Starting phenix.real_space_refine on Thu Feb 15 17:41:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0g_8947/02_2024/6e0g_8947.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0g_8947/02_2024/6e0g_8947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0g_8947/02_2024/6e0g_8947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0g_8947/02_2024/6e0g_8947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0g_8947/02_2024/6e0g_8947.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e0g_8947/02_2024/6e0g_8947.pdb" } resolution = 2.9 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= 0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 8240 2.51 5 N 2190 2.21 5 O 2420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12910 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1291 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain: "A" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1291 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain: "B" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1291 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain: "C" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1291 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain: "D" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1291 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain: "E" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1291 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain: "F" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1291 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain: "G" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1291 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain: "H" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1291 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Chain: "I" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1291 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Time building chain proxies: 7.24, per 1000 atoms: 0.56 Number of scatterers: 12910 At special positions: 0 Unit cell: (137.256, 142.416, 65.016, 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 60 16.00 O 2420 8.00 N 2190 7.00 C 8240 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: 4.69 Conformation dependent library (CDL) restraints added in 2.2 seconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 35 sheets defined 35.8% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS J 64 " --> pdb=" O ASN J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 82 through 90 Processing helix chain 'J' and resid 92 through 97 Processing helix chain 'J' and resid 109 through 118 Processing helix chain 'J' and resid 120 through 124 Processing helix chain 'J' and resid 139 through 145 Processing helix chain 'J' and resid 181 through 198 removed outlier: 3.531A pdb=" N ALA J 185 " --> pdb=" O ASN J 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS A 64 " --> pdb=" O ASN A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 181 through 198 removed outlier: 3.532A pdb=" N ALA A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS B 64 " --> pdb=" O ASN B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'B' and resid 181 through 198 removed outlier: 3.532A pdb=" N ALA B 185 " --> pdb=" O ASN B 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS C 64 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 181 through 198 removed outlier: 3.531A pdb=" N ALA C 185 " --> pdb=" O ASN C 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS D 64 " --> pdb=" O ASN D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 181 through 198 removed outlier: 3.531A pdb=" N ALA D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS E 64 " --> pdb=" O ASN E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 92 through 97 Processing helix chain 'E' and resid 109 through 118 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 139 through 145 Processing helix chain 'E' and resid 181 through 198 removed outlier: 3.531A pdb=" N ALA E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS F 64 " --> pdb=" O ASN F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 82 through 90 Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'F' and resid 109 through 118 Processing helix chain 'F' and resid 120 through 124 Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'F' and resid 181 through 198 removed outlier: 3.532A pdb=" N ALA F 185 " --> pdb=" O ASN F 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.518A pdb=" N LYS G 64 " --> pdb=" O ASN G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 82 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 109 through 118 Processing helix chain 'G' and resid 120 through 124 Processing helix chain 'G' and resid 139 through 145 Processing helix chain 