Starting phenix.real_space_refine on Fri Mar 15 11:47:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgj_11208/03_2024/6zgj_11208.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgj_11208/03_2024/6zgj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgj_11208/03_2024/6zgj_11208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgj_11208/03_2024/6zgj_11208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgj_11208/03_2024/6zgj_11208.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zgj_11208/03_2024/6zgj_11208.pdb" } 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 Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 136": "OD1" <-> "OD2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 136": "OD1" <-> "OD2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 243": "OE1" <-> "OE2" Residue "E PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.52, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 4.09 Conformation dependent library (CDL) restraints added in 2.3 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: 1.29 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: 3.66 Time building geometry restraints manager: 4.49 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: 99.78 - 106.62: 395 106.62 - 113.46: 6599 113.46 - 120.29: 4133 120.29 - 127.13: 5060 127.13 - 133.97: 143 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 2.520 nonbonded pdb=" ND2 ASN B 80 " pdb=" O VAL B 110 " model vdw 2.192 2.520 nonbonded pdb=" ND2 ASN D 80 " pdb=" O VAL D 110 " model vdw 2.193 2.520 nonbonded pdb=" ND2 ASN C 80 " pdb=" O VAL C 110 " model vdw 2.193 2.520 nonbonded pdb=" ND2 ASN A 80 " pdb=" O VAL A 110 " model vdw 2.194 2.520 ... (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 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 4.160 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 33.910 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.650 ------------------------------------------------------------------------------- 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= 0.305 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.271 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.3146 time to fit residues: 75.7332 Evaluate side-chains 121 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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: 0.6980 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 E 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1003 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= 0.309 Angle : 0.588 7.185 16330 Z= 0.309 Chirality : 0.043 0.124 1975 Planarity : 0.005 0.046 2040 Dihedral : 4.931 19.445 1665 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.64 % Allowed : 9.32 % Favored : 89.04 % 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: 1.98 (0.22), residues: 495 sheet: -1.00 (0.28), residues: 300 loop : -3.10 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 160 HIS 0.003 0.001 HIS A 277 PHE 0.016 0.001 PHE D 37 TYR 0.010 0.001 TYR E 102 ARG 0.004 0.001 ARG A 105 *********************** 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 144 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.131 Fit side-chains REVERT: C 106 PHE cc_start: 0.8539 (p90) cc_final: 0.8266 (p90) outliers start: 18 outliers final: 11 residues processed: 136 average time/residue: 0.2834 time to fit residues: 53.4447 Evaluate side-chains 116 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 103 LEU Chi-restraints excluded: chain C residue 19 ASN 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 75 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 121 optimal weight: 0.1980 chunk 135 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN C 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1314 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= 0.243 Angle : 0.560 6.708 16330 Z= 0.290 Chirality : 0.043 0.126 1975 Planarity : 0.004 0.043 2040 Dihedral : 4.793 18.859 1665 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.37 % Allowed : 11.78 % Favored : 85.84 % 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: 2.13 (0.22), residues: 495 sheet: -0.89 (0.28), residues: 300 loop : -3.07 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 47 HIS 0.002 0.001 HIS D 277 PHE 0.016 0.001 PHE E 37 TYR 0.011 0.001 TYR E 102 ARG 0.003 0.000 ARG A 105 *********************** 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 146 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.112 Fit side-chains outliers start: 26 outliers final: 17 residues processed: 137 average time/residue: 0.2830 time to fit residues: 52.7996 Evaluate side-chains 122 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 103 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 196 SER 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 196 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 50.0000 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 50.0000 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 193 GLN B 127 HIS C 127 HIS D 187 GLN D 193 GLN E 187 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1724 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= 