Starting phenix.real_space_refine on Sat Mar 16 22:52:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl1_16709/03_2024/8cl1_16709.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl1_16709/03_2024/8cl1_16709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl1_16709/03_2024/8cl1_16709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl1_16709/03_2024/8cl1_16709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl1_16709/03_2024/8cl1_16709.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl1_16709/03_2024/8cl1_16709.pdb" } resolution = 3.35 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= 0.002 sd= 0.067 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 5472 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 6660 2.51 5 N 1818 2.21 5 O 1944 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-5265/modules/chem_data/mon_lib" Total number of atoms: 10494 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1646 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 103 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1646 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 103 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1646 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 103 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1646 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 103 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1646 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 103 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1646 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 103 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.79, per 1000 atoms: 0.55 Number of scatterers: 10494 At special positions: 0 Unit cell: (116.25, 108.81, 70.68, 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 1944 8.00 N 1818 7.00 C 6660 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: 4.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 69.2% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 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 146 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.651A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 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 146 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.651A pdb=" N GLY C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 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 146 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.650A pdb=" N GLY E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'G' and resid 16 through 31 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 119 Processing helix chain 'G' and resid 125 through 146 Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA G 174 " --> pdb=" O LYS G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.651A pdb=" N GLY G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 219 Processing helix chain 'I' and resid 16 through 31 Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 48 through 58 Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 110 through 119 Processing helix chain 'I' and resid 125 through 146 Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA I 174 " --> pdb=" O LYS I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 206 removed outlier: 3.651A pdb=" N GLY I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 219 Processing helix chain 'K' and resid 16 through 31 Processing helix chain 'K' and resid 35 through 44 Processing helix chain 'K' and resid 48 through 58 Processing helix chain 'K' and resid 62 through 84 Processing helix chain 'K' and resid 100 through 105 Processing helix chain 'K' and resid 110 through 119 Processing helix chain 'K' and resid 125 through 146 Processing helix chain 'K' and resid 149 through 153 Processing helix chain 'K' and resid 160 through 175 removed outlier: 3.723A pdb=" N ALA K 174 " --> pdb=" O LYS