Starting phenix.real_space_refine on Thu Feb 15 00:36:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckv_16703/02_2024/8ckv_16703.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckv_16703/02_2024/8ckv_16703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckv_16703/02_2024/8ckv_16703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckv_16703/02_2024/8ckv_16703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckv_16703/02_2024/8ckv_16703.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckv_16703/02_2024/8ckv_16703.pdb" } resolution = 2.89 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= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 732 atoms to isotropic. 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 72 5.16 5 C 6252 2.51 5 N 1716 2.21 5 O 1860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9900 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1650 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1650 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1650 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1650 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1650 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1650 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 5.48, per 1000 atoms: 0.55 Number of scatterers: 9900 At special positions: 0 Unit cell: (110.67, 112.53, 77.19, 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 72 16.00 O 1860 8.00 N 1716 7.00 C 6252 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: 4.24 Conformation dependent library (CDL) restraints added in 2.0 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2388 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 72.6% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.848A pdb=" N ALA A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.333A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.647A pdb=" N THR A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'B' and resid 16 through 31 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.848A pdb=" N ALA B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.333A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.647A pdb=" N THR B 200 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.849A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.333A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.647A pdb=" N THR C 200 " --> pdb=" O PRO C 196 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 119 Processing helix chain 'D' and resid 125 through 145 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.848A pdb=" N ALA D 174 " --> pdb=" O LYS D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.333A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.647A pdb=" N THR D 200 " --> pdb=" O PRO D 196 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 125 through 145 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 175 removed outlier: 3.848A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.333A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.647A pdb=" N THR E 200 " --> pdb=" O PRO E 196 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 16 through 31 Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 119 Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 175 removed outlier: 3.849A pdb=" N ALA F 174 " --> pdb=" O LYS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.333A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.647A pdb=" N THR F 200 " --> pdb=" O PRO F 196 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 205 " --> pdb=" O ILE F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 218 Processing sheet with id= 1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= 2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id= 3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= 4, first strand: chain 'D' and resid 2 through 4 Processing sheet with id= 5, first strand: chain 'E' and resid 2 through 4 Processing sheet with id= 6, first strand: chain 'F' and resid 2 through 4 618 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3300 1.34 - 1.46: 1250 1.46 - 1.58: 5428 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 10110 Sorted by residual: bond pdb=" CB PRO E 1 " pdb=" CG PRO E 1 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.38e+00 bond pdb=" CB PRO B 1 " pdb=" CG PRO B 1 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.38e+00 bond pdb=" CB PRO F 1 " pdb=" CG PRO F 1 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.37e+00 bond pdb=" CB PRO C 1 " pdb=" CG PRO C 1 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.37e+00 bond pdb=" CB PRO A 1 " pdb=" CG PRO A 1 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.37e+00 ... (remaining 10105 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.26: 