C 231 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" CB THR B 231 " pdb=" CG2 THR B 231 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 ... (remaining 11870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 15370 1.15 - 2.30: 747 2.30 - 3.46: 178 3.46 - 4.61: 10 4.61 - 5.76: 25 Bond angle restraints: 16330 Sorted by residual: angle pdb=" C ILE D 140 " pdb=" N VAL D 141 " pdb=" CA VAL D 141 " ideal model delta sigma weight residual 120.62 123.76 -3.14 1.64e+00 3.72e-01 3.67e+00 angle pdb=" C ILE E 140 " pdb=" N VAL E 141 " pdb=" CA VAL E 141 " ideal model delta sigma weight residual 120.62 123.76 -3.14 1.64e+00 3.72e-01 3.67e+00 angle pdb=" C ILE C 140 " pdb=" N VAL C 141 " pdb=" CA VAL C 141 " ideal model delta sigma weight residual 120.62 123.75 -3.13 1.64e+00 3.72e-01 3.64e+00 angle pdb=" C ILE B 140 " pdb=" N VAL B 141 " pdb=" CA VAL B 141 " ideal model delta sigma weight residual 120.62 123.72 -3.10 1.64e+00 3.72e-01 3.58e+00 angle pdb=" C ILE A 140 " pdb=" N VAL A 141 " pdb=" CA VAL A 141 " ideal model delta sigma weight residual 120.62 123.71 -3.09 1.64e+00 3.72e-01 3.56e+00 ... (remaining 16325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6445 17.96 - 35.91: 435 35.91 - 53.87: 55 53.87 - 71.83: 5 71.83 - 89.79: 5 Dihedral angle restraints: 6945 sinusoidal: 2315 harmonic: 4630 Sorted by residual: dihedral pdb=" CA CYS A 27 " pdb=" C CYS A 27 " pdb=" N TYR A 28 " pdb=" CA TYR A 28 " ideal model delta harmonic sigma weight residual 180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA CYS C 27 " pdb=" C CYS C 27 " pdb=" N TYR C 28 " pdb=" CA TYR C 28 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA CYS B 27 " pdb=" C CYS B 27 " pdb=" N TYR B 28 " pdb=" CA TYR B 28 " ideal model delta harmonic sigma weight residual -180.00 -159.45 -20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 6942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 972 0.024 - 0.048: 522 0.048 - 0.072: 255 0.072 - 0.096: 137 0.096 - 0.120: 89 Chirality restraints: 1975 Sorted by residual: chirality pdb=" CA LEU D 203 " pdb=" N LEU D 203 " pdb=" C LEU D 203 " pdb=" CB LEU D 203 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA LEU A 203 " pdb=" N LEU A 203 " pdb=" C LEU A 203 " pdb=" CB LEU A 203 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" CA ILE E 128 " pdb=" N ILE E 128 " pdb=" C ILE E 128 " pdb=" CB ILE E 128 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 1972 not shown) Planarity restraints: 2040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 6 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO D 7 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 7 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 7 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 6 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.25e+00 pdb=" N PRO C 7 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 6 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO E 7 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 7 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 7 " 0.029 5.00e-02 4.00e+02 ... (remaining 2037 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 709 2.73 - 3.28: 11793 3.28 - 3.82: 19088 3.82 - 4.36: 21520 4.36 - 4.90: 37585 Nonbonded interactions: 90695 Sorted by model distance: nonbonded pdb=" ND2 ASN E 80 " pdb=" O VAL E 110 " model vdw 2.192 3.120 nonbonded pdb=" ND2 ASN B 80 " pdb=" O VAL B 110 " model vdw 2.192 3.120 nonbonded pdb=" ND2 ASN D 80 " pdb=" O VAL D 110 " model vdw 2.193 3.120 nonbonded pdb=" ND2 ASN C 80 " pdb=" O VAL C 110 " model vdw 2.193 3.120 nonbonded pdb=" ND2 ASN A 80 " pdb=" O VAL A 110 " model vdw 2.194 3.120 ... (remaining 90690 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.220 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 0.043 11875 Z= 0.196 Angle : 0.609 5.761 16330 Z= 0.336 Chirality : 0.043 0.120 1975 Planarity : 0.004 0.052 2040 Dihedral : 12.361 89.785 3915 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.21), residues: 1520 helix: 1.97 (0.22), residues: 495 sheet: -1.13 (0.27), residues: 300 loop : -3.02 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 293 TYR 0.011 0.002 TYR B 102 PHE 0.012 0.001 PHE C 37 TRP 0.009 0.001 TRP E 160 HIS 0.003 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00464 (11875) covalent geometry : angle 0.60870 (16330) hydrogen bonds : bond 0.09599 ( 605) hydrogen bonds : angle 6.13837 ( 1920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.387 