K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 193 removed outlier: 4.505A pdb=" N LEU K 190 " --> pdb=" O THR K 186 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 206 removed outlier: 3.650A pdb=" N GLY K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 219 Processing sheet with id= 1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= 2, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= 3, first strand: chain 'E' and resid 2 through 4 Processing sheet with id= 4, first strand: chain 'G' and resid 2 through 4 Processing sheet with id= 5, first strand: chain 'I' and resid 2 through 4 Processing sheet with id= 6, first strand: chain 'K' and resid 2 through 4 648 hydrogen bonds defined for protein. 1908 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: 2.75 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1776 1.29 - 1.42: 2508 1.42 - 1.55: 6312 1.55 - 1.68: 18 1.68 - 1.81: 132 Bond restraints: 10746 Sorted by residual: bond pdb=" CA ALA I 177 " pdb=" C ALA I 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.74e+01 bond pdb=" CA ALA C 177 " pdb=" C ALA C 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.74e+01 bond pdb=" CA ALA G 177 " pdb=" C ALA G 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.72e+01 bond pdb=" CA ALA A 177 " pdb=" C ALA A 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.72e+01 bond pdb=" CA ALA E 177 " pdb=" C ALA E 177 " ideal model delta sigma weight residual 1.525 1.428 0.097 1.28e-02 6.10e+03 5.68e+01 ... (remaining 10741 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.49: 618 106.49 - 113.40: 5688 113.40 - 120.31: 4204 120.31 - 127.22: 3908 127.22 - 134.14: 204 Bond angle restraints: 14622 Sorted by residual: angle pdb=" N ALA C 177 " pdb=" CA ALA C 177 " pdb=" C ALA C 177 " ideal model delta sigma weight residual 110.35 117.30 -6.95 1.36e+00 5.41e-01 2.61e+01 angle pdb=" N ALA I 177 " pdb=" CA ALA I 177 " pdb=" C ALA I 177 " ideal model delta sigma weight residual 110.35 117.30 -6.95 1.36e+00 5.41e-01 2.61e+01 angle pdb=" N ALA K 177 " pdb=" CA ALA K 177 " pdb=" C ALA K 177 " ideal model delta sigma weight residual 110.35 117.29 -6.94 1.36e+00 5.41e-01 2.60e+01 angle pdb=" N ALA E 177 " pdb=" CA ALA E 177 " pdb=" C ALA E 177 " ideal model delta sigma weight residual 110.35 117.29 -6.94 1.36e+00 5.41e-01 2.60e+01 angle pdb=" N ALA G 177 " pdb=" CA ALA G 177 " pdb=" C ALA G 177 " ideal model delta sigma weight residual 110.35 117.25 -6.90 1.36e+00 5.41e-01 2.57e+01 ... (remaining 14617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 6012 15.12 - 30.23: 396 30.23 - 45.35: 96 45.35 - 60.46: 30 60.46 - 75.58: 12 Dihedral angle restraints: 6546 sinusoidal: 2634 harmonic: 3912 Sorted by residual: dihedral pdb=" CA PHE C 32 " pdb=" C PHE C 32 " pdb=" N SER C 33 " pdb=" CA SER C 33 " ideal model delta harmonic sigma weight residual 180.00 149.91 30.09 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA PHE I 32 " pdb=" C PHE I 32 " pdb=" N SER I 33 " pdb=" CA SER I 33 " ideal model delta harmonic sigma weight residual 180.00 149.91 30.09 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA PHE K 32 " pdb=" C PHE K 32 " pdb=" N SER K 33 " pdb=" CA SER K 33 " ideal model delta harmonic sigma weight residual 180.00 149.92 30.08 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 6543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1452 0.084 - 0.167: 162 0.167 - 0.250: 18 0.250 - 0.334: 0 0.334 - 0.417: 6 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CA ALA C 177 " pdb=" N ALA C 177 " pdb=" C ALA C 177 " pdb=" CB ALA C 177 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA ALA I 177 " pdb=" N ALA I 177 " pdb=" C ALA I 177 " pdb=" CB ALA I 177 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA ALA K 177 " pdb=" N ALA K 177 " pdb=" C ALA K 177 " pdb=" CB ALA K 177 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 1635 not shown) Planarity restraints: 