'G' and resid 181 through 198 removed outlier: 3.532A pdb=" N ALA G 185 " --> pdb=" O ASN G 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.518A pdb=" N LYS H 64 " --> pdb=" O ASN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 82 through 90 Processing helix chain 'H' and resid 92 through 97 Processing helix chain 'H' and resid 109 through 118 Processing helix chain 'H' and resid 120 through 124 Processing helix chain 'H' and resid 139 through 145 Processing helix chain 'H' and resid 181 through 198 removed outlier: 3.531A pdb=" N ALA H 185 " --> pdb=" O ASN H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS I 64 " --> pdb=" O ASN I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 92 through 97 Processing helix chain 'I' and resid 109 through 118 Processing helix chain 'I' and resid 120 through 124 Processing helix chain 'I' and resid 139 through 145 Processing helix chain 'I' and resid 181 through 198 removed outlier: 3.531A pdb=" N ALA I 185 " --> pdb=" O ASN I 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 46 through 47 Processing sheet with id=AA2, first strand: chain 'J' and resid 50 through 51 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 135 removed outlier: 7.446A pdb=" N LEU J 134 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA J 104 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU A 134 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA A 104 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE J 154 " --> pdb=" O ILE J 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA7, first strand: chain 'A' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE A 154 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 47 Processing sheet with id=AA9, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AB1, first strand: chain 'B' and resid 133 through 135 removed outlier: 7.446A pdb=" N LEU B 134 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA B 104 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU F 134 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA F 104 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE B 154 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 46 through 47 Processing sheet with id=AB4, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AB5, first strand: chain 'C' and resid 133 through 135 removed outlier: 7.446A pdb=" N LEU C 134 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 104 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU G 134 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA G 104 " --> pdb=" O LEU G 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE C 154 " --> pdb=" O ILE C 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AB8, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB9, first strand: chain 'D' and resid 133 through 135 removed outlier: 7.446A pdb=" N LEU D 134 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA D 104 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU H 134 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA H 104 " --> pdb=" O LEU H 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE D 154 " --> pdb=" O ILE D 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 46 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 50 through 51 Processing sheet with id=AC4, first strand: chain 'E' and resid 133 through 135 removed outlier: 7.446A pdb=" N LEU E 134 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA E 104 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU I 134 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA I 104 " --> pdb=" O LEU I 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE E 154 " --> pdb=" O ILE E 149 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 46 through 47 Processing sheet with id=AC7, first strand: chain 'F' and resid 50 through 51 Processing sheet with id=AC8, first strand: chain 'F' and resid 148 through 149 removed outlier: 3.502A pdb=" N ILE F 154 " --> pdb=" O ILE F 149 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 46 through 47 Processing sheet with id=AD1, first strand: chain 'G' and resid 50 through 51 Processing sheet with id=AD2, first strand: chain 'G' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE G 154 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 46 through 47 Processing sheet with id=AD4, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=AD5, first strand: chain 'H' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE H 154 " --> pdb=" O ILE H 149 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 46 through 47 Processing sheet with id=AD7, first strand: chain 'I' and resid 50 through 51 Processing sheet with id=AD8, first strand: chain 'I' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE I 154 " --> pdb=" O ILE I 