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1406 time to fit residues: 33.8147 Evaluate side-chains 121 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN C 193 GLN D 245 ASN E 193 GLN E 245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.192832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.143036 restraints weight = 11437.471| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.41 r_work: 0.3052 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11875 Z= 0.173 Angle : 0.595 7.089 16330 Z= 0.313 Chirality : 0.044 0.122 1975 Planarity : 0.005 0.046 2040 Dihedral : 4.909 19.166 1665 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.46 % Allowed : 9.59 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.21), residues: 1520 helix: 2.03 (0.22), residues: 495 sheet: -1.05 (0.28), residues: 300 loop : -3.16 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 189 TYR 0.009 0.001 TYR E 102 PHE 0.017 0.001 PHE D 37 TRP 0.005 0.001 TRP B 160 HIS 0.003 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00418 (11875) covalent geometry : angle 0.59503 (16330) hydrogen bonds : bond 0.03900 ( 605) hydrogen bonds : angle 4.98773 ( 1920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.391 Fit side-chains REVERT: A 80 ASN cc_start: 0.8584 (p0) cc_final: 0.8070 (p0) REVERT: B 80 ASN cc_start: 0.8691 (p0) cc_final: 0.8184 (p0) REVERT: C 80 ASN cc_start: 0.8699 (p0) cc_final: 0.8419 (p0) REVERT: C 106 PHE cc_start: 0.8513 (p90) cc_final: 0.8305 (p90) REVERT: D 80 ASN cc_start: 0.8748 (p0) cc_final: 0.8324 (p0) REVERT: E 80 ASN cc_start: 0.8761 (p0) cc_final: 0.8245 (p0) outliers start: 16 outliers final: 10 residues processed: 153 average time/residue: 0.1470 time to fit residues: 29.4769 Evaluate side-chains 127 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 196 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 3 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 104 optimal weight: 0.0170 chunk 6 optimal weight: 0.0770 chunk 33 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 overall best weight: 0.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.194427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 153)---------------| | r_work = 0.3489 r_free = 0.3489 target = 0.139351 restraints weight = 11458.565| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.34 r_work: 0.3145 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11875 Z= 0.118 Angle : 0.557 6.720 16330 Z= 0.289 Chirality : 0.043 0.153 1975 Planarity : 0.004 0.043 2040 Dihedral : 4.688 18.068 1665 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.19 % Allowed : 12.69 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.21), residues: 1520 helix: 2.29 (0.22), residues: 495 sheet: -0.94 (0.28), residues: 295 loop : -3.09 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 192 TYR 0.011 0.001 TYR D 197 PHE 0.017 0.001 PHE E 37 TRP 0.002 0.001 TRP A 213 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00272 (11875) covalent geometry : angle 0.55722 (16330) hydrogen bonds : bond 0.03466 ( 605) hydrogen bonds : angle 4.57995 ( 1920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.249 Fit side-chains REVERT: A 80 ASN cc_start: 0.8296 (p0) cc_final: 0.7878 (p0) REVERT: B 80 ASN cc_start: 0.8523 (p0) cc_final: 0.8048 (p0) REVERT: C 80 ASN cc_start: 0.8447 (p0) cc_final: 0.8211 (p0) REVERT: D 80 ASN cc_start: 0.8461 (p0) cc_final: 0.7774 (p0) REVERT: E 80 ASN cc_start: 0.8701 (p0) cc_final: 0.8197 (p0) outliers start: 24 outliers final: 18 residues processed: 140 average time/residue: 0.1193 time to fit residues: 23.3758 Evaluate side-chains 130 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 196 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 62 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 245 ASN B 187 GLN B 245 ASN C 127 HIS C 187 GLN C 193 GLN C 245 ASN D 187 GLN D 245 ASN E 187 GLN E 245 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.184390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 157)---------------| | r_work = 0.3385 r_free = 0.3385 target = 0.129962 restraints weight = 11779.633| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.17 r_work: 0.2978 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.074 11875 Z= 0.412 Angle : 0.725 6.809 16330 Z= 0.389 Chirality : 0.049 0.169 1975 Planarity : 0.005 0.041 2040 Dihedral : 5.251 22.784 1665 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.47 % Allowed : 15.89 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.21), residues: 