Starting phenix.real_space_refine on Tue Jul 29 11:47:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zgj_11208/07_2025/6zgj_11208.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zgj_11208/07_2025/6zgj_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_11208/07_2025/6zgj_11208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zgj_11208/07_2025/6zgj_11208.map" model { file = "/net/cci-nas-00/data/ceres_data/6zgj_11208/07_2025/6zgj_11208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zgj_11208/07_2025/6zgj_11208.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 123 Time building chain proxies: 7.12, per 1000 atoms: 0.62 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: 2.48 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.20 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: 3.32 Time building geometry restraints manager: 3.01 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.140 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.870 ------------------------------------------------------------------------------- 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 (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: -1.35 (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 TRP 0.009 0.001 TRP E 160 HIS 0.003 0.001 HIS A 277 PHE 0.012 0.001 PHE C 37 TYR 0.011 0.002 TYR B 102 ARG 0.010 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.09599 ( 605) hydrogen bonds : angle 6.13837 ( 1920) covalent geometry : bond 0.00464 (11875) covalent geometry : angle 0.60870 (16330) *********************** 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 : 1.080 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.3041 time to fit residues: 73.2808 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 : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 76 optimal weight: 0.0980 chunk 60 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.191380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.143001 restraints weight = 11360.144| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.45 r_work: 0.3114 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11875 Z= 0.204 Angle : 0.608 7.201 16330 Z= 0.322 Chirality : 0.044 0.124 1975 Planarity : 0.005 0.046 2040 Dihedral : 4.967 19.720 1665 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.46 % Allowed : 10.14 % Favored : 88.40 % 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: -1.44 (0.21), residues: 1520 helix: 1.92 (0.22), residues: 495 sheet: -1.04 (0.28), residues: 300 loop : -3.18 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 160 HIS 0.003 0.001 HIS A 277 PHE 0.016 0.001 PHE B 37 TYR 0.010 0.002 TYR E 102 ARG 0.004 0.001 ARG D 189 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 605) hydrogen bonds : angle 5.08516 ( 1920) covalent geometry : bond 0.00503 (11875) covalent geometry : angle 0.60798 (16330) *********************** 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 155 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 1.478 Fit side-chains REVERT: A 80 ASN cc_start: 0.8605 (p0) cc_final: 0.7996 (p0) REVERT: B 80 ASN cc_start: 0.8723 (p0) cc_final: 0.8185 (p0) REVERT: C 80 ASN cc_start: 0.8683 (p0) cc_final: 0.8252 (p0) REVERT: C 106 PHE cc_start: 0.8562 (p90) cc_final: 0.8332 (p90) REVERT: D 80 ASN cc_start: 0.8759 (p0) cc_final: 0.8269 (p0) REVERT: E 80 ASN cc_start: 0.8786 (p0) cc_final: 0.8287 (p0) outliers start: 16 outliers final: 9 residues processed: 149 average time/residue: 0.3194 time to fit residues: 65.5029 Evaluate side-chains 127 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 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 47 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 146 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN B 127 HIS B 187 GLN C 127 HIS C 187 GLN D 187 GLN E 187 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.186772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 191)---------------| | r_work = 0.3388 r_free = 0.3388 target = 0.130226 restraints weight = 11668.546| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.17 r_work: 0.3006 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 11875 Z= 0.296 Angle : 0.653 7.007 16330 Z= 0.346 Chirality : 0.046 0.147 1975 Planarity : 0.005 0.043 2040 Dihedral : 5.165 22.089 1665 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.47 % Allowed : 13.61 % Favored : 82.92 % 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: -1.59 (0.21), residues: 1520 helix: 1.67 (0.22), residues: 495 sheet: -1.12 (0.28), residues: 300 loop : -3.15 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 213 HIS 0.004 0.002 HIS E 277 PHE 0.016 0.002 PHE C 37 TYR 0.014 0.002 TYR D 266 ARG 0.003 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 605) hydrogen bonds : angle 4.91181 ( 1920) covalent geometry : bond 0.00733 (11875) covalent geometry : angle 0.65327 (16330) *********************** 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 162 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 1.988 Fit side-chains REVERT: B 80 ASN cc_start: 0.8728 (p0) cc_final: 0.8138 (p0) REVERT: C 80 ASN cc_start: 0.8736 (p0) cc_final: 0.8383 (p0) REVERT: C 133 ARG cc_start: 0.7239 (mtm-85) cc_final: 0.7032 (ttm170) REVERT: D 80 ASN cc_start: 0.8769 (p0) cc_final: 0.8271 (p0) REVERT: D 133 ARG cc_start: 0.7286 (mtm-85) cc_final: 0.7046 (ttm170) REVERT: E 80 ASN cc_start: 0.8799 (p0) cc_final: 