149 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1500 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: 4.00 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3620 1.33 - 1.45: 2287 1.45 - 1.57: 7163 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 13170 Sorted by residual: bond pdb=" CA LEU F 189 " pdb=" C LEU F 189 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.24e-02 6.50e+03 1.02e+01 bond pdb=" CA LEU E 189 " pdb=" C LEU E 189 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.24e-02 6.50e+03 1.02e+01 bond pdb=" CA LEU C 189 " pdb=" C LEU C 189 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.24e-02 6.50e+03 1.02e+01 bond pdb=" CA LEU B 189 " pdb=" C LEU B 189 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.24e-02 6.50e+03 1.00e+01 bond pdb=" CA LEU G 189 " pdb=" C LEU G 189 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.24e-02 6.50e+03 9.99e+00 ... (remaining 13165 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.83: 441 106.83 - 113.56: 7155 113.56 - 120.28: 4835 120.28 - 127.00: 5269 127.00 - 133.72: 130 Bond angle restraints: 17830 Sorted by residual: angle pdb=" N PHE E 192 " pdb=" CA PHE E 192 " pdb=" C PHE E 192 " ideal model delta sigma weight residual 111.82 105.56 6.26 1.16e+00 7.43e-01 2.91e+01 angle pdb=" N PHE G 192 " pdb=" CA PHE G 192 " pdb=" C PHE G 192 " ideal model delta sigma weight residual 111.82 105.56 6.26 1.16e+00 7.43e-01 2.91e+01 angle pdb=" N PHE H 192 " pdb=" CA PHE H 192 " pdb=" C PHE H 192 " ideal model delta sigma weight residual 111.82 105.57 6.25 1.16e+00 7.43e-01 2.91e+01 angle pdb=" N PHE C 192 " pdb=" CA PHE C 192 " pdb=" C PHE C 192 " ideal model delta sigma weight residual 111.82 105.58 6.24 1.16e+00 7.43e-01 2.89e+01 angle pdb=" N PHE B 192 " pdb=" CA PHE B 192 " pdb=" C PHE B 192 " ideal model delta sigma weight residual 111.82 105.59 6.23 1.16e+00 7.43e-01 2.89e+01 ... (remaining 17825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.69: 7430 15.69 - 31.37: 350 31.37 - 47.06: 60 47.06 - 62.75: 10 62.75 - 78.44: 10 Dihedral angle restraints: 7860 sinusoidal: 3100 harmonic: 4760 Sorted by residual: dihedral pdb=" CA TRP I 116 " pdb=" C TRP I 116 " pdb=" N VAL I 117 " pdb=" CA VAL I 117 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA TRP F 116 " pdb=" C TRP F 116 " pdb=" N VAL F 117 " pdb=" CA VAL F 117 " ideal model delta harmonic sigma weight residual 180.00 156.56 23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA TRP J 116 " pdb=" C TRP J 116 " pdb=" N VAL J 117 " pdb=" CA VAL J 117 " ideal model delta harmonic sigma weight residual 180.00 156.57 23.43 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 7857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1014 0.039 - 0.077: 599 0.077 - 0.116: 205 0.116 - 0.155: 136 0.155 - 0.194: 46 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CB VAL C 110 " pdb=" CA VAL C 110 " pdb=" CG1 VAL C 110 " pdb=" CG2 VAL C 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" CB VAL F 110 " pdb=" CA VAL F 110 " pdb=" CG1 VAL F 110 " pdb=" CG2 VAL F 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CB VAL H 110 " pdb=" CA VAL H 110 " pdb=" CG1 VAL H 110 " pdb=" CG2 VAL H 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 1997 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 116 " 0.028 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP I 116 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP I 116 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP I 116 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP I 116 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP I 116 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP I 116 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 116 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 116 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP I 116 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 116 " 0.028 2.00e-02 2.50e+03 2.49e-02 1.55e+01 pdb=" CG TRP A 116 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP A 116 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 116 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 116 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 116 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 116 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 116 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 116 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 116 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 116 " -0.028 2.00e-02 2.50e+03 2.48e-02 1.54e+01 pdb=" CG TRP B 116 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP B 116 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 116 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 116 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 