1520 helix: 1.44 (0.21), residues: 490 sheet: -0.85 (0.28), residues: 315 loop : -3.19 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 77 TYR 0.022 0.003 TYR E 266 PHE 0.025 0.002 PHE C 106 TRP 0.012 0.002 TRP A 213 HIS 0.006 0.002 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.01025 (11875) covalent geometry : angle 0.72537 (16330) hydrogen bonds : bond 0.05163 ( 605) hydrogen bonds : angle 4.98289 ( 1920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.398 Fit side-chains REVERT: A 80 ASN cc_start: 0.8642 (p0) cc_final: 0.8041 (p0) REVERT: B 80 ASN cc_start: 0.8727 (p0) cc_final: 0.8233 (p0) REVERT: C 80 ASN cc_start: 0.8728 (p0) cc_final: 0.8425 (p0) REVERT: D 80 ASN cc_start: 0.8784 (p0) cc_final: 0.8181 (p0) REVERT: E 80 ASN cc_start: 0.8766 (p0) cc_final: 0.8212 (p0) outliers start: 38 outliers final: 32 residues processed: 157 average time/residue: 0.1260 time to fit residues: 27.1114 Evaluate side-chains 153 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 245 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 143 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 126 optimal weight: 0.0040 chunk 5 optimal weight: 50.0000 chunk 46 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS E 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.191092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.141825 restraints weight = 11488.861| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.44 r_work: 0.3041 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11875 Z= 0.134 Angle : 0.578 6.969 16330 Z= 0.299 Chirality : 0.043 0.127 1975 Planarity : 0.004 0.041 2040 Dihedral : 4.852 19.055 1665 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.74 % Allowed : 19.36 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.21), residues: 1520 helix: 1.90 (0.22), residues: 510 sheet: -1.03 (0.29), residues: 300 loop : -3.17 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 77 TYR 0.010 0.001 TYR A 102 PHE 0.020 0.001 PHE C 106 TRP 0.004 0.001 TRP B 213 HIS 0.001 0.000 HIS E 235 Details of bonding type rmsd covalent geometry : bond 0.00317 (11875) covalent geometry : angle 0.57813 (16330) hydrogen bonds : bond 0.03624 ( 605) hydrogen bonds : angle 4.56743 ( 1920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.406 Fit side-chains REVERT: A 80 ASN cc_start: 0.8483 (p0) cc_final: 0.7986 (p0) REVERT: B 80 ASN cc_start: 0.8553 (p0) cc_final: 0.8182 (p0) REVERT: C 80 ASN cc_start: 0.8540 (p0) cc_final: 0.8291 (p0) REVERT: D 80 ASN cc_start: 0.8585 (p0) cc_final: 0.7938 (p0) REVERT: D 133 ARG cc_start: 0.7257 (mtm-85) cc_final: 0.6977 (ttm170) REVERT: E 80 ASN cc_start: 0.8635 (p0) cc_final: 0.8001 (p0) outliers start: 19 outliers final: 17 residues processed: 138 average time/residue: 0.1352 time to fit residues: 25.3183 Evaluate side-chains 133 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 245 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 136 optimal weight: 50.0000 chunk 36 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 95 optimal weight: 50.0000 chunk 81 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.186131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.137749 restraints weight = 11615.343| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.36 r_work: 0.3014 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 11875 Z= 0.295 Angle : 0.649 6.758 16330 Z= 0.342 Chirality : 0.046 0.142 1975 Planarity : 0.005 0.040 2040 Dihedral : 5.063 21.056 1665 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 4.02 % Allowed : 18.72 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.21), residues: 1520 helix: 1.76 (0.22), residues: 490 sheet: -1.06 (0.29), residues: 300 loop : -3.16 (0.20), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 77 TYR 0.015 0.002 TYR E 266 PHE 0.017 0.002 PHE C 106 TRP 0.009 0.002 TRP C 213 HIS 0.005 0.002 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00738 (11875) covalent geometry : angle 0.64867 (16330) hydrogen bonds : bond 0.04518 ( 605) hydrogen bonds : angle 4.69010 ( 1920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 0.356 Fit side-chains REVERT: A 80 ASN cc_start: 0.8583 (p0) cc_final: 0.8111 (p0) REVERT: B 80 ASN cc_start: 0.8681 (p0) cc_final: 0.8220 (p0) REVERT: C 80 ASN cc_start: 0.8681 (p0) cc_final: 0.8407 (p0) REVERT: D 80 ASN cc_start: 0.8709 (p0) cc_final: 0.8172 (p0) REVERT: E 80 ASN cc_start: 0.8742 (p0) cc_final: 0.8221 (p0) outliers start: 44 outliers