1902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 175 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C GLU E 175 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU E 175 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN E 176 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 175 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C GLU K 175 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU K 175 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN K 176 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 175 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C GLU C 175 " 0.050 2.00e-02 2.50e+03 pdb=" O GLU C 175 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN C 176 " -0.017 2.00e-02 2.50e+03 ... (remaining 1899 not shown) Histogram of nonbonded interaction distances: 0.39 - 1.29: 24 1.29 - 2.20: 78 2.20 - 3.10: 8266 3.10 - 4.00: 27982 4.00 - 4.90: 51006 Warning: very small nonbonded interaction distances. Nonbonded interactions: 87356 Sorted by model distance: nonbonded pdb=" CZ TYR G 145 " pdb=" NH2 ARG I 162 " model vdw 0.393 3.340 nonbonded pdb=" CZ TYR A 145 " pdb=" NH2 ARG C 162 " model vdw 0.393 3.340 nonbonded pdb=" CZ TYR C 145 " pdb=" NH2 ARG E 162 " model vdw 0.393 3.340 nonbonded pdb=" CZ TYR I 145 " pdb=" NH2 ARG K 162 " model vdw 0.393 3.340 nonbonded pdb=" NH2 ARG A 162 " pdb=" CZ TYR K 145 " model vdw 0.393 3.340 ... (remaining 87351 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } 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: 0.010 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 12.110 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 30.150 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 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 : 0.008 0.097 10746 Z= 0.536 Angle : 0.929 6.951 14622 Z= 0.576 Chirality : 0.059 0.417 1638 Planarity : 0.008 0.055 1902 Dihedral : 12.178 75.578 4002 Min Nonbonded Distance : 0.393 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.90 % Allowed : 0.00 % Favored : 99.10 % Rotamer: Outliers : 0.54 % Allowed : 0.00 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -1.05 (0.20), residues: 1326 helix: -0.93 (0.14), residues: 870 sheet: -3.06 (0.31), residues: 54 loop : 0.80 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP E 23 HIS 0.008 0.002 HIS C 84 PHE 0.014 0.003 PHE B 321 TYR 0.026 0.006 TYR C 145 ARG 0.015 0.002 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 226 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7951 (tpt) cc_final: 0.7734 (tpp) REVERT: A 75 GLU cc_start: 0.7905 (pt0) cc_final: 0.7666 (pt0) REVERT: C 39 MET cc_start: 0.7700 (tpt) cc_final: 0.7151 (tpp) REVERT: G 39 MET cc_start: 0.7952 (tpt) cc_final: 0.7732 (tpp) REVERT: G 75 GLU cc_start: 0.7907 (pt0) cc_final: 0.7669 (pt0) REVERT: I 39 MET cc_start: 0.7691 (tpt) cc_final: 0.7151 (tpp) outliers start: 6 outliers final: 2 residues processed: 226 average time/residue: 0.2783 time to fit residues: 83.3649 Evaluate side-chains 142 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain G residue 176 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 119 optimal weight: 0.0060 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN E 74 ASN G 74 ASN ** G 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN K 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10746 Z= 0.240 Angle : 0.635 7.234 14622 Z= 0.334 Chirality : 0.042 0.150 1638 Planarity : 0.006 0.043 1902 Dihedral : 5.148 38.771 1434 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.90 % Allowed : 0.45 % Favored : 98.64 % Rotamer: Outliers : 1.08 % Allowed : 3.41 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.05 (0.22), residues: 1326 helix: 0.88 (0.16), residues: 876 sheet: -2.03 (0.33), residues: 54 loop : 1.07 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 117 HIS 0.001 0.001 HIS I 84 PHE 0.006 0.001 PHE L 321 TYR 0.010 0.002 TYR C 169 