0.474 Angle : 0.642 6.726 16330 Z= 0.338 Chirality : 0.045 0.143 1975 Planarity : 0.005 0.041 2040 Dihedral : 5.064 21.646 1665 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.56 % Allowed : 16.26 % Favored : 81.19 % 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: -1.42 (0.21), residues: 1520 helix: 1.73 (0.22), residues: 495 sheet: -0.91 (0.28), residues: 300 loop : -3.05 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 213 HIS 0.005 0.002 HIS E 235 PHE 0.014 0.002 PHE E 37 TYR 0.016 0.002 TYR E 266 ARG 0.006 0.001 ARG D 192 *********************** 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 147 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 1.251 Fit side-chains outliers start: 28 outliers final: 25 residues processed: 140 average time/residue: 0.2835 time to fit residues: 54.2596 Evaluate side-chains 130 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 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 190 ILE Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 304 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 20.0000 chunk 82 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 0.0370 overall best weight: 1.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11875 Z= 0.274 Angle : 0.569 6.950 16330 Z= 0.295 Chirality : 0.043 0.147 1975 Planarity : 0.004 0.040 2040 Dihedral : 4.872 19.709 1665 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.19 % Allowed : 18.17 % Favored : 79.63 % 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: -1.20 (0.21), residues: 1520 helix: 2.04 (0.22), residues: 495 sheet: -0.86 (0.28), residues: 300 loop : -2.98 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 47 HIS 0.002 0.001 HIS D 277 PHE 0.015 0.001 PHE C 37 TYR 0.011 0.001 TYR A 102 ARG 0.003 0.000 ARG B 77 *********************** 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 138 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 1.218 Fit side-chains outliers start: 24 outliers final: 22 residues processed: 130 average time/residue: 0.2668 time to fit residues: 48.0605 Evaluate side-chains 132 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 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 190 ILE Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain C residue 19 ASN Chi-restraints excluded: chain C residue 27 CYS 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 190 ILE Chi-restraints excluded: chain D residue 196 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 50.0000 chunk 145 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 76 optimal weight: 50.0000 chunk 139 optimal weight: 0.8980 overall best weight: 3.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 11875 Z= 0.520 Angle : 0.656 6.811 16330 Z= 0.345 Chirality : 0.046 0.145 1975 Planarity : 0.005 0.039 2040 Dihedral : 5.163 21.593 1665 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.93 % Allowed : 17.81 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1520 helix: 1.63 (0.22), residues: 495 sheet: -0.88 (0.28), residues: 300 loop : -3.01 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 160 HIS 0.005 0.002 HIS A 277 PHE 0.015 0.002 PHE B 238 TYR 0.015 0.002 TYR A 266 ARG 0.003 0.000 ARG D 192 *********************** 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 163 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 1.361 Fit side-chains outliers start: 43 outliers final: 36 residues processed: 154 average time/residue: 0.2569 time to fit residues: 55.4328 Evaluate side-chains 150 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 270 VAL Chi-restraints excluded: chain A residue 304 LEU 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 242 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 308 ILE 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 196 SER Chi-restraints excluded: chain C residue 242 VAL 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 190 ILE Chi-restraints excluded: chain D residue 196 SER Chi-restraints excluded: chain D residue 242 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 40.0000 chunk 82 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11875 Z= 0.184 Angle : 0.545 7.293 16330 Z= 0.281 Chirality : 0.042 0.154 1975 Planarity : 0.004 0.040 2040 Dihedral : 4.803 18.736 1665 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.56 % Allowed : 18.81 % Favored : 77.63 % 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: -1.03 (0.21), residues: 1520 helix: 2.22 (0.22), residues: 495 sheet: -0.82 (0.28), residues: 300 loop : -2.89 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 213 HIS 0.002 0.000 HIS D 235 PHE 0.020 0.001 PHE A 37 TYR 0.012 0.001 TYR E 102 ARG 0.004 0.000 ARG E 77 *********************** 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 160 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 121 time to evaluate : 1.192 Fit side-chains outliers start: 39 outliers final: 26 residues processed: 155 average time/residue: 0.2504 time to fit residues: 54.3422 Evaluate side-chains 138 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 242 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 