0.8391 (p0) outliers start: 38 outliers final: 29 residues processed: 149 average time/residue: 0.3823 time to fit residues: 79.7148 Evaluate side-chains 141 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS 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 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 190 ILE Chi-restraints excluded: chain B residue 196 SER 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 103 LEU Chi-restraints excluded: chain C residue 242 VAL 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 103 LEU Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain E residue 242 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 137 optimal weight: 8.9990 chunk 146 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.192081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.3468 r_free = 0.3468 target = 0.137284 restraints weight = 11482.206| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.31 r_work: 0.3136 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11875 Z= 0.127 Angle : 0.559 6.851 16330 Z= 0.290 Chirality : 0.043 0.125 1975 Planarity : 0.004 0.041 2040 Dihedral : 4.823 18.199 1665 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.74 % Allowed : 18.72 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.21), residues: 1520 helix: 2.16 (0.22), residues: 495 sheet: -1.03 (0.28), residues: 300 loop : -3.04 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 213 HIS 0.002 0.001 HIS E 235 PHE 0.016 0.001 PHE C 37 TYR 0.009 0.001 TYR D 119 ARG 0.004 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 605) hydrogen bonds : angle 4.52773 ( 1920) covalent geometry : bond 0.00299 (11875) covalent geometry : angle 0.55905 (16330) *********************** 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 148 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.231 Fit side-chains REVERT: B 80 ASN cc_start: 0.8572 (p0) cc_final: 0.8084 (p0) REVERT: D 80 ASN cc_start: 0.8696 (p0) cc_final: 0.8328 (p0) REVERT: D 133 ARG cc_start: 0.7340 (mtm-85) cc_final: 0.7066 (ttm170) REVERT: E 80 ASN cc_start: 0.8737 (p0) cc_final: 0.8371 (p0) outliers start: 19 outliers final: 15 residues processed: 143 average time/residue: 0.2761 time to fit residues: 54.8493 Evaluate side-chains 137 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 245 ASN 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 103 LEU Chi-restraints excluded: chain E residue 196 SER 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 148 optimal weight: 0.8980 chunk 65 optimal weight: 50.0000 chunk 124 optimal weight: 8.9990 chunk 125 optimal weight: 50.0000 chunk 63 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.191654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.142116 restraints weight = 11419.180| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.34 r_work: 0.3049 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11875 Z= 0.136 Angle : 0.564 6.967 16330 Z= 0.292 Chirality : 0.043 0.187 1975 Planarity : 0.004 0.040 2040 Dihedral : 4.710 18.066 1665 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.37 % Allowed : 19.27 % Favored : 78.36 % 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: -1.16 (0.21), residues: 1520 helix: 2.30 (0.22), residues: 495 sheet: -1.03 (0.28), residues: 300 loop : -3.05 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 160 HIS 0.003 0.001 HIS E 277 PHE 0.015 0.001 PHE E 37 TYR 0.013 0.001 TYR E 129 ARG 0.005 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 605) hydrogen bonds : angle 4.42262 ( 1920) covalent geometry : bond 0.00327 (11875) covalent geometry : angle 0.56411 (16330) *********************** 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 154 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.406 Fit side-chains REVERT: B 80 ASN cc_start: 0.8563 (p0) cc_final: 0.8094 (p0) REVERT: D 80 ASN cc_start: 0.8536 (p0) cc_final: 0.7929 (p0) REVERT: E 80 ASN cc_start: 0.8628 (p0) cc_final: 0.7988 (p0) outliers start: 26 outliers final: 21 residues processed: 150 average time/residue: 0.2738 time to fit residues: 57.4437 Evaluate side-chains 135 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 190 ILE 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 103 LEU 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 245 ASN Chi-restraints excluded: chain D residue 27 CYS 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 27 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 196 SER 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 65 optimal weight: 50.0000 chunk 40 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 50.0000 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 16 optimal weight: 30.