ARG 0.007 0.001 ARG C 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 1.199 Fit side-chains REVERT: A 145 TYR cc_start: 0.7226 (m-80) cc_final: 0.6590 (m-80) REVERT: C 39 MET cc_start: 0.7492 (tpt) cc_final: 0.6718 (tpp) REVERT: C 145 TYR cc_start: 0.7402 (m-80) cc_final: 0.6558 (m-80) REVERT: C 176 GLN cc_start: 0.6879 (pt0) cc_final: 0.6631 (pm20) REVERT: E 145 TYR cc_start: 0.7343 (m-80) cc_final: 0.6453 (m-10) REVERT: G 145 TYR cc_start: 0.7226 (m-80) cc_final: 0.6587 (m-80) REVERT: I 39 MET cc_start: 0.7493 (tpt) cc_final: 0.6719 (tpp) REVERT: I 145 TYR cc_start: 0.7403 (m-80) cc_final: 0.6559 (m-80) REVERT: I 176 GLN cc_start: 0.6884 (pt0) cc_final: 0.6633 (pm20) REVERT: K 145 TYR cc_start: 0.7340 (m-80) cc_final: 0.6455 (m-10) outliers start: 12 outliers final: 4 residues processed: 176 average time/residue: 0.2486 time to fit residues: 59.8888 Evaluate side-chains 166 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 162 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain K residue 104 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 10746 Z= 0.483 Angle : 0.712 6.872 14622 Z= 0.371 Chirality : 0.047 0.195 1638 Planarity : 0.006 0.045 1902 Dihedral : 5.056 43.447 1434 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.45 % Allowed : 2.26 % Favored : 97.29 % Rotamer: Outliers : 1.79 % Allowed : 5.38 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1326 helix: 0.81 (0.17), residues: 870 sheet: -1.57 (0.36), residues: 54 loop : 1.06 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 117 HIS 0.005 0.001 HIS E 12 PHE 0.010 0.002 PHE G 168 TYR 0.007 0.002 TYR C 169 ARG 0.007 0.001 ARG C 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 1.325 Fit side-chains REVERT: A 25 LYS cc_start: 0.8520 (mttt) cc_final: 0.8102 (mttm) REVERT: A 104 ILE cc_start: 0.8183 (mt) cc_final: 0.7967 (mm) REVERT: A 185 MET cc_start: 0.8120 (mtm) cc_final: 0.7909 (mtt) REVERT: C 25 LYS cc_start: 0.8489 (mttt) cc_final: 0.7958 (mttm) REVERT: E 25 LYS cc_start: 0.8594 (mttt) cc_final: 0.8159 (mttm) REVERT: G 25 LYS cc_start: 0.8520 (mttt) cc_final: 0.8101 (mttm) REVERT: G 104 ILE cc_start: 0.8181 (mt) cc_final: 0.7967 (mm) REVERT: G 185 MET cc_start: 0.8122 (mtm) cc_final: 0.7896 (mtt) REVERT: I 25 LYS cc_start: 0.8498 (mttt) cc_final: 0.7966 (mttm) REVERT: K 25 LYS cc_start: 0.8594 (mttt) cc_final: 0.8159 (mttm) outliers start: 20 outliers final: 11 residues processed: 180 average time/residue: 0.2514 time to fit residues: 61.9982 Evaluate side-chains 168 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 191 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 127 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10746 Z= 0.244 Angle : 0.577 7.325 14622 Z= 0.294 Chirality : 0.040 0.154 1638 Planarity : 0.005 0.039 1902 Dihedral : 4.695 42.900 1434 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.51 % Favored : 98.04 % Rotamer: Outliers : 1.16 % Allowed : 6.99 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.39 (0.23), residues: 1326 helix: 1.14 (0.17), residues: 870 sheet: -1.07 (0.46), residues: 54 loop : 1.04 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 117 HIS 0.002 0.001 HIS G 12 PHE 0.005 0.001 PHE E 32 TYR 0.008 0.001 TYR C 169 ARG 0.005 0.001 ARG C 162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 1.095 Fit side-chains REVERT: C 15 ILE cc_start: 0.8170 (mt) cc_final: 0.7938 (mm) REVERT: C 39 MET cc_start: 0.7338 (tpp) cc_final: 0.6764 (tpp) REVERT: C 144 MET cc_start: 0.8113 (tpp) cc_final: 0.7769 (tpp) REVERT: G 82 ARG cc_start: 0.6731 (ttm170) cc_final: 0.6357 (ttm170) REVERT: I 15 ILE cc_start: 0.8172 (mt) cc_final: 0.7939 (mm) REVERT: I 39 MET cc_start: 0.7335 (tpp) cc_final: 0.6763 (tpp) REVERT: I 144 MET cc_start: 0.8114 (tpp) cc_final: 0.7771 (tpp) outliers start: 13 outliers final: 9 residues processed: 175 average time/residue: 0.2318 time to fit residues: 56.0652 Evaluate side-chains 