Starting phenix.real_space_refine on Fri Jul 19 03:11:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhs_18416/07_2024/8qhs_18416.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhs_18416/07_2024/8qhs_18416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhs_18416/07_2024/8qhs_18416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhs_18416/07_2024/8qhs_18416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhs_18416/07_2024/8qhs_18416.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhs_18416/07_2024/8qhs_18416.cif" } resolution = 2.3 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= 0.055 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 30 5.16 5 C 3725 2.51 5 N 935 2.21 5 O 1522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 5": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "C GLU 5": "OE1" <-> "OE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C ASP 125": "OD1" <-> "OD2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 150": "OD1" <-> "OD2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "D GLU 5": "OE1" <-> "OE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D ASP 125": "OD1" <-> "OD2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 150": "OD1" <-> "OD2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "E GLU 5": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E ASP 86": "OD1" <-> "OD2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F ASP 86": "OD1" <-> "OD2" Residue "F ASP 125": "OD1" <-> "OD2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "F GLU 155": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6212 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1175 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 1 Chain: "C" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1175 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 1 Chain: "D" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1175 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 1 Chain: "E" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1175 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 1 Chain: "F" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1175 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 1 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Time building chain proxies: 4.82, per 1000 atoms: 0.78 Number of scatterers: 6212 At special positions: 0 Unit cell: (72.688, 99.12, 159.418, 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 30 16.00 O 1522 8.00 N 935 7.00 C 3725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS C 104 " distance=3.00 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: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 3 sheets defined 14.1% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.514A pdb=" N ASN A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 7' Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 87 through 100 Processing helix chain 'C' and resid 3 through 7 removed outlier: 3.906A pdb=" N LEU C 7 " --> pdb=" O PHE C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3 through 7' Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'D' and resid 3 through 7 removed outlier: 3.907A pdb=" N LEU D 7 " --> pdb=" O PHE D 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3 through 7' Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 87 through 100 Processing helix chain 'E' and resid 3 through 7 removed outlier: 3.906A pdb=" N LEU E 7 " --> pdb=" O PHE E 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3 through 7' Processing helix chain 'E' and resid 20 through 22 No H-bonds generated for 'chain 'E' and resid 20 through 22' Processing helix chain 'E' and resid 87 through 100 Processing helix chain 'F' and resid 3 through 7 removed outlier: 3.907A pdb=" N LEU F 7 " --> pdb=" O PHE F 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 3 through 7' Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 87 through 100 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 36 through 38 current: chain 'A' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 82 current: chain 'A' and resid 114 through 129 removed outlier: 6.281A pdb=" N LYS A 141 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR A 126 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER A 139 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE A 128 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR A 137 " --> pdb=" O PHE A 128 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 137 through 144 current: chain 'D' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 36 through 38 current: chain 'D' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 82 current: chain 'D' and resid 114 through 129 removed outlier: 6.281A pdb=" N LYS