116 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 116 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 116 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 116 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 116 " -0.006 2.00e-02 2.50e+03 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 179 2.60 - 3.18: 10776 3.18 - 3.75: 20200 3.75 - 4.33: 31088 4.33 - 4.90: 49695 Nonbonded interactions: 111938 Sorted by model distance: nonbonded pdb=" O GLU E 190 " pdb=" N GLN E 193 " model vdw 2.030 2.520 nonbonded pdb=" O GLU C 190 " pdb=" N GLN C 193 " model vdw 2.030 2.520 nonbonded pdb=" O GLU A 190 " pdb=" N GLN A 193 " model vdw 2.031 2.520 nonbonded pdb=" O GLU G 190 " pdb=" N GLN G 193 " model vdw 2.031 2.520 nonbonded pdb=" O GLU J 190 " pdb=" N GLN J 193 " model vdw 2.031 2.520 ... (remaining 111933 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.160 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 36.410 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 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 : 0.010 0.061 13170 Z= 0.663 Angle : 1.035 10.077 17830 Z= 0.595 Chirality : 0.064 0.194 2000 Planarity : 0.008 0.052 2320 Dihedral : 10.035 78.437 4800 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.75 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % 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: -3.72 (0.18), residues: 1630 helix: -4.10 (0.10), residues: 550 sheet: -2.55 (0.28), residues: 270 loop : -1.00 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.015 TRP I 116 HIS 0.011 0.003 HIS H 113 PHE 0.044 0.006 PHE C 88 TYR 0.037 0.005 TYR C 145 ARG 0.006 0.001 ARG I 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 165 LYS cc_start: 0.6588 (mttt) cc_final: 0.6295 (mmmt) REVERT: A 123 LYS cc_start: 0.7811 (mttt) cc_final: 0.7592 (mmtp) REVERT: B 57 ASP cc_start: 0.7173 (t0) cc_final: 0.6915 (t0) REVERT: B 165 LYS cc_start: 0.6391 (mttt) cc_final: 0.6090 (mmmt) REVERT: C 165 LYS cc_start: 0.6560 (mttt) cc_final: 0.6337 (mmmt) REVERT: E 165 LYS cc_start: 0.6449 (mttt) cc_final: 0.6181 (mmmt) REVERT: F 165 LYS cc_start: 0.6495 (mttt) cc_final: 0.6265 (mmmt) REVERT: F 190 GLU cc_start: 0.6766 (tt0) cc_final: 0.6236 (mt-10) REVERT: G 40 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6590 (pt0) REVERT: H 165 LYS cc_start: 0.6552 (mttt) cc_final: 0.6227 (mmmt) REVERT: I 165 LYS cc_start: 0.6283 (mttt) cc_final: 0.6052 (mmmt) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 1.3760 time to fit residues: 514.1372 Evaluate side-chains 292 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 44 GLN J 101 GLN J 118 ASN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN F 101 GLN ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13170 Z= 0.196 Angle : 0.596 6.249 17830 Z= 0.320 Chirality : 0.047 0.144 2000 Planarity : 0.005 0.051 2320 Dihedral : 5.470 23.837 1780 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.42 % Allowed : 9.93 % Favored : 85.65 % 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: -2.63 (0.19), residues: 1630 helix: -2.78 (0.14), residues: 550 sheet: -1.77 (0.31), residues: 270 loop : -0.77 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP J 116 HIS 0.005 0.001 HIS I 113 PHE 0.027 0.003 PHE H 71 TYR 0.017 0.002 TYR B 145 ARG 0.005 0.000 ARG E 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 317 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 165 LYS cc_start: 0.6262 (mttt) cc_final: 0.5940 (mmmt) REVERT: A 123 LYS cc_start: 0.7877 (mttt) cc_final: 0.7632 (mmtp) REVERT: C 129 MET cc_start: 0.7022 (tpp) cc_final: 0.6814 (tpt) REVERT: C 138 SER cc_start: 0.8437 (p) cc_final: 0.7666 (p) REVERT: D 140 GLU cc_start: 0.7097 (pt0) cc_final: 0.6761 (mt-10) REVERT: D 165 LYS cc_start: 0.6399 (mtmm) cc_final: 0.5615 (mmmt) REVERT: E 165 LYS cc_start: 0.6205 (mttt) cc_final: 0.5961 (mmmt) REVERT: F 75 MET cc_start: 0.7806 (ptm) cc_final: 0.7488 (ptt) REVERT: F 111 TYR cc_start: 0.7412 (m-80) cc_final: 0.7170 (m-80) REVERT: G 40 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6565 (pt0) REVERT: H 91 ARG cc_start: 0.7381 (mmm-85) cc_final: 0.7170 (mtp-110) outliers start: 61 outliers final: 24 residues processed: 354 average time/residue: 1.1721 time to fit residues: 453.4046 Evaluate side-chains 282 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 258 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 116 TRP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 116 TRP Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 116 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 116 TRP Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 116 TRP Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 116 TRP Chi-restraints excluded: chain I residue 138 