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 18 VAL Chi-restraints excluded: chain C residue 27 CYS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 27 CYS 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 126 optimal weight: 0.0020 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11875 Z= 0.398 Angle : 0.611 7.711 16330 Z= 0.316 Chirality : 0.044 0.147 1975 Planarity : 0.004 0.040 2040 Dihedral : 4.929 19.982 1665 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.20 % Allowed : 19.09 % 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: -1.18 (0.21), residues: 1520 helix: 2.00 (0.22), residues: 495 sheet: -0.78 (0.28), residues: 300 loop : -2.95 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 213 HIS 0.005 0.002 HIS C 277 PHE 0.016 0.002 PHE A 37 TYR 0.012 0.002 TYR A 102 ARG 0.004 0.000 ARG B 77 *********************** 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 154 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 1.256 Fit side-chains REVERT: E 110 VAL cc_start: 0.7571 (OUTLIER) cc_final: 0.7339 (t) outliers start: 35 outliers final: 28 residues processed: 149 average time/residue: 0.2702 time to fit residues: 56.2109 Evaluate side-chains 138 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 242 VAL 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 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 27 CYS Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 270 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 110 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11875 Z= 0.218 Angle : 0.550 7.475 16330 Z= 0.282 Chirality : 0.042 0.147 1975 Planarity : 0.004 0.041 2040 Dihedral : 4.733 18.510 1665 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.37 % Allowed : 19.82 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.21), residues: 1520 helix: 2.32 (0.22), residues: 495 sheet: -0.82 (0.28), residues: 300 loop : -2.86 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 47 HIS 0.002 0.001 HIS D 235 PHE 0.017 0.001 PHE A 37 TYR 0.011 0.001 TYR E 102 ARG 0.003 0.000 ARG E 77 *********************** 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 146 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.218 Fit side-chains outliers start: 26 outliers final: 23 residues processed: 142 average time/residue: 0.2546 time to fit residues: 50.6609 Evaluate side-chains 139 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 242 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 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 27 CYS 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 E residue 27 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 0.0970 chunk 36 optimal weight: 0.0570 overall best weight: 0.8302 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11875 Z= 0.201 Angle : 0.549 9.355 16330 Z= 0.279 Chirality : 0.042 0.142 1975 Planarity : 0.004 0.041 2040 Dihedral : 4.613 17.852 1665 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.28 % Allowed : 20.46 % 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: -0.76 (0.21), residues: 1520 helix: 2.49 (0.21), residues: 495 sheet: -0.51 (0.28), residues: 315 loop : -2.88 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 47 HIS 0.002 0.001 HIS B 277 PHE 0.017 0.001 PHE E 37 TYR 0.010 0.001 TYR E 102 ARG 0.004 0.000 ARG E 77 ********************** 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 141 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.188 Fit side-chains outliers start: 25 outliers final: 25 residues processed: 138 average time/residue: 0.2554 time to fit residues: 49.4740 Evaluate side-chains 139 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 242 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 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 27 CYS Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 242 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 E residue 27 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 6 optimal weight: 0.0040 chunk 86 optimal weight: 3.9990 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 HIS E 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.191123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3471 r_free = 0.3471 target = 0.137687 restraints weight = 11349.058| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.31 r_work: 0.3104 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2274 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= 0.257 Angle : 0.560 8.372 16330 Z= 0.286 Chirality : 0.043 0.145 1975 Planarity : 0.004 0.041 2040 Dihedral : 4.638 18.387 1665 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.74 % Allowed : 20.55 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.21), residues: 1520 helix: 2.39 (0.21), residues: 495 sheet: -0.76 (0.28), residues: 300 loop : -2.80 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 160 HIS 0.003 0.001 HIS B 277 PHE 0.017 0.001 PHE A 37 TYR 0.011 0.001 TYR E 102 ARG 0.004 0.000 ARG D 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2193.02 seconds wall clock time: 40 minutes 14.25 seconds (2414.25 seconds total)