D 141 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR D 126 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER D 139 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE D 128 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR D 137 " --> pdb=" O PHE D 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 36 through 38 current: chain 'C' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 82 current: chain 'C' and resid 114 through 129 removed outlier: 6.282A pdb=" N LYS C 141 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR C 126 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER C 139 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE C 128 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR C 137 " --> pdb=" O PHE C 128 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 137 through 144 current: chain 'E' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 36 through 38 current: chain 'E' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 68 through 82 current: chain 'E' and resid 114 through 129 removed outlier: 6.281A pdb=" N LYS E 141 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR E 126 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER E 139 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE E 128 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR E 137 " --> pdb=" O PHE E 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 36 through 38 current: chain 'F' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 82 current: chain 'F' and resid 114 through 129 removed outlier: 6.281A pdb=" N LYS F 141 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR F 126 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER F 139 " --> pdb=" O TYR F 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE F 128 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR F 137 " --> pdb=" O PHE F 128 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 213 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: 1.26 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1915 1.34 - 1.45: 1011 1.45 - 1.57: 2989 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 5965 Sorted by residual: bond pdb=" C ILE D 56 " pdb=" O ILE D 56 " ideal model delta sigma weight residual 1.236 1.223 0.014 1.19e-02 7.06e+03 1.31e+00 bond pdb=" N GLY C 44 " pdb=" CA GLY C 44 " ideal model delta sigma weight residual 1.454 1.443 0.011 9.90e-03 1.02e+04 1.29e+00 bond pdb=" C ILE C 56 " pdb=" O ILE C 56 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.27e+00 bond pdb=" C ILE A 56 " pdb=" O ILE A 56 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.25e+00 bond pdb=" C ILE E 56 " pdb=" O ILE E 56 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.25e+00 ... (remaining 5960 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.26: 133 107.26 - 113.96: 3394 113.96 - 120.66: 2360 120.66 - 127.36: 2110 127.36 - 134.06: 38 Bond angle restraints: 8035 Sorted by residual: angle pdb=" C SER E 112 " pdb=" N LYS E 113 " pdb=" CA LYS E 113 " ideal model delta sigma weight residual 122.19 125.30 -3.11 1.41e+00 5.03e-01 4.87e+00 angle pdb=" C SER A 112 " pdb=" N LYS A 113 " pdb=" CA LYS A 113 " ideal model delta sigma weight residual 122.19 125.30 -3.11 1.41e+00 5.03e-01 4.87e+00 angle pdb=" C SER C 112 " pdb=" N LYS C 113 " pdb=" CA LYS C 113 " ideal model delta sigma weight residual 122.19 125.28 -3.09 1.41e+00 5.03e-01 4.80e+00 angle pdb=" C SER D 112 " pdb=" N LYS D 113 " pdb=" CA LYS D 113 " ideal model delta sigma weight residual 122.19 125.27 -3.08 1.41e+00 5.03e-01 4.76e+00 angle pdb=" C SER F 112 " pdb=" N LYS F 113 " pdb=" CA LYS F 113 " ideal model delta sigma weight residual 122.19 125.26 -3.07 1.41e+00 5.03e-01 4.75e+00 ... (remaining 8030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 3160 16.62 - 33.24: 202 33.24 - 49.85: 101 49.85 - 66.47: 55 66.47 - 83.09: 20 Dihedral angle restraints: 3538 sinusoidal: 1333 harmonic: 2205 Sorted by residual: dihedral pdb=" CA ALA F 121 " pdb=" C ALA F 121 " pdb=" N ILE F 122 " pdb=" CA ILE F 122 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ALA A 121 " pdb=" C ALA A 121 " pdb=" N ILE A 122 " pdb=" CA ILE A 122 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ALA D 121 " pdb=" C ALA D 121 " pdb=" N ILE D 122 " pdb=" CA ILE D 122 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 453 0.028 - 0.055: 257 0.055 - 0.083: 115 0.083 - 0.110: 50 0.110 - 0.138: 20 Chirality restraints: 895 Sorted by residual: chirality pdb=" CA ILE F 122 " pdb=" N ILE F 122 " pdb=" C ILE F 122 " pdb=" CB ILE F 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE C 122 " pdb=" N ILE C 122 " pdb=" C ILE C 122 " pdb=" CB ILE C 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE E 122 " pdb=" N ILE E 