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13170 Z= 0.227 Angle : 0.576 6.084 17830 Z= 0.308 Chirality : 0.047 0.146 2000 Planarity : 0.005 0.048 2320 Dihedral : 5.142 22.442 1780 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.49 % Allowed : 12.03 % Favored : 83.48 % 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: -1.69 (0.20), residues: 1630 helix: -1.49 (0.18), residues: 550 sheet: -1.43 (0.33), residues: 270 loop : -0.56 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP I 116 HIS 0.003 0.001 HIS A 113 PHE 0.024 0.003 PHE E 71 TYR 0.018 0.002 TYR B 145 ARG 0.006 0.001 ARG J 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 269 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: J 165 LYS cc_start: 0.6212 (mttt) cc_final: 0.5996 (mmmt) REVERT: A 40 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.5754 (mp0) REVERT: A 94 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: A 123 LYS cc_start: 0.7880 (mttt) cc_final: 0.7663 (mmtp) REVERT: B 116 TRP cc_start: 0.6465 (OUTLIER) cc_final: 0.6239 (t60) REVERT: C 129 MET cc_start: 0.7122 (tpp) cc_final: 0.6824 (tpt) REVERT: D 140 GLU cc_start: 0.7208 (pt0) cc_final: 0.6978 (mt-10) REVERT: D 165 LYS cc_start: 0.6069 (mtmm) cc_final: 0.5515 (mmmt) REVERT: E 165 LYS cc_start: 0.6114 (mttt) cc_final: 0.5878 (mmmt) REVERT: F 111 TYR cc_start: 0.7408 (m-80) cc_final: 0.7056 (m-80) REVERT: H 40 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.5572 (mp0) REVERT: H 80 VAL cc_start: 0.8079 (m) cc_final: 0.7814 (t) REVERT: I 91 ARG cc_start: 0.7458 (mmm-85) cc_final: 0.6999 (mtp-110) REVERT: I 165 LYS cc_start: 0.6299 (mttt) cc_final: 0.5935 (mmmt) outliers start: 62 outliers final: 27 residues processed: 297 average time/residue: 1.1568 time to fit residues: 375.2647 Evaluate side-chains 276 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 245 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 116 TRP Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 116 TRP Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 116 TRP Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 116 TRP Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain I residue 116 TRP Chi-restraints excluded: chain I residue 138 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13170 Z= 0.225 Angle : 0.565 6.361 17830 Z= 0.298 Chirality : 0.047 0.145 2000 Planarity : 0.004 0.046 2320 Dihedral : 4.965 22.196 1780 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.07 % Allowed : 11.88 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.21), residues: 1630 helix: -0.85 (0.20), residues: 550 sheet: -1.11 (0.34), residues: 270 loop : -0.46 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP I 116 HIS 0.003 0.001 HIS A 113 PHE 0.017 0.003 PHE E 71 TYR 0.016 0.002 TYR D 145 ARG 0.007 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 256 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.5815 (mp0) REVERT: A 94 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: A 123 LYS cc_start: 0.7860 (mttt) cc_final: 0.7625 (mmtp) REVERT: A 175 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6646 (m-30) REVERT: C 129 MET cc_start: 0.7082 (tpp) cc_final: 0.6763 (tpt) REVERT: D 140 GLU cc_start: 0.7181 (pt0) cc_final: 0.6957 (mt-10) REVERT: D 165 LYS cc_start: 0.5837 (mtmm) cc_final: 0.5320 (mmmt) REVERT: H 40 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.5434 (mp0) REVERT: H 80 VAL cc_start: 0.8067 (m) cc_final: 0.7813 (t) REVERT: H 91 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.7160 (mtp-110) REVERT: H 94 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: H 129 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6494 (tpt) REVERT: I 91 ARG cc_start: 0.7413 (mmm-85) cc_final: 0.7026 (mtp-110) outliers start: 70 outliers final: 35 residues processed: 294 average time/residue: 1.1530 time to fit residues: 370.5219 Evaluate side-chains 283 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 242 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 116 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 116 TRP Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 116 TRP Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 175 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13170 Z= 0.379 Angle : 0.668 7.073 17830 Z= 0.349 Chirality : 0.051 0.151 2000 Planarity : 0.005 0.047 2320 Dihedral : 5.384 20.671 1780 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.93 % Allowed : 12.68 % Favored : 82.39 % 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: -1.17 (0.22), residues: 1630 helix: -0.91 (0.20), residues: 550 sheet: -1.02 (0.36), residues: 270 loop : -0.41 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.006 TRP A 116 HIS 0.004 0.001 HIS H 113 PHE 0.019 0.003 PHE B 88 TYR 0.023 0.003 TYR D 