final: 43 residues processed: 159 average time/residue: 0.1182 time to fit residues: 25.9585 Evaluate side-chains 162 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 270 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 131 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 0.0570 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 112 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 0.0470 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.192392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.144424 restraints weight = 11447.961| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.41 r_work: 0.3092 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11875 Z= 0.113 Angle : 0.555 8.126 16330 Z= 0.287 Chirality : 0.043 0.130 1975 Planarity : 0.004 0.040 2040 Dihedral : 4.741 18.511 1665 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.65 % Allowed : 20.55 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.21), residues: 1520 helix: 2.27 (0.22), residues: 495 sheet: -0.96 (0.29), residues: 300 loop : -3.02 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 77 TYR 0.012 0.001 TYR E 102 PHE 0.017 0.001 PHE C 106 TRP 0.005 0.001 TRP C 213 HIS 0.002 0.000 HIS D 235 Details of bonding type rmsd covalent geometry : bond 0.00256 (11875) covalent geometry : angle 0.55532 (16330) hydrogen bonds : bond 0.03355 ( 605) hydrogen bonds : angle 4.38256 ( 1920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.345 Fit side-chains REVERT: A 80 ASN cc_start: 0.8455 (p0) cc_final: 0.8040 (p0) REVERT: B 80 ASN cc_start: 0.8474 (p0) cc_final: 0.8155 (p0) REVERT: C 80 ASN cc_start: 0.8490 (p0) cc_final: 0.8158 (p0) REVERT: D 80 ASN cc_start: 0.8511 (p0) cc_final: 0.7852 (p0) REVERT: E 80 ASN cc_start: 0.8550 (p0) cc_final: 0.7957 (p0) outliers start: 29 outliers final: 19 residues processed: 147 average time/residue: 0.1218 time to fit residues: 24.6262 Evaluate side-chains 138 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 245 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 83 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.190808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.143862 restraints weight = 11543.307| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.46 r_work: 0.3063 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11875 Z= 0.157 Angle : 0.565 7.112 16330 Z= 0.293 Chirality : 0.043 0.126 1975 Planarity : 0.004 0.040 2040 Dihedral : 4.706 18.330 1665 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.01 % Allowed : 20.00 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.21), residues: 1520 helix: 2.25 (0.22), residues: 495 sheet: -0.91 (0.28), residues: 300 loop : -3.07 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 77 TYR 0.011 0.001 TYR E 102 PHE 0.015 0.001 PHE E 37 TRP 0.004 0.001 TRP C 160 HIS 0.003 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00383 (11875) covalent geometry : angle 0.56502 (16330) hydrogen bonds : bond 0.03642 ( 605) hydrogen bonds : angle 4.35479 ( 1920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.404 Fit side-chains REVERT: A 80 ASN cc_start: 0.8511 (p0) cc_final: 0.8118 (p0) REVERT: A 163 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7196 (mm-30) REVERT: B 80 ASN cc_start: 0.8547 (p0) cc_final: 0.8186 (p0) REVERT: C 80 ASN cc_start: 0.8571 (p0) cc_final: 0.8288 (p0) REVERT: D 80 ASN cc_start: 0.8610 (p0) cc_final: 0.7989 (p0) REVERT: D 133 ARG cc_start: 0.7186 (mtm-85) cc_final: 0.6953 (ttm170) REVERT: E 80 ASN cc_start: 0.8601 (p0) cc_final: 0.8028 (p0) outliers start: 33 outliers final: 27 residues processed: 139 average time/residue: 0.1233 time to fit residues: 23.8773 Evaluate side-chains 139 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 245 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 46 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 128 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 68 optimal weight: 0.0470 chunk 37 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.193789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 129)---------------| | r_work = 0.3486 r_free = 0.3486 target = 0.139038 restraints weight = 11288.311| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.34 r_work: 0.3053 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11875 Z= 0.113 Angle : 0.543 7.496 16330 Z= 0.279 Chirality : 0.043 0.128 1975 Planarity : 0.004 0.041 2040 Dihedral : 4.555 17.574 1665 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.56 % Allowed : 20.82 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.21), residues: 1520 helix: 2.32 (0.21), residues: 515 sheet: -0.89 (0.28), residues: 300 loop : -3.05 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 77 TYR 0.009 0.001 TYR A 102 PHE 0.016 0.001 PHE C 37 TRP 0.006 0.001 TRP D 160 HIS 0.001 0.001 HIS E 235 Details of bonding type rmsd covalent geometry : bond 0.00263 (11875) covalent geometry : angle 0.54306 (16330) hydrogen bonds : bond 0.03228 ( 605) hydrogen bonds : angle 4.21353 ( 1920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.397 Fit side-chains REVERT: A 80 ASN cc_start: 0.8434 (p0) cc_final: 0.8064 (p0) REVERT: A 163 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7195 (mm-30) REVERT: B 80 ASN cc_start: 0.8480 (p0) cc_final: 0.8199 (p0) REVERT: C 80 ASN cc_start: 0.8516 (p0) cc_final: 0.8253 (p0) REVERT: D 80 ASN cc_start: 0.8544 (p0) cc_final: 0.7897 (p0) REVERT: D 133 ARG cc_start: 0.7236 (mtm-85) cc_final: 0.6973 (ttm170) REVERT: E 80 ASN cc_start: 0.8504 (p0) cc_final: 0.7871 (p0) outliers start: 28 outliers final: 25 residues processed: 145 average time/residue: 0.1199 time to fit residues: 24.3793 Evaluate side-chains 148 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 245 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 147 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 121 optimal weight: 0.3980 chunk 75 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.190227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 129)---------------| | r_work = 0.3445 r_free = 0.3445 target = 0.135492 restraints weight = 11552.370| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.27 r_work: 0.3104 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11875 Z= 0.199 Angle : 0.593 8.615 16330 Z= 0.305 Chirality : 0.044 0.128 1975 Planarity : 0.004 0.040 2040 Dihedral : 4.683 18.672 1665 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.74 % Allowed : 21.19 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.21), residues: 1520 helix: 2.28 (0.21), residues: 495 sheet: -0.86 (0.28), residues: 300 loop : -3.03 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 77 TYR 0.012 0.001 TYR E 102 PHE 0.016 0.001 PHE E 37 TRP 0.008 0.001 TRP D 160 HIS 0.004 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00493 (11875) covalent geometry : angle 0.59301 (16330) hydrogen bonds : bond 0.03855 ( 605) hydrogen bonds : angle 4.34101 ( 1920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.379 Fit side-chains REVERT: A 80 ASN cc_start: 0.8597 (p0) cc_final: 0.8187 (p0) REVERT: A 163 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7177 (mm-30) REVERT: B 80 ASN cc_start: 0.8554 (p0) cc_final: 0.8199 (p0) REVERT: C 80 ASN cc_start: 0.8633 (p0) cc_final: 0.8351 (p0) REVERT: D 80 ASN cc_start: 0.8657 (p0) cc_final: 0.8089 (p0) REVERT: D 133 ARG cc_start: 0.7104 (mtm-85) cc_final: 0.6878 (ttm170) REVERT: E 80 ASN cc_start: 0.8637 (p0) cc_final: 0.8053 (p0) outliers start: 30 outliers final: 24 residues processed: 139 average time/residue: 0.1154 time to fit residues: 22.7576 Evaluate side-chains 139 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 245 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 140 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 142 optimal weight: 0.4980 chunk 47 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.193287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 146)---------------| | r_work = 0.3497 r_free = 0.3497 target = 0.140139 restraints weight = 11468.186| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.30 r_work: 0.3054 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11875 Z= 0.123 Angle : 0.549 8.467 16330 Z= 0.282 Chirality : 0.043 0.129 1975 Planarity : 0.004 0.041 2040 Dihedral : 4.555 17.435 1665 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.37 % Allowed : 21.74 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.21), residues: 1520 helix: 2.51 (0.21), residues: 495 sheet: -0.88 (0.28), residues: 300 loop : -2.91 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 77 TYR 0.010 0.001 TYR E 102 PHE 0.017 0.001 PHE C 37 TRP 0.003 0.001 TRP C 72 HIS 0.002 0.001 HIS E 277 Details of bonding type rmsd covalent geometry : bond 0.00294 (11875) covalent geometry : angle 0.54938 (16330) hydrogen bonds : bond 0.03319 ( 605) hydrogen bonds : angle 4.20998 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3003.23 seconds wall clock time: 51 minutes 48.93 seconds (3108.93 seconds total)