122 " pdb=" C ILE E 122 " pdb=" CB ILE E 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 892 not shown) Planarity restraints: 1035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 101 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO E 102 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO E 102 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 102 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 101 " -0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO D 102 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 102 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 102 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 101 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO F 102 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO F 102 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 102 " -0.016 5.00e-02 4.00e+02 ... (remaining 1032 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 215 2.65 - 3.21: 5559 3.21 - 3.78: 10780 3.78 - 4.34: 14721 4.34 - 4.90: 22938 Nonbonded interactions: 54213 Sorted by model distance: nonbonded pdb=" OD1 ASP E 60 " pdb=" O HOH E 201 " model vdw 2.089 2.440 nonbonded pdb=" O HOH C 222 " pdb=" O HOH C 243 " model vdw 2.147 2.440 nonbonded pdb=" OD1 ASP F 150 " pdb=" OG1 THR F 152 " model vdw 2.158 2.440 nonbonded pdb=" OD1 ASP D 150 " pdb=" OG1 THR D 152 " model vdw 2.159 2.440 nonbonded pdb=" OD1 ASP C 150 " pdb=" OG1 THR C 152 " model vdw 2.159 2.440 ... (remaining 54208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.740 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 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 : 0.006 0.029 5965 Z= 0.428 Angle : 0.676 4.546 8035 Z= 0.402 Chirality : 0.045 0.138 895 Planarity : 0.003 0.028 1035 Dihedral : 17.608 83.088 2135 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 6.56 % Allowed : 6.56 % Favored : 86.89 % 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: -0.18 (0.27), residues: 765 helix: -0.27 (0.50), residues: 70 sheet: 0.11 (0.29), residues: 290 loop : -0.15 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP D 75 HIS 0.005 0.003 HIS E 90 PHE 0.015 0.002 PHE D 128 TYR 0.006 0.002 TYR F 138 ARG 0.000 0.000 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 0.729 Fit side-chains REVERT: C 17 LYS cc_start: 0.7992 (ttmt) cc_final: 0.6800 (ttpt) REVERT: C 145 MET cc_start: 0.9166 (mtp) cc_final: 0.8881 (mtp) REVERT: E 17 LYS cc_start: 0.7917 (ttmt) cc_final: 0.6997 (ttpt) REVERT: F 145 MET cc_start: 0.9120 (mtp) cc_final: 0.8795 (mtp) outliers start: 40 outliers final: 1 residues processed: 141 average time/residue: 1.4951 time to fit residues: 218.6839 Evaluate side-chains 96 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 159 GLN C 43 GLN C 159 GLN D 43 GLN D 159 GLN E 43 GLN E 159 GLN F 43 GLN F 159 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5965 Z= 0.265 Angle : 0.484 4.183 8035 Z= 0.270 Chirality : 0.044 0.151 895 Planarity : 0.003 0.023 1035 Dihedral : 5.507 52.057 812 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.15 % Allowed : 13.93 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.28), residues: 765 helix: 1.70 (0.62), residues: 70 sheet: 0.24 (0.27), residues: 325 loop : 0.42 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 75 HIS 0.004 0.002 HIS E 90 PHE 0.017 0.002 PHE C 128 TYR 0.007 0.002 TYR F 83 ARG 0.001 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.694 Fit side-chains REVERT: C 17 LYS cc_start: 0.7960 (ttmt) cc_final: 0.6796 (ttpt) REVERT: E 17 LYS cc_start: 0.7905 (ttmt) cc_final: 0.6905 (ttpt) REVERT: E 113 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8208 (mppt) REVERT: F 113 LYS cc_start: 0.8487 (mtmm) cc_final: 0.7975 (mptp) outliers start: 7 outliers final: 0 residues processed: 99 average time/residue: 1.8006 time to fit residues: 184.3210 Evaluate side-chains 95 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 113 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 73 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5965 Z= 0.135 Angle : 0.379 3.050 8035 Z= 0.217 Chirality : 0.042 0.143 895 Planarity : 0.002 0.016 1035 Dihedral : 4.454 16.096 810 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.48 % Allowed : 14.26 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.29), residues: 765 helix: 2.45 (0.66), residues: 70 sheet: 0.38 (0.27), residues: 325 loop : 0.67 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 65 HIS 0.002 0.001 HIS F 90 PHE 0.010 0.001 PHE C 128 TYR 0.004 0.001 TYR E 96 ARG 0.001 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.725 Fit side-chains REVERT: C 5 GLU cc_start: 0.7789 (mp0) cc_final: 0.7181 (mp0) REVERT: C 17 LYS cc_start: 0.7853 (ttmt) cc_final: 0.6726 (ttpt) REVERT: E 17 