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.190619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.140425 restraints weight = 11550.971| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.35 r_work: 0.3050 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11875 Z= 0.171 Angle : 0.577 8.136 16330 Z= 0.298 Chirality : 0.043 0.138 1975 Planarity : 0.004 0.039 2040 Dihedral : 4.728 18.733 1665 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.84 % Allowed : 18.90 % 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 (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: -1.16 (0.21), residues: 1520 helix: 2.25 (0.22), residues: 495 sheet: -0.99 (0.28), residues: 300 loop : -3.03 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 160 HIS 0.004 0.001 HIS E 277 PHE 0.015 0.001 PHE D 37 TYR 0.013 0.001 TYR E 102 ARG 0.003 0.000 ARG E 77 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 605) hydrogen bonds : angle 4.37550 ( 1920) covalent geometry : bond 0.00420 (11875) covalent geometry : angle 0.57713 (16330) *********************** 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 159 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 1.124 Fit side-chains REVERT: B 80 ASN cc_start: 0.8628 (p0) cc_final: 0.8189 (p0) REVERT: D 80 ASN cc_start: 0.8623 (p0) cc_final: 0.8012 (p0) REVERT: E 80 ASN cc_start: 0.8650 (p0) cc_final: 0.8012 (p0) outliers start: 42 outliers final: 40 residues processed: 149 average time/residue: 0.2592 time to fit residues: 54.0007 Evaluate side-chains 151 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 45 LEU 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 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 245 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 76 ILE 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 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 44 SER Chi-restraints excluded: chain E residue 79 VAL 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 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 58 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 119 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.189845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.143629 restraints weight = 11600.413| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.52 r_work: 0.3057 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11875 Z= 0.189 Angle : 0.580 7.057 16330 Z= 0.302 Chirality : 0.043 0.131 1975 Planarity : 0.004 0.039 2040 Dihedral : 4.763 18.854 1665 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.02 % Allowed : 17.81 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1520 helix: 2.25 (0.22), residues: 495 sheet: -0.93 (0.28), residues: 300 loop : -3.04 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 160 HIS 0.003 0.001 HIS E 277 PHE 0.014 0.001 PHE C 37 TYR 0.014 0.001 TYR A 102 ARG 0.004 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 605) hydrogen bonds : angle 4.36978 ( 1920) covalent geometry : bond 0.00467 (11875) covalent geometry : angle 0.57961 (16330) *********************** 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 174 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 119 time to evaluate : 1.092 Fit side-chains REVERT: B 80 ASN cc_start: 0.8650 (p0) cc_final: 0.8141 (p0) REVERT: D 80 ASN cc_start: 0.8580 (p0) cc_final: 0.8060 (p0) REVERT: E 80 ASN cc_start: 0.8595 (p0) cc_final: 0.8014 (p0) outliers start: 55 outliers final: 42 residues processed: 162 average time/residue: 0.2476 time to fit residues: 56.4314 Evaluate side-chains 154 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 44 SER 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 B residue 18 VAL 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 45 LEU 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 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 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 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 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 103 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 40.0000 chunk 136 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 65 optimal weight: 50.0000 chunk 3 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.189326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 152)---------------| | r_work = 0.3405 r_free = 0.3405 target = 0.131934 restraints weight = 11549.680| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.23 r_work: 0.3042 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11875 Z= 0.197 Angle : 0.586 7.136 16330 Z= 0.305 Chirality : 0.043 0.125 1975 Planarity : 0.004 0.039 2040 Dihedral : 4.797 18.902 1665 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.47 % Allowed : 17.81 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1520 helix: 2.20 (0.21), residues: 495 sheet: -0.89 (0.28), residues: 300 loop : -3.04 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 160 HIS 0.004 0.001 HIS B 277 PHE 0.017 0.001 PHE B 37 TYR 0.014 0.001 TYR C 102 ARG 0.003 0.000 ARG E 77 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 605) hydrogen bonds : angle 4.38783 ( 1920) covalent geometry : bond 0.00486 (11875) covalent geometry : angle 0.58599 (16330) *********************** 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 162 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 113 time to evaluate : 2.312 Fit side-chains REVERT: D 80 ASN cc_start: 0.8630 (p0) cc_final: 0.8156 (p0) REVERT: E 80 ASN cc_start: 0.8620 (p0) cc_final: 0.8062 (p0) outliers start: 49 outliers final: 44 residues processed: 152 average time/residue: 0.3643 time to fit residues: 78.8598 Evaluate side-chains 153 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 44 SER 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 B residue 18 VAL Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 45 LEU 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 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 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 76 ILE 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 D residue 304 LEU 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 