514 107.26 - 113.96: 5684 113.96 - 120.67: 4194 120.67 - 127.37: 3172 127.37 - 134.08: 170 Bond angle restraints: 13734 Sorted by residual: angle pdb=" C GLU C 175 " pdb=" N GLN C 176 " pdb=" CA GLN C 176 " ideal model delta sigma weight residual 120.31 124.78 -4.47 1.52e+00 4.33e-01 8.66e+00 angle pdb=" C GLU F 175 " pdb=" N GLN F 176 " pdb=" CA GLN F 176 " ideal model delta sigma weight residual 120.31 124.78 -4.47 1.52e+00 4.33e-01 8.66e+00 angle pdb=" C GLU A 175 " pdb=" N GLN A 176 " pdb=" CA GLN A 176 " ideal model delta sigma weight residual 120.31 124.78 -4.47 1.52e+00 4.33e-01 8.63e+00 angle pdb=" C GLU D 175 " pdb=" N GLN D 176 " pdb=" CA GLN D 176 " ideal model delta sigma weight residual 120.31 124.78 -4.47 1.52e+00 4.33e-01 8.63e+00 angle pdb=" C GLU B 175 " pdb=" N GLN B 176 " pdb=" CA GLN B 176 " ideal model delta sigma weight residual 120.31 124.78 -4.47 1.52e+00 4.33e-01 8.63e+00 ... (remaining 13729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 5610 15.32 - 30.63: 432 30.63 - 45.95: 132 45.95 - 61.26: 12 61.26 - 76.57: 6 Dihedral angle restraints: 6192 sinusoidal: 2520 harmonic: 3672 Sorted by residual: dihedral pdb=" CA ASN D 121 " pdb=" C ASN D 121 " pdb=" N PRO D 122 " pdb=" CA PRO D 122 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASN A 121 " pdb=" C ASN A 121 " pdb=" N PRO A 122 " pdb=" CA PRO A 122 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASN E 121 " pdb=" C ASN E 121 " pdb=" N PRO E 122 " pdb=" CA PRO E 122 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 736 0.032 - 0.064: 534 0.064 - 0.095: 178 0.095 - 0.127: 76 0.127 - 0.159: 30 Chirality restraints: 1554 Sorted by residual: chirality pdb=" CA PHE F 32 " pdb=" N PHE F 32 " pdb=" C PHE F 32 " pdb=" CB PHE F 32 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA PHE C 32 " pdb=" N PHE C 32 " pdb=" C PHE C 32 " pdb=" CB PHE C 32 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA PHE D 32 " pdb=" N PHE D 32 " pdb=" C PHE D 32 " pdb=" CB PHE D 32 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 1551 not shown) Planarity restraints: 1776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 173 " -0.207 9.50e-02 1.11e+02 9.29e-02 5.33e+00 pdb=" NE ARG B 173 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 173 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 173 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 173 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 173 " 0.207 9.50e-02 1.11e+02 9.29e-02 5.33e+00 pdb=" NE ARG E 173 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 173 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG E 173 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 173 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 173 " -0.206 9.50e-02 1.11e+02 9.24e-02 5.28e+00 pdb=" NE ARG C 173 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 173 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 173 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 173 " -0.006 2.00e-02 2.50e+03 ... (remaining 1773 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 12 1.90 - 2.65: 54 2.65 - 3.40: 14330 3.40 - 4.15: 24026 4.15 - 4.90: 44676 Nonbonded interactions: 83098 Sorted by model distance: nonbonded pdb=" NH2 ARG B 18 " pdb=" NH1 ARG C 18 " model vdw 1.152 3.200 nonbonded pdb=" NH2 ARG E 18 " pdb=" NH1 ARG F 18 " model vdw 1.152 3.200 nonbonded pdb=" NH2 ARG A 18 " pdb=" NH1 ARG B 18 " model vdw 1.152 3.200 nonbonded pdb=" NH2 ARG D 18 " pdb=" NH1 ARG E 18 " model vdw 1.152 3.200 nonbonded pdb=" NH2 ARG C 18 " pdb=" NH1 ARG D 18 " model vdw 1.153 3.200 ... (remaining 83093 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' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 12.340 Check model and map are aligned: 0.170 Set scattering table: 0.080 Process input model: 29.600 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 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:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.004 0.077 10110 Z= 0.283 Angle : 0.823 5.537 13734 Z= 0.498 Chirality : 0.050 0.159 1554 Planarity : 0.011 0.093 1776 Dihedral : 12.341 76.573 3804 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.51 (0.20), residues: 1248 helix: -0.38 (0.15), residues: 840 sheet: -0.62 (0.39), residues: 54 loop : 0.31 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.004 TRP F 117 HIS 0.012 0.005 HIS A 12 PHE 0.011 0.003 PHE E 40 TYR 0.018 0.005 TYR D 145 ARG 0.016 0.003 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.120 Fit side-chains REVERT: A 167 ARG cc_start: 0.8054 (mtp180) cc_final: 0.7780 (mtp-110) REVERT: A 215 MET cc_start: 0.7895 (mtp) cc_final: 0.7523 (mtp) REVERT: B 33 SER cc_start: 0.8336 (t) cc_final: 0.8081 (m) REVERT: B 68 MET cc_start: 0.8460 (mtp) cc_final: 0.8157 (mtp) REVERT: B 163 ASP cc_start: 0.7498 (m-30) cc_final: 0.7276 (m-30) REVERT: B 170 LYS cc_start: 0.8290 (tttm) cc_final: 0.8067 (tttp) REVERT: C 68 MET cc_start: 0.8434 (mtp) cc_final: 0.8205 (mtm) REVERT: D 167 ARG cc_start: 0.8055 (mtp180) cc_final: 0.7781 (mtp-110) REVERT: D 215 MET cc_start: 0.7897 (mtp) cc_final: 0.7524 (mtp) REVERT: E 33 SER cc_start: 0.8339 (t) cc_final: 0.8083 (m) REVERT: E 68 MET cc_start: 0.8459 (mtp) cc_final: 0.8157 (mtp) REVERT: E 163 ASP cc_start: 0.7495 (m-30) cc_final: 0.7275 (m-30) REVERT: E 170 LYS cc_start: 0.8290 (tttm) cc_final: 0.8067 (tttp) REVERT: F 68 MET cc_start: 0.8433 (mtp) cc_final: 0.8205 (mtm) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 1.3153 time to fit residues: 316.4838 Evaluate side-chains 180 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 0.0370 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN E 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10110 Z= 0.245 Angle : 0.552 5.389 13734 Z= 0.281 Chirality : 0.042 0.130 1554 Planarity : 0.007 0.079 1776 Dihedral : 5.095 29.355 1344 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.87 % Allowed : 7.30 % Favored : 90.82 % 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: 1.30 (0.22), residues: 1248 helix: 1.29 (0.17), residues: 858 sheet: -0.01 (0.49), residues: 54 loop : 0.10 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 117 HIS 0.003 0.001 HIS B 120 PHE 0.012 0.002 PHE E 32 TYR 0.012 0.001 TYR D 169 ARG 0.003 0.001 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 1.111 Fit side-chains REVERT: A 79 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6210 (mt-10) REVERT: A 144 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7225 (mtp) REVERT: C 55 MET cc_start: 0.8532 (mtp) cc_final: 0.8280 (mtp) REVERT: D 79 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.6210 (mt-10) REVERT: D 144 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7226 (mtp) REVERT: F 55 MET cc_start: 0.8531 (mtp) cc_final: 0.8280 (mtp) outliers start: 20 outliers final: 2 residues processed: 154 average time/residue: 1.3051 time to fit residues: 214.7352 Evaluate side-chains 140 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 83 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 0.0050 chunk 113 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN E 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10110 Z= 0.253 Angle : 0.526 5.311 13734 Z= 0.264 Chirality : 0.042 0.135 1554 Planarity : 0.005 0.036 1776 Dihedral : 4.803 28.252 1344 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.25 % Allowed : 9.36 % Favored : 88.39 % 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: 1.47 (0.23), residues: 1248 helix: 1.43 (0.17), residues: 858 sheet: 0.14 (0.50), residues: 54 loop : 0.12 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 117 HIS 0.003 0.001 HIS A 84 PHE 0.012 0.002 PHE B 32 TYR 0.013 0.001 TYR C 169 ARG 0.002 0.000 ARG F 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 1.196 Fit side-chains REVERT: A 79 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6237 (mt-10) REVERT: A 144 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7143 (mtp) REVERT: C 55 MET cc_start: 0.8531 (mtp) cc_final: 0.8275 (mtp) REVERT: D 79 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6239 (mt-10) REVERT: D 144 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7143 (mtp) REVERT: F 55 MET cc_start: 0.8531 (mtp) cc_final: 0.8276 (mtp) outliers start: 24 outliers final: 8 residues processed: 148 average time/residue: 1.2958 time to fit residues: 205.0845 Evaluate side-chains 134 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 0.1980 chunk 121 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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: 0.7265 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10110 Z= 0.214 Angle : 0.494 5.219 13734 Z= 0.246 Chirality : 0.040 0.130 1554 Planarity : 0.005 0.037 1776 Dihedral : 4.529 27.589 1344 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.81 % Allowed : 10.67 % Favored : 86.52 % 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: 1.64 (0.23), residues: 1248 helix: 1.56 (0.18), residues: 858 sheet: 0.37 (0.54), residues: 54 loop : 0.15 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.003 0.001 HIS D 84 PHE 0.011 0.002 PHE B 32 TYR 0.012 0.001 TYR F 169 ARG 0.002 0.000 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.126 Fit side-chains REVERT: A 79 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6292 (mt-10) REVERT: C 55 MET cc_start: 0.8472 (mtp) cc_final: 0.8239 (mtp) REVERT: C 96 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.5094 (mtt) REVERT: D 79 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6292 (mt-10) REVERT: F 55 MET cc_start: 0.8472 (mtp) cc_final: 