LYS cc_start: 0.7794 (ttmt) cc_final: 0.6846 (ttpt) REVERT: E 113 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8136 (mptp) REVERT: F 113 LYS cc_start: 0.8410 (mtmm) cc_final: 0.7962 (mptp) outliers start: 9 outliers final: 1 residues processed: 103 average time/residue: 1.6947 time to fit residues: 180.5932 Evaluate side-chains 95 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain E residue 113 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5965 Z= 0.241 Angle : 0.458 3.723 8035 Z= 0.257 Chirality : 0.044 0.152 895 Planarity : 0.002 0.018 1035 Dihedral : 4.903 19.065 810 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.48 % Allowed : 14.26 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.29), residues: 765 helix: 2.36 (0.65), residues: 70 sheet: 0.38 (0.27), residues: 325 loop : 0.83 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 75 HIS 0.004 0.002 HIS A 90 PHE 0.014 0.002 PHE C 128 TYR 0.006 0.002 TYR A 138 ARG 0.001 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.722 Fit side-chains REVERT: C 5 GLU cc_start: 0.7779 (mp0) cc_final: 0.7173 (mp0) REVERT: C 17 LYS cc_start: 0.7926 (ttmt) cc_final: 0.6767 (ttpt) REVERT: E 17 LYS cc_start: 0.7895 (ttmt) cc_final: 0.6952 (ttpp) REVERT: F 113 LYS cc_start: 0.8443 (mtmm) cc_final: 0.7969 (mptp) outliers start: 9 outliers final: 1 residues processed: 105 average time/residue: 1.7864 time to fit residues: 193.8677 Evaluate side-chains 100 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 101 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 0.0030 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5965 Z= 0.339 Angle : 0.529 4.557 8035 Z= 0.294 Chirality : 0.045 0.155 895 Planarity : 0.003 0.022 1035 Dihedral : 5.247 20.230 810 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.46 % Allowed : 13.11 % Favored : 84.43 % 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: 0.99 (0.29), residues: 765 helix: 2.12 (0.63), residues: 70 sheet: 0.37 (0.27), residues: 325 loop : 0.84 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP E 75 HIS 0.005 0.003 HIS A 90 PHE 0.017 0.002 PHE C 128 TYR 0.009 0.002 TYR A 138 ARG 0.002 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.660 Fit side-chains REVERT: C 5 GLU cc_start: 0.7795 (mp0) cc_final: 0.7199 (mp0) REVERT: C 17 LYS cc_start: 0.7938 (ttmt) cc_final: 0.6744 (ttpt) REVERT: E 17 LYS cc_start: 0.7940 (ttmt) cc_final: 0.6892 (ttpt) REVERT: F 113 LYS cc_start: 0.8489 (mtmm) cc_final: 0.7983 (mptp) outliers start: 15 outliers final: 7 residues processed: 112 average time/residue: 1.7642 time to fit residues: 204.2121 Evaluate side-chains 104 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 155 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 9.9990 chunk 14 optimal weight: 0.0050 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 0.0010 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5965 Z= 0.124 Angle : 0.374 3.496 8035 Z= 0.216 Chirality : 0.042 0.141 895 Planarity : 0.002 0.018 1035 Dihedral : 4.344 15.499 810 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.98 % Allowed : 14.59 % Favored : 84.43 % 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: 1.34 (0.29), residues: 765 helix: 2.77 (0.68), residues: 70 sheet: 0.51 (0.28), residues: 315 loop : 1.08 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 65 HIS 0.002 0.001 HIS F 90 PHE 0.009 0.001 PHE C 128 TYR 0.005 0.001 TYR C 96 ARG 0.001 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.637 Fit side-chains REVERT: C 5 GLU cc_start: 0.7718 (mp0) cc_final: 0.7128 (mp0) REVERT: C 17 LYS cc_start: 0.7842 (ttmt) cc_final: 0.6717 (ttpt) REVERT: E 17 LYS cc_start: 0.7808 (ttmt) cc_final: 0.6886 (ttpt) REVERT: F 113 LYS cc_start: 0.8399 (mtmm) cc_final: 0.7988 (mptp) outliers start: 6 outliers final: 1 residues processed: 100 average time/residue: 1.7142 time to fit residues: 177.2692 Evaluate side-chains 94 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 0.0470 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5965 Z= 0.151 Angle : 0.395 3.124 8035 Z= 0.227 Chirality : 0.042 0.145 895 Planarity : 0.002 0.018 1035 Dihedral : 4.370 16.374 810 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.49 % Allowed : 15.41 % Favored : 84.10 % 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: 1.39 (0.29), residues: 765 helix: 2.76 (0.68), residues: 70 sheet: 0.52 (0.28), residues: 315 loop : 1.14 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 65 HIS 0.002 0.001 HIS A 90 PHE 0.011 0.001 PHE C 128 TYR 0.005 0.001 TYR A 83 ARG 0.000 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.705 Fit side-chains REVERT: C 5 GLU cc_start: 0.7745 (mp0) cc_final: 0.7146 (mp0) REVERT: C 17 LYS cc_start: 0.7843 (ttmt) cc_final: 0.6708 (ttpt) REVERT: E 17 LYS cc_start: 0.7798 (ttmt) cc_final: 0.6876 (ttpt) REVERT: F 113 LYS cc_start: 0.8419 (mtmm) cc_final: 0.8022 (mptp) outliers start: 3 outliers final: 3 residues processed: 99 average time/residue: 1.7778 time to fit residues: 181.8745 Evaluate side-chains 101 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain C residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5965 Z= 0.245 Angle : 0.468 3.736 8035 Z= 0.263 Chirality : 0.043 0.150 895 Planarity : 0.003 0.018 1035 Dihedral : 4.821 18.823 810 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.98 % Allowed : 15.41 % Favored : 83.61 % 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: 1.32 (0.29), residues: 765 helix: 2.46 (0.66), residues: 70 sheet: 0.49 (0.28), residues: 315 loop : 1.12 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 75 HIS 0.004 0.002 HIS A 90 PHE 0.014 0.002 PHE C 128 TYR 0.006 0.002 TYR A 138 ARG 0.001 0.000 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.862 Fit side-chains REVERT: A 62 VAL cc_start: 0.8618 (m) cc_final: 0.8398 (t) REVERT: C 5 GLU cc_start: 0.7752 (mp0) cc_final: 0.7149 (mp0) REVERT: C 17 LYS cc_start: 0.7924 (ttmt) cc_final: 0.6733 (ttpt) REVERT: E 17 LYS cc_start: 0.7879 (ttmt) cc_final: 0.6922 (ttpt) REVERT: F 113 LYS cc_start: 0.8479 (mtmm) cc_final: 0.8021 (mptp) outliers start: 6 outliers final: 4 residues processed: 106 average time/residue: 1.7968 time to fit residues: 196.9006 Evaluate side-chains 99 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain C residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5965 Z= 0.284 Angle : 0.498 4.124 8035 Z= 0.277 Chirality : 0.044 0.154 895 Planarity : 0.003 0.019 1035 Dihedral : 5.046 19.693 810 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.31 % Allowed : 15.57 % Favored : 83.11 % 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: 1.26 (0.29), residues: 765 helix: 2.25 (0.64), residues: 70 sheet: 0.48 (0.28), residues: 315 loop : 1.10 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 75 HIS 0.005 0.003 HIS A 90 PHE 0.016 0.002 PHE C 128 TYR 0.007 0.002 TYR A 138 ARG 0.002 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.642 Fit side-chains REVERT: A 62 VAL cc_start: 0.8646 (m) cc_final: 0.8430 (t) REVERT: C 5 GLU cc_start: 0.7777 (mp0) cc_final: 0.7167 (mp0) REVERT: C 17 LYS cc_start: 0.7932 (ttmt) cc_final: 0.6732 (ttpt) REVERT: E 17 LYS cc_start: 0.7912 (ttmt) cc_final: 0.6941 (ttpt) REVERT: F 113 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8050 (mptp) outliers start: 8 outliers final: 6 residues processed: 104 average time/residue: 1.8389 time to fit residues: 197.3972 Evaluate side-chains 103 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain E residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5965 Z= 0.173 Angle : 0.422 4.232 8035 Z= 0.240 Chirality : 0.042 0.145 895 Planarity : 0.002 0.019 1035 Dihedral : 4.572 17.307 810 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.82 % Allowed : 16.72 % Favored : 82.46 % 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: 1.40 (0.29), residues: 765 helix: 2.65 (0.67), residues: 70 sheet: 0.51 (0.28), residues: 315 loop : 1.19 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 65 HIS 0.003 0.002 HIS A 90 PHE 0.012 0.001 PHE C 128 TYR 0.005 0.001 TYR E 96 ARG 0.000 0.000 ARG D 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.687 Fit side-chains REVERT: C 5 GLU cc_start: 0.7750 (mp0) cc_final: 0.7150 (mp0) REVERT: C 17 LYS cc_start: 0.7871 (ttmt) cc_final: 0.6717 (ttpt) REVERT: E 17 LYS cc_start: 0.7827 (ttmt) cc_final: 0.6897 (ttpt) REVERT: F 113 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8041 (mptp) outliers start: 5 outliers final: 5 residues processed: 99 average time/residue: 1.8099 time to fit residues: 185.0978 Evaluate side-chains 97 residues out of total 610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 103 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.106718 restraints weight = 5936.563| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.06 r_work: 0.3157 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5965 Z= 0.171 Angle : 0.417 3.553 8035 Z= 0.238 Chirality : 0.042 0.145 895 Planarity : 0.003 0.019 1035 Dihedral : 4.513 17.253 810 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.82 % Allowed : 16.72 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.29), residues: 765 helix: 2.71 (0.67), residues: 70 sheet: 0.49 (0.28), residues: 315 loop : 1.22 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 65 HIS 0.003 0.002 HIS A 90 PHE 0.012 0.001 PHE C 128 TYR 0.005 0.001 TYR F 138 ARG 0.000 0.000 ARG E 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3524.20 seconds wall clock time: 62 minutes 4.34 seconds (3724.34 seconds total)