169 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain I residue 212 GLU Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.0030 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 65 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10746 Z= 0.212 Angle : 0.555 7.140 14622 Z= 0.283 Chirality : 0.040 0.145 1638 Planarity : 0.005 0.042 1902 Dihedral : 4.496 40.175 1434 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.66 % Favored : 97.89 % Rotamer: Outliers : 0.99 % Allowed : 8.24 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1326 helix: 1.37 (0.17), residues: 870 sheet: -0.64 (0.55), residues: 54 loop : 1.14 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 117 HIS 0.002 0.001 HIS E 12 PHE 0.007 0.001 PHE E 32 TYR 0.008 0.001 TYR I 169 ARG 0.003 0.000 ARG I 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 162 time to evaluate : 1.241 Fit side-chains REVERT: A 25 LYS cc_start: 0.8589 (mttt) cc_final: 0.8068 (mttm) REVERT: A 39 MET cc_start: 0.7407 (tpp) cc_final: 0.7002 (tpp) REVERT: A 82 ARG cc_start: 0.6961 (ttm170) cc_final: 0.6621 (ttm170) REVERT: C 39 MET cc_start: 0.7322 (tpp) cc_final: 0.6783 (tpp) REVERT: C 144 MET cc_start: 0.8052 (tpp) cc_final: 0.7741 (tpp) REVERT: C 176 GLN cc_start: 0.6679 (pt0) cc_final: 0.6454 (pm20) REVERT: G 25 LYS cc_start: 0.8588 (mttt) cc_final: 0.8067 (mttm) REVERT: G 39 MET cc_start: 0.7404 (tpp) cc_final: 0.6999 (tpp) REVERT: G 82 ARG cc_start: 0.6882 (ttm170) cc_final: 0.6499 (ttm170) REVERT: I 39 MET cc_start: 0.7322 (tpp) cc_final: 0.6781 (tpp) REVERT: I 144 MET cc_start: 0.8051 (tpp) cc_final: 0.7736 (tpp) REVERT: I 176 GLN cc_start: 0.6685 (pt0) cc_final: 0.6458 (pm20) outliers start: 11 outliers final: 7 residues processed: 169 average time/residue: 0.2537 time to fit residues: 59.5038 Evaluate side-chains 155 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10746 Z= 0.219 Angle : 0.559 7.193 14622 Z= 0.289 Chirality : 0.040 0.146 1638 Planarity : 0.005 0.044 1902 Dihedral : 4.459 37.472 1434 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.66 % Favored : 97.89 % Rotamer: Outliers : 1.43 % Allowed : 8.06 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.89 (0.23), residues: 1326 helix: 1.46 (0.18), residues: 864 sheet: -0.60 (0.58), residues: 54 loop : 1.39 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 117 HIS 0.002 0.001 HIS E 12 PHE 0.007 0.001 PHE K 32 TYR 0.008 0.001 TYR I 169 ARG 0.003 0.000 ARG C 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 1.288 Fit side-chains REVERT: A 82 ARG cc_start: 0.6869 (ttm170) cc_final: 0.6528 (ttm170) REVERT: C 39 MET cc_start: 0.7339 (tpp) cc_final: 0.6785 (tpp) REVERT: C 176 GLN cc_start: 0.6736 (pt0) cc_final: 0.6533 (pm20) REVERT: G 82 ARG cc_start: 0.6864 (ttm170) cc_final: 0.6508 (ttm170) REVERT: I 39 MET cc_start: 0.7339 (tpp) cc_final: 0.6782 (tpp) REVERT: I 176 GLN cc_start: 0.6747 (pt0) cc_final: 0.6538 (pm20) outliers start: 16 outliers final: 11 residues processed: 159 average time/residue: 0.2697 time to fit residues: 59.5038 Evaluate side-chains 153 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 142 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10746 Z= 0.233 Angle : 0.558 7.278 14622 Z= 0.288 Chirality : 0.040 0.149 1638 Planarity : 0.005 0.045 1902 Dihedral : 4.460 37.805 1434 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.96 % Favored : 97.59 % Rotamer: Outliers : 1.61 % Allowed : 8.51 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.86 (0.23), residues: 1326 helix: 1.44 (0.18), residues: 864 sheet: -0.55 (0.60), residues: 54 loop : 1.35 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 23 HIS 0.002 0.001 HIS K 12 PHE 0.007 0.001 PHE K 32 TYR 0.007 0.001 TYR C 169 ARG 0.003 0.000 ARG C 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 1.185 Fit side-chains REVERT: A 39 MET cc_start: 0.7381 (tpp) cc_final: 0.6942 (tpp) REVERT: A 82 ARG cc_start: 0.6858 (ttm170) cc_final: 0.6540 (ttm170) REVERT: A 185 MET cc_start: 0.8177 (mtm) cc_final: 0.7915 (mtt) REVERT: C 39 MET cc_start: 0.7410 (tpp) cc_final: 0.6841 (tpp) REVERT: G 39 MET cc_start: 0.7376 (tpp) cc_final: 0.6935 (tpp) REVERT: G 82 ARG cc_start: 0.6862 (ttm170) cc_final: 0.6517 (ttm170) REVERT: G 185 MET cc_start: 0.8178 (mtm) cc_final: 0.7901 (mtt) REVERT: I 39 MET cc_start: 0.7412 (tpp) cc_final: 0.6840 (tpp) outliers start: 18 outliers final: 14 residues processed: 161 average time/residue: 0.2435 time to fit residues: 53.9165 Evaluate side-chains 152 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.0270 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.0470 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN ** J 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10746 Z= 0.160 Angle : 0.524 7.417 14622 Z= 0.268 Chirality : 0.038 0.135 1638 Planarity : 0.005 0.044 1902 Dihedral : 4.299 35.503 1434 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.21 % Favored : 98.34 % Rotamer: Outliers : 1.08 % Allowed : 9.50 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.95 (0.23), residues: 1326 helix: 1.55 (0.17), residues: 870 sheet: -0.32 (0.63), residues: 54 loop : 1.22 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 23 HIS 0.001 0.000 HIS G 84 PHE 0.008 0.001 PHE E 32 TYR 0.007 0.001 TYR G 169 ARG 0.003 0.000 ARG K 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.154 Fit side-chains REVERT: A 39 MET cc_start: 0.7360 (tpp) cc_final: 0.6827 (tpp) REVERT: A 82 ARG cc_start: 0.6875 (ttm170) cc_final: 0.6559 (ttm170) REVERT: A 185 MET cc_start: 0.8203 (mtm) cc_final: 0.7952 (mtt) REVERT: C 39 MET cc_start: 0.7370 (tpp) cc_final: 0.6857 (tpp) REVERT: C 117 TRP cc_start: 0.6095 (m-10) cc_final: 0.5842 (m-10) REVERT: E 39 MET cc_start: 0.7135 (tpp) cc_final: 0.6818 (mmt) REVERT: F 319 GLN cc_start: 0.8160 (mm110) cc_final: 0.7488 (pt0) REVERT: G 39 MET cc_start: 0.7359 (tpp) cc_final: 0.6823 (tpp) REVERT: G 82 ARG cc_start: 0.6847 (ttm170) cc_final: 0.6523 (ttm170) REVERT: G 185 MET cc_start: 0.8190 (mtm) cc_final: 0.7931 (mtt) REVERT: I 39 MET cc_start: 0.7375 (tpp) cc_final: 0.6856 (tpp) REVERT: I 117 TRP cc_start: 0.6089 (m-10) cc_final: 0.5840 (m-10) REVERT: K 39 MET cc_start: 0.7135 (tpp) cc_final: 0.6821 (mmt) REVERT: L 319 GLN cc_start: 0.8156 (mm110) cc_final: 0.7484 (pt0) outliers start: 12 outliers final: 6 residues processed: 148 average time/residue: 0.2354 time to fit residues: 48.4126 Evaluate side-chains 146 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 77 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10746 Z= 0.244 Angle : 0.562 7.297 14622 Z= 0.289 Chirality : 0.040 0.148 1638 Planarity : 0.005 0.045 1902 Dihedral : 4.385 36.050 1434 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.96 % Favored : 97.59 % Rotamer: Outliers : 0.72 % Allowed : 10.30 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1326 helix: 1.46 (0.18), residues: 870 sheet: -0.33 (0.63), residues: 54 loop : 1.14 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 23 HIS 0.002 0.001 HIS E 12 PHE 0.007 0.001 PHE E 32 TYR 0.007 0.001 TYR C 169 ARG 0.003 0.000 ARG K 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 1.222 Fit side-chains REVERT: A 39 MET cc_start: 0.7389 (tpp) cc_final: 0.6884 (tpp) REVERT: A 82 ARG cc_start: 0.6829 (ttm170) cc_final: 0.6514 (ttm170) REVERT: A 185 MET cc_start: 0.8270 (mtm) cc_final: 0.8021 (mtt) REVERT: C 39 MET cc_start: 0.7400 (tpp) cc_final: 0.6869 (tpp) REVERT: C 117 TRP cc_start: 0.6109 (m-10) cc_final: 0.5873 (m-10) REVERT: C 144 MET cc_start: 0.7995 (tpp) cc_final: 0.7726 (tpt) REVERT: E 39 MET cc_start: 0.7206 (tpp) cc_final: 0.6878 (mmt) REVERT: F 319 GLN cc_start: 0.8166 (mm110) cc_final: 0.7587 (pt0) REVERT: G 39 MET cc_start: 0.7389 (tpp) cc_final: 0.6881 (tpp) REVERT: G 82 ARG cc_start: 0.6820 (ttm170) cc_final: 0.6495 (ttm170) REVERT: G 185 MET cc_start: 