0.8239 (mtp) REVERT: F 96 MET cc_start: 0.5813 (OUTLIER) cc_final: 0.5094 (mtt) outliers start: 30 outliers final: 6 residues processed: 140 average time/residue: 1.3335 time to fit residues: 199.6915 Evaluate side-chains 126 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 96 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7310 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10110 Z= 0.288 Angle : 0.525 5.135 13734 Z= 0.261 Chirality : 0.042 0.134 1554 Planarity : 0.005 0.039 1776 Dihedral : 4.722 27.470 1344 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.06 % Allowed : 11.42 % Favored : 86.52 % 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 (0.23), residues: 1248 helix: 1.34 (0.17), residues: 858 sheet: 0.62 (0.51), residues: 54 loop : 0.23 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 184 HIS 0.004 0.002 HIS A 84 PHE 0.011 0.002 PHE E 32 TYR 0.015 0.001 TYR F 169 ARG 0.002 0.000 ARG F 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 1.053 Fit side-chains REVERT: A 79 GLU cc_start: 0.6461 (mt-10) cc_final: 0.6260 (mt-10) REVERT: D 79 GLU cc_start: 0.6463 (mt-10) cc_final: 0.6261 (mt-10) outliers start: 22 outliers final: 8 residues processed: 132 average time/residue: 1.3101 time to fit residues: 185.1186 Evaluate side-chains 124 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 83 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.0020 chunk 109 optimal weight: 0.5980 chunk 24 optimal weight: 0.0270 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 chunk 117 optimal weight: 0.6980 overall best weight: 0.3446 ------------------------------------------------------------------------------- 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: 0.7239 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10110 Z= 0.169 Angle : 0.461 5.803 13734 Z= 0.228 Chirality : 0.039 0.124 1554 Planarity : 0.004 0.038 1776 Dihedral : 4.249 25.960 1344 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.25 % Allowed : 11.61 % Favored : 86.14 % 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: 1.84 (0.23), residues: 1248 helix: 1.66 (0.18), residues: 858 sheet: 0.59 (0.57), residues: 54 loop : 0.36 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 117 HIS 0.003 0.001 HIS F 120 PHE 0.012 0.002 PHE B 32 TYR 0.011 0.001 TYR F 169 ARG 0.001 0.000 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 1.146 Fit side-chains REVERT: A 83 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7598 (mm) REVERT: C 96 MET cc_start: 0.5998 (OUTLIER) cc_final: 0.5072 (mtt) REVERT: D 83 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7600 (mm) REVERT: F 96 MET cc_start: 0.5998 (OUTLIER) cc_final: 0.5072 (mtt) outliers start: 24 outliers final: 6 residues processed: 136 average time/residue: 1.4308 time to fit residues: 207.3191 Evaluate side-chains 118 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 148 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 76 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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: 0.7271 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10110 Z= 0.211 Angle : 0.485 5.500 13734 Z= 0.238 Chirality : 0.040 0.126 1554 Planarity : 0.005 0.038 1776 Dihedral : 4.315 25.577 1344 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.87 % Allowed : 12.17 % Favored : 85.96 % 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: 1.80 (0.23), residues: 1248 helix: 1.58 (0.18), residues: 858 sheet: 0.62 (0.58), residues: 54 loop : 0.47 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 184 HIS 0.003 0.001 HIS D 120 PHE 0.011 0.002 PHE B 32 TYR 0.012 0.001 TYR A 169 ARG 0.001 0.000 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 1.158 Fit side-chains REVERT: A 83 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7639 (mm) REVERT: D 83 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7651 (mm) outliers start: 20 outliers final: 12 residues processed: 132 average time/residue: 1.4186 time to fit residues: 199.7041 Evaluate side-chains 126 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 148 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 95 optimal weight: 0.4980 chunk 110 optimal weight: 0.2980 chunk 116 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7279 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10110 Z= 0.220 Angle : 0.487 6.212 13734 Z= 0.239 Chirality : 0.041 0.126 1554 Planarity : 0.005 0.039 1776 Dihedral : 4.347 25.535 1344 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.97 % Allowed : 12.45 % Favored : 85.58 % 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: 1.75 (0.23), residues: 1248 helix: 1.53 (0.18), residues: 858 sheet: 0.57 (0.57), residues: 54 loop : 0.53 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 