145 ARG 0.009 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 262 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.5874 (mp0) REVERT: A 91 ARG cc_start: 0.7589 (mtp180) cc_final: 0.7299 (mtm-85) REVERT: A 94 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: A 123 LYS cc_start: 0.7951 (mttt) cc_final: 0.7726 (mmtp) REVERT: A 165 LYS cc_start: 0.6154 (mtmm) cc_final: 0.5301 (mmmt) REVERT: B 91 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.7355 (mtp180) REVERT: B 111 TYR cc_start: 0.7399 (m-80) cc_final: 0.7174 (m-80) REVERT: B 165 LYS cc_start: 0.6395 (mttt) cc_final: 0.5922 (mmmt) REVERT: C 129 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6931 (tpt) REVERT: D 98 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7502 (tt) REVERT: D 165 LYS cc_start: 0.6073 (mtmm) cc_final: 0.5673 (mmmt) REVERT: E 98 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7646 (tp) REVERT: E 129 MET cc_start: 0.6647 (tpt) cc_final: 0.6345 (tpt) REVERT: E 165 LYS cc_start: 0.6425 (mttt) cc_final: 0.6081 (mmmt) REVERT: F 129 MET cc_start: 0.7270 (tpp) cc_final: 0.7066 (tpt) REVERT: H 40 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.5382 (mp0) REVERT: H 75 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7540 (ptm) REVERT: H 123 LYS cc_start: 0.7758 (mmtp) cc_final: 0.7538 (mmtp) REVERT: I 94 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7253 (m-30) REVERT: I 165 LYS cc_start: 0.6404 (mttt) cc_final: 0.6056 (mmmt) outliers start: 68 outliers final: 39 residues processed: 295 average time/residue: 1.2947 time to fit residues: 417.5820 Evaluate side-chains 288 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 241 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 116 TRP Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 116 TRP Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain I residue 116 TRP Chi-restraints excluded: chain I residue 138 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13170 Z= 0.173 Angle : 0.574 14.876 17830 Z= 0.293 Chirality : 0.046 0.143 2000 Planarity : 0.004 0.052 2320 Dihedral : 4.730 20.944 1780 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.91 % Allowed : 14.49 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.21), residues: 1630 helix: -0.39 (0.20), residues: 550 sheet: -0.81 (0.35), residues: 270 loop : -0.48 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP I 116 HIS 0.005 0.001 HIS E 113 PHE 0.014 0.002 PHE E 71 TYR 0.017 0.002 TYR H 67 ARG 0.005 0.000 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 241 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 40 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5987 (mp0) REVERT: A 40 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.5616 (mp0) REVERT: A 94 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: A 123 LYS cc_start: 0.7940 (mttt) cc_final: 0.7699 (mmtp) REVERT: A 175 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6724 (m-30) REVERT: B 91 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7383 (mtp180) REVERT: B 175 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6807 (m-30) REVERT: C 129 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6875 (tpt) REVERT: D 140 GLU cc_start: 0.7070 (pt0) cc_final: 0.6638 (mt-10) REVERT: E 180 ARG cc_start: 0.7136 (mpp80) cc_final: 0.6208 (mpp80) REVERT: G 91 ARG cc_start: 0.7540 (mtm-85) cc_final: 0.7325 (mtp180) REVERT: G 175 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.6805 (m-30) REVERT: H 75 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7514 (ptm) REVERT: I 91 ARG cc_start: 0.7383 (mmm-85) cc_final: 0.7158 (mtp-110) outliers start: 54 outliers final: 26 residues processed: 269 average time/residue: 1.2323 time to fit residues: 360.8943 Evaluate side-chains 259 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 225 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 40 GLU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 116 TRP Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 116 TRP Chi-restraints excluded: chain I residue 175 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13170 Z= 0.203 Angle : 0.588 12.702 17830 Z= 0.297 Chirality : 0.047 0.146 2000 Planarity : 0.004 0.050 2320 Dihedral : 4.684 20.578 1780 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.13 % Allowed : 14.86 % Favored : 81.01 % 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: -0.66 (0.21), residues: 1630 helix: -0.05 (0.20), residues: 550 sheet: -0.72 (0.35), residues: 270 loop : -0.48 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP I 116 HIS 0.003 0.001 HIS I 113 PHE 0.014 0.002 PHE E 71 TYR 0.018 0.002 TYR H 67 ARG 0.005 0.000 ARG D 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 243 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.5699 (mp0) REVERT: A 94 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: A 123 LYS cc_start: 0.7926 (mttt) cc_final: 0.7679 (mmtp) REVERT: A 175 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6776 (m-30) REVERT: B 91 ARG cc_start: 0.7511 (mtm-85) cc_final: 0.7306 (mtp180) REVERT: B 175 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6779 (m-30) REVERT: C 40 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.5410 (mp0) REVERT: C 129 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6819 (tpt) REVERT: D 140 GLU cc_start: 0.7117 (pt0) cc_final: 0.6730 (mt-10) REVERT: F 40 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.5419 (mp0) REVERT: F 91 ARG cc_start: 0.7515 (mtm-85) cc_final: 0.7300 (mtp-110) REVERT: G 175 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6788 (m-30) REVERT: H 40 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.5556 (mp0) REVERT: H 75 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7549 (ptm) REVERT: H 94 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: I 129 MET cc_start: 0.6689 (tpt) cc_final: 0.6182 (tpp) outliers start: 57 outliers final: 33 residues processed: 269 average time/residue: 1.2189 time to fit residues: 357.9522 Evaluate side-chains 274 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 230 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 116 TRP Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 116 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 13170 Z= 0.448 Angle : 0.723 12.677 17830 Z= 0.371 Chirality : 0.053 0.166 2000 Planarity : 0.005 0.049 2320 Dihedral : 5.376 20.389 1780 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.99 % Allowed : 16.09 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.21), residues: 1630 helix: -0.55 (0.20), residues: 550 sheet: -0.98 (0.36), residues: 270 loop : -0.42 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.006 TRP E 116 HIS 0.004 0.001 HIS G 113 PHE 0.017 0.003 PHE B 88 TYR 0.023 0.003 TYR D 145 ARG 0.009 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 226 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 40 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6050 (mp0) REVERT: J 98 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7413 (tt) REVERT: A 40 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.5836 (mp0) REVERT: A 75 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7621 (ptm) REVERT: A 91 ARG cc_start: 0.7532 (mtm-85) cc_final: 0.6987 (mtm-85) REVERT: A 94 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7792 (m-30) REVERT: A 123 LYS cc_start: 0.7932 (mttt) cc_final: 0.7732 (mmtp) REVERT: A 129 MET cc_start: 0.7099 (tpp) cc_final: 0.6709 (tpt) REVERT: A 165 LYS cc_start: 0.6114 (mtmm) cc_final: 0.5237 (mmmt) REVERT: A 175 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6919 (m-30) REVERT: B 165 LYS cc_start: 0.6428 (mttt) cc_final: 0.5963 (mmmt) REVERT: C 40 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.5356 (mp0) REVERT: C 129 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6927 (tpt) REVERT: D 140 GLU cc_start: 0.7240 (pt0) cc_final: 0.6975 (mt-10) REVERT: D 165 LYS cc_start: 0.6050 (mtmm) cc_final: 0.5768 (mmmt) REVERT: D 193 GLN cc_start: 0.5557 (mt0) cc_final: 0.5288 (mt0) REVERT: E 40 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6136 (mp0) REVERT: E 94 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7506 (m-30) REVERT: E 165 LYS cc_start: 0.6519 (mttt) cc_final: 0.6163 (mmmt) REVERT: F 40 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.5346 (mp0) REVERT: F 129 MET cc_start: 0.7297 (tpp) cc_final: 0.6947 (tpt) REVERT: H 123 LYS cc_start: 0.7745 (mmtp) cc_final: 0.7521 (mmtp) REVERT: I 165 LYS cc_start: 0.6448 (mttt) cc_final: 0.6096 (mmmt) outliers start: 55 outliers final: 32 residues processed: 259 average time/residue: 1.2276 time to fit residues: 346.2665 Evaluate side-chains 265 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 222 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 40 GLU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 139 MET Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 116 TRP Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 116 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 0.0040 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 GLN ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13170 Z= 0.194 Angle : 0.590 13.837 17830 Z= 0.302 Chirality : 0.047 0.144 2000 Planarity : 0.004 0.051 2320 Dihedral : 4.723 20.942 1780 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.33 % Allowed : 16.74 % Favored : 79.93 % 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: -0.66 (0.21), residues: 1630 helix: 0.01 (0.20), residues: 550 sheet: -0.77 (0.36), residues: 270 loop : -0.51 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP I 116 HIS 0.003 0.001 HIS I 113 PHE 0.013 0.002 PHE E 71 TYR 0.022 0.002 TYR B 67 ARG 0.005 0.001 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 229 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.5563 (mp0) REVERT: A 129 MET cc_start: 0.7039 (tpp) cc_final: 0.6590 (tpt) REVERT: A 175 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6775 (m-30) REVERT: C 40 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5547 (mp0) REVERT: C 129 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6811 (tpt) REVERT: D 140 GLU cc_start: 0.7154 (pt0) cc_final: 0.6814 (mt-10) REVERT: E 91 ARG cc_start: 0.7382 (mtm-85) cc_final: 0.7077 (mtm180) REVERT: E 94 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: F 40 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5560 (mp0) REVERT: F 91 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.7296 (mtp-110) REVERT: H 75 MET cc_start: 0.7726 (ptt) cc_final: 0.7525 (ptm) REVERT: H 91 ARG cc_start: 0.7344 (mtm-85) cc_final: 0.6968 (mtm-85) REVERT: I 91 ARG cc_start: 0.7727 (mtp-110) cc_final: 0.7454 (mtm-85) REVERT: I 129 MET cc_start: 0.6634 (tpt) cc_final: 0.6407 (tpp) outliers start: 46 outliers final: 28 residues processed: 258 average time/residue: 1.2098 time to fit residues: 340.6582 Evaluate side-chains 247 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 213 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 116 TRP Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 116 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 105 optimal weight: 0.2980 chunk 159 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13170 Z= 0.348 Angle : 0.703 17.459 17830 Z= 0.352 Chirality : 0.050 0.148 2000 Planarity : 0.005 0.047 2320 Dihedral : 5.161 20.853 1780 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.97 % Allowed : 17.39 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.83 (0.21), residues: 1630 helix: -0.24 (0.20), residues: 550 sheet: -0.97 (0.36), residues: 270 loop : -0.47 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP E 116 HIS 0.004 0.001 HIS B 113 PHE 0.014 0.003 PHE J 45 TYR 0.029 0.003 TYR B 67 ARG 0.011 0.001 ARG C 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 228 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.5898 (mp0) REVERT: A 129 MET cc_start: 0.7032 (tpp) cc_final: 0.6583 (tpt) REVERT: A 175 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6808 (m-30) REVERT: B 165 LYS cc_start: 0.6452 (mttt) cc_final: 0.5988 (mmmt) REVERT: C 40 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.5347 (mp0) REVERT: C 129 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6926 (tpt) REVERT: D 140 GLU cc_start: 0.7158 (pt0) cc_final: 0.6742 (mt-10) REVERT: E 91 ARG cc_start: 0.7555 (mtm-85) cc_final: 0.7168 (mtm180) REVERT: E 94 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: E 165 LYS cc_start: 0.6288 (mttt) cc_final: 0.6050 (mmmt) REVERT: F 40 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.5331 (mp0) REVERT: F 91 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.7306 (mtp-110) REVERT: H 40 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.5512 (mp0) REVERT: H 75 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7538 (ptm) REVERT: I 129 MET cc_start: 0.6775 (tpt) cc_final: 0.6357 (tpp) REVERT: I 165 LYS cc_start: 0.6294 (mttt) cc_final: 0.6049 (mmmt) outliers start: 41 outliers final: 32 residues processed: 253 average time/residue: 1.2236 time to fit residues: 337.7201 Evaluate side-chains 262 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 222 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 116 TRP Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 116 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 GLN ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 ASN I 193 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.201509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.177114 restraints weight = 14169.200| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.68 r_work: 0.3764 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13170 Z= 0.318 Angle : 0.694 17.039 17830 Z= 0.348 Chirality : 0.049 0.143 2000 Planarity : 0.005 0.047 2320 Dihedral : 5.126 20.928 1780 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.41 % Allowed : 17.46 % Favored : 79.13 % 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: -0.84 (0.21), residues: 1630 helix: -0.25 (0.20), residues: 550 sheet: -1.03 (0.35), residues: 270 loop : -0.45 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP A 116 HIS 0.003 0.001 HIS B 113 PHE 0.014 0.003 PHE J 45 TYR 0.033 0.003 TYR C 67 ARG 0.009 0.001 ARG C 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5672.73 seconds wall clock time: 101 minutes 7.87 seconds (6067.87 seconds total)