0.8269 (mtm) cc_final: 0.8007 (mtt) REVERT: I 39 MET cc_start: 0.7403 (tpp) cc_final: 0.6868 (tpp) REVERT: I 117 TRP cc_start: 0.6103 (m-10) cc_final: 0.5873 (m-10) REVERT: I 144 MET cc_start: 0.7994 (tpp) cc_final: 0.7726 (tpt) REVERT: K 39 MET cc_start: 0.7215 (tpp) cc_final: 0.6886 (mmt) REVERT: L 319 GLN cc_start: 0.8158 (mm110) cc_final: 0.7581 (pt0) outliers start: 8 outliers final: 6 residues processed: 152 average time/residue: 0.2616 time to fit residues: 54.6586 Evaluate side-chains 149 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 131 optimal weight: 0.0670 chunk 121 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10746 Z= 0.178 Angle : 0.531 7.312 14622 Z= 0.273 Chirality : 0.039 0.138 1638 Planarity : 0.005 0.045 1902 Dihedral : 4.278 35.764 1434 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.45 % Allowed : 1.51 % Favored : 98.04 % Rotamer: Outliers : 0.72 % Allowed : 10.66 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.91 (0.23), residues: 1326 helix: 1.55 (0.17), residues: 870 sheet: -0.17 (0.65), residues: 54 loop : 1.12 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 23 HIS 0.001 0.000 HIS G 84 PHE 0.008 0.001 PHE E 32 TYR 0.007 0.001 TYR C 169 ARG 0.003 0.000 ARG K 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 1.283 Fit side-chains REVERT: A 39 MET cc_start: 0.7334 (tpp) cc_final: 0.6816 (tpp) REVERT: A 82 ARG cc_start: 0.6854 (ttm170) cc_final: 0.6562 (ttm170) REVERT: A 185 MET cc_start: 0.8221 (mtm) cc_final: 0.7977 (mtt) REVERT: C 39 MET cc_start: 0.7388 (tpp) cc_final: 0.6855 (tpp) REVERT: C 117 TRP cc_start: 0.6091 (m-10) cc_final: 0.5870 (m-10) REVERT: C 144 MET cc_start: 0.8054 (tpp) cc_final: 0.7757 (tpt) REVERT: D 319 GLN cc_start: 0.8196 (mm110) cc_final: 0.7556 (pt0) REVERT: E 39 MET cc_start: 0.7152 (tpp) cc_final: 0.6808 (mmt) REVERT: E 187 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6022 (mp0) REVERT: F 319 GLN cc_start: 0.8129 (mm110) cc_final: 0.7573 (pt0) REVERT: G 39 MET cc_start: 0.7334 (tpp) cc_final: 0.6813 (tpp) REVERT: G 82 ARG cc_start: 0.6838 (ttm170) cc_final: 0.6533 (ttm170) REVERT: G 185 MET cc_start: 0.8221 (mtm) cc_final: 0.7964 (mtt) REVERT: I 39 MET cc_start: 0.7388 (tpp) cc_final: 0.6848 (tpp) REVERT: I 117 TRP cc_start: 0.6085 (m-10) cc_final: 0.5870 (m-10) REVERT: I 144 MET cc_start: 0.8056 (tpp) cc_final: 0.7759 (tpt) REVERT: J 319 GLN cc_start: 0.8194 (mm110) cc_final: 0.7555 (pt0) REVERT: K 39 MET cc_start: 0.7159 (tpp) cc_final: 0.6813 (mmt) REVERT: K 187 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6031 (mp0) REVERT: L 319 GLN cc_start: 0.8121 (mm110) cc_final: 0.7568 (pt0) outliers start: 8 outliers final: 6 residues processed: 149 average time/residue: 0.2416 time to fit residues: 49.7011 Evaluate side-chains 149 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain K residue 187 GLU Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 0.0670 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.203409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.174734 restraints weight = 10736.829| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.64 r_work: 0.3428 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10746 Z= 0.203 Angle : 0.539 7.285 14622 Z= 0.277 Chirality : 0.039 0.142 1638 Planarity : 0.005 0.045 1902 Dihedral : 4.279 36.662 1434 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.45 % Allowed : 2.11 % Favored : 97.44 % Rotamer: Outliers : 0.72 % Allowed : 10.75 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.93 (0.23), residues: 1326 helix: 1.58 (0.18), residues: 870 sheet: -0.12 (0.66), residues: 54 loop : 1.09 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 23 HIS 0.002 0.000 HIS K 12 PHE 0.008 0.001 PHE E 32 TYR 0.007 0.001 TYR I 169 ARG 0.003 0.000 ARG K 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2273.47 seconds wall clock time: 41 minutes 33.76 seconds (2493.76 seconds total)