242 VAL Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 50.0000 chunk 58 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN D 127 HIS D 245 ASN E 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.185704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 212)---------------| | r_work = 0.3362 r_free = 0.3362 target = 0.127980 restraints weight = 11651.322| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.23 r_work: 0.2995 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 11875 Z= 0.326 Angle : 0.665 7.061 16330 Z= 0.352 Chirality : 0.046 0.143 1975 Planarity : 0.005 0.038 2040 Dihedral : 5.136 21.213 1665 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 4.38 % Allowed : 18.54 % Favored : 77.08 % 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: -1.49 (0.21), residues: 1520 helix: 1.83 (0.21), residues: 490 sheet: -1.18 (0.27), residues: 330 loop : -3.13 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 160 HIS 0.006 0.002 HIS A 277 PHE 0.015 0.002 PHE E 37 TYR 0.017 0.002 TYR A 266 ARG 0.004 0.000 ARG B 77 Details of bonding type rmsd hydrogen bonds : bond 0.04719 ( 605) hydrogen bonds : angle 4.65262 ( 1920) covalent geometry : bond 0.00809 (11875) covalent geometry : angle 0.66539 (16330) *********************** 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 175 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 1.167 Fit side-chains REVERT: D 80 ASN cc_start: 0.8740 (p0) cc_final: 0.8372 (p0) REVERT: E 80 ASN cc_start: 0.8716 (p0) cc_final: 0.8287 (p0) outliers start: 48 outliers final: 39 residues processed: 165 average time/residue: 0.3681 time to fit residues: 85.1659 Evaluate side-chains 165 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS 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 B residue 18 VAL 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 B residue 270 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 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 C residue 308 ILE Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 76 ILE 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 D residue 304 LEU Chi-restraints excluded: chain E residue 27 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 50.0000 chunk 120 optimal weight: 20.0000 chunk 71 optimal weight: 0.5980 chunk 14 optimal weight: 0.0060 chunk 92 optimal weight: 9.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.190501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 156)---------------| | r_work = 0.3326 r_free = 0.3326 target = 0.125401 restraints weight = 11452.559| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.80 r_work: 0.3046 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11875 Z= 0.132 Angle : 0.578 7.603 16330 Z= 0.300 Chirality : 0.043 0.157 1975 Planarity : 0.004 0.039 2040 Dihedral : 4.855 19.028 1665 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.64 % Allowed : 21.92 % Favored : 76.44 % 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: -1.01 (0.21), residues: 1520 helix: 2.32 (0.22), residues: 490 sheet: -0.66 (0.28), residues: 315 loop : -3.03 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 213 HIS 0.001 0.001 HIS B 277 PHE 0.015 0.001 PHE C 37 TYR 0.016 0.001 TYR E 119 ARG 0.004 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 605) hydrogen bonds : angle 4.40670 ( 1920) covalent geometry : bond 0.00307 (11875) covalent geometry : angle 0.57819 (16330) ********************** 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 140 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.497 Fit side-chains REVERT: D 80 ASN cc_start: 0.8591 (p0) cc_final: 0.8184 (p0) REVERT: E 80 ASN cc_start: 0.8560 (p0) cc_final: 0.8096 (p0) outliers start: 18 outliers final: 17 residues processed: 136 average time/residue: 0.4166 time to fit residues: 77.6439 Evaluate side-chains 134 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain B residue 18 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 270 VAL 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 D residue 27 CYS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 196 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 70 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 0.0470 chunk 98 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.189592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.147533 restraints weight = 11388.954| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.52 r_work: 0.3053 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11875 Z= 0.178 Angle : 0.585 8.973 16330 Z= 0.304 Chirality : 0.043 0.147 1975 Planarity : 0.004 0.040 2040 Dihedral : 4.822 19.009 1665 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.74 % Allowed : 22.19 % 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 (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: -1.04 (0.21), residues: 1520 helix: 2.24 (0.22), residues: 495 sheet: -0.64 (0.28), residues: 315 loop : -3.06 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 160 HIS 0.003 0.001 HIS E 277 PHE 0.015 0.001 PHE C 37 TYR 0.013 0.001 TYR C 102 ARG 0.004 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 605) hydrogen bonds : angle 4.37208 ( 1920) covalent geometry : bond 0.00438 (11875) covalent geometry : angle 0.58517 (16330) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6732.76 seconds wall clock time: 124 minutes 8.21 seconds (7448.21 seconds total)