184 HIS 0.003 0.001 HIS F 120 PHE 0.011 0.002 PHE B 32 TYR 0.012 0.001 TYR F 169 ARG 0.001 0.000 ARG C 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.990 Fit side-chains REVERT: A 79 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6160 (mt-10) REVERT: A 83 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7619 (mm) REVERT: C 180 GLU cc_start: 0.7169 (tt0) cc_final: 0.6939 (tp30) REVERT: D 79 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6162 (mt-10) REVERT: D 83 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7618 (mm) REVERT: F 180 GLU cc_start: 0.7171 (tt0) cc_final: 0.6940 (tp30) outliers start: 21 outliers final: 9 residues processed: 127 average time/residue: 1.3834 time to fit residues: 187.3329 Evaluate side-chains 127 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 144 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.0270 chunk 116 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 0.0070 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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: 0.7257 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10110 Z= 0.190 Angle : 0.482 6.570 13734 Z= 0.235 Chirality : 0.040 0.123 1554 Planarity : 0.004 0.038 1776 Dihedral : 4.223 24.905 1344 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.78 % Allowed : 12.45 % Favored : 85.77 % 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: 1.82 (0.23), residues: 1248 helix: 1.58 (0.18), residues: 858 sheet: 0.45 (0.59), residues: 54 loop : 0.56 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 184 HIS 0.003 0.001 HIS D 120 PHE 0.012 0.002 PHE B 32 TYR 0.011 0.001 TYR B 169 ARG 0.001 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.335 Fit side-chains REVERT: A 79 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6203 (mt-10) REVERT: A 83 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7598 (mm) REVERT: C 180 GLU cc_start: 0.7141 (tt0) cc_final: 0.6895 (tp30) REVERT: D 79 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6202 (mt-10) REVERT: D 83 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7599 (mm) REVERT: F 180 GLU cc_start: 0.7143 (tt0) cc_final: 0.6895 (tp30) outliers start: 19 outliers final: 9 residues processed: 127 average time/residue: 1.3613 time to fit residues: 184.5933 Evaluate side-chains 125 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 15 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7278 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10110 Z= 0.229 Angle : 0.500 8.769 13734 Z= 0.243 Chirality : 0.041 0.126 1554 Planarity : 0.005 0.039 1776 Dihedral : 4.324 25.046 1344 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.06 % Allowed : 11.89 % Favored : 86.05 % 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: 1.70 (0.23), residues: 1248 helix: 1.48 (0.18), residues: 858 sheet: 0.43 (0.56), residues: 54 loop : 0.56 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 184 HIS 0.003 0.001 HIS D 84 PHE 0.011 0.002 PHE B 32 TYR 0.013 0.001 TYR C 169 ARG 0.001 0.000 ARG C 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.173 Fit side-chains REVERT: A 79 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6158 (mt-10) REVERT: A 83 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7613 (mm) REVERT: C 180 GLU cc_start: 0.7164 (tt0) cc_final: 0.6913 (tp30) REVERT: D 79 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6158 (mt-10) REVERT: D 83 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7613 (mm) REVERT: F 180 GLU cc_start: 0.7168 (tt0) cc_final: 0.6915 (tp30) outliers start: 22 outliers final: 12 residues processed: 128 average time/residue: 1.3892 time to fit residues: 189.8683 Evaluate side-chains 128 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 75 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 41 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.165621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.129194 restraints weight = 9578.164| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.71 r_work: 0.3125 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10110 Z= 0.263 Angle : 0.518 8.544 13734 Z= 0.253 Chirality : 0.041 0.128 1554 Planarity : 0.005 0.039 1776 Dihedral : 4.471 25.490 1344 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.97 % Allowed : 12.08 % Favored : 85.96 % 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: 1.54 (0.23), residues: 1248 helix: 1.35 (0.18), residues: 858 sheet: 0.39 (0.53), residues: 54 loop : 0.52 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 184 HIS 0.004 0.002 HIS A 84 PHE 0.011 0.002 PHE E 32 TYR 0.013 0.001 TYR F 169 ARG 0.002 0.000 ARG C 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3940.50 seconds wall clock time: 70 minutes 54.97 seconds (4254.97 seconds total)