Starting phenix.real_space_refine on Thu Feb 15 06:04:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfs_25879/02_2024/7tfs_25879_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfs_25879/02_2024/7tfs_25879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfs_25879/02_2024/7tfs_25879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfs_25879/02_2024/7tfs_25879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfs_25879/02_2024/7tfs_25879_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfs_25879/02_2024/7tfs_25879_updated.pdb" } resolution = 4.3 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 ------------------------------------------------------------------------------- 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= 0.017 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: 5 Type Number sf(0) Gaussians Fe 28 7.16 5 S 91 5.16 5 C 7168 2.51 5 N 1918 2.21 5 O 2177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11382 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1626 Unusual residues: {'HEC': 4} Classifications: {'peptide': 202, 'undetermined': 4} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 190, None: 4} Not linked: pdbres="LYS B 231 " pdbres="HEC B 301 " Not linked: pdbres="HEC B 301 " pdbres="HEC B 302 " Not linked: pdbres="HEC B 302 " pdbres="HEC B 303 " Not linked: pdbres="HEC B 303 " pdbres="HEC B 304 " Chain: "C" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1626 Unusual residues: {'HEC': 4} Classifications: {'peptide': 202, 'undetermined': 4} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 190, None: 4} Not linked: pdbres="LYS C 231 " pdbres="HEC C 301 " Not linked: pdbres="HEC C 301 " pdbres="HEC C 302 " Not linked: pdbres="HEC C 302 " pdbres="HEC C 303 " Not linked: pdbres="HEC C 303 " pdbres="HEC C 304 " Chain: "D" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1626 Unusual residues: {'HEC': 4} Classifications: {'peptide': 202, 'undetermined': 4} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 190, None: 4} Not linked: pdbres="LYS D 231 " pdbres="HEC D 301 " Not linked: pdbres="HEC D 301 " pdbres="HEC D 302 " Not linked: pdbres="HEC D 302 " pdbres="HEC D 303 " Not linked: pdbres="HEC D 303 " pdbres="HEC D 304 " Chain: "A" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1626 Unusual residues: {'HEC': 4} Classifications: {'peptide': 202, 'undetermined': 4} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 190, None: 4} Not linked: pdbres="LYS A 231 " pdbres="HEC A 301 " Not linked: pdbres="HEC A 301 " pdbres="HEC A 302 " Not linked: pdbres="HEC A 302 " pdbres="HEC A 303 " Not linked: pdbres="HEC A 303 " pdbres="HEC A 304 " Chain: "E" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1626 Unusual residues: {'HEC': 4} Classifications: {'peptide': 202, 'undetermined': 4} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 190, None: 4} Not linked: pdbres="LYS E 231 " pdbres="HEC E 301 " Not linked: pdbres="HEC E 301 " pdbres="HEC E 302 " Not linked: pdbres="HEC E 302 " pdbres="HEC E 303 " Not linked: pdbres="HEC E 303 " pdbres="HEC E 304 " Chain: "F" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1626 Unusual residues: {'HEC': 4} Classifications: {'peptide': 202, 'undetermined': 4} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 190, None: 4} Not linked: pdbres="LYS F 231 " pdbres="HEC F 301 " Not linked: pdbres="HEC F 301 " pdbres="HEC F 302 " Not linked: pdbres="HEC F 302 " pdbres="HEC F 303 " Not linked: pdbres="HEC F 303 " pdbres="HEC F 304 " Chain: "G" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1626 Unusual residues: {'HEC': 4} Classifications: {'peptide': 202, 'undetermined': 4} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 190, None: 4} Not linked: pdbres="LYS G 231 " pdbres="HEC G 301 " Not linked: pdbres="HEC G 301 " pdbres="HEC G 302 " Not linked: pdbres="HEC G 302 " pdbres="HEC G 303 " Not linked: pdbres="HEC G 303 " pdbres="HEC G 304 " Time building chain proxies: 6.34, per 1000 atoms: 0.56 Number of scatterers: 11382 At special positions: 0 Unit cell: (72.36, 72.36, 267.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 28 26.01 S 91 16.00 O 2177 8.00 N 1918 7.00 C 7168 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=96, symmetry=0 Number of additional bonds: simple=96, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.76 Conformation dependent library (CDL) restraints added in 2.2 seconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 7 sheets defined 16.3% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 99 through 106 removed outlier: 4.152A pdb=" N CYS B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 157 through 163 Processing helix chain 'B' and resid 224 through 229 removed outlier: 4.050A pdb=" N CYS B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 99 through 106 removed outlier: 4.152A pdb=" N CYS C 106 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 157 through 163 Processing helix chain 'C' and resid 224 through 229 removed outlier: 4.050A pdb=" N CYS C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 53 No H-bonds generated for 'chain 'D' and resid 51 through 53' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 99 through 106 removed outlier: 4.151A pdb=" N CYS D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 157 through 163 Processing helix chain 'D' and resid 224 through 229 removed outlier: 4.050A pdb=" N CYS D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 99 through 106 removed outlier: 4.151A pdb=" N CYS A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 157 through 163 Processing helix chain 'A' and resid 224 through 229 removed outlier: 4.050A pdb=" N CYS A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 53 No H-bonds generated for 'chain 'E' and resid 51 through 53' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 99 through 106 removed outlier: 4.152A pdb=" N CYS E 106 " --> pdb=" O PHE E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 131 No H-bonds generated for 'chain 'E' and resid 129 through 131' Processing helix chain 'E' and resid 157 through 163 Processing helix chain 'E' and resid 224 through 229 removed outlier: 4.051A pdb=" N CYS E 229 " --> pdb=" O LEU E 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 99 through 106 removed outlier: 4.152A pdb=" N CYS F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 131 No H-bonds generated for 'chain 'F' and resid 129 through 131' Processing helix chain 'F' and resid 157 through 163 Processing helix chain 'F' and resid 224 through 229 removed outlier: 4.050A pdb=" N CYS F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 53 No H-bonds generated for 'chain 'G' and resid 51 through 53' Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 99 through 106 removed outlier: 4.151A pdb=" N CYS G 106 " --> pdb=" O PHE G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 131 No H-bonds generated for 'chain 'G' and resid 129 through 131' Processing helix chain 'G' and resid 157 through 163 Processing helix chain 'G' and resid 224 through 229 removed outlier: 4.050A pdb=" N CYS G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 168 through 170 Processing sheet with id= B, first strand: chain 'C' and resid 168 through 170 Processing sheet with id= C, first strand: chain 'D' and resid 168 through 170 Processing sheet with id= D, first strand: chain 'A' and resid 168 through 170 Processing sheet with id= E, first strand: chain 'E' and resid 168 through 170 Processing sheet with id= F, first strand: chain 'F' and resid 168 through 170 Processing sheet with id= G, first strand: chain 'G' and resid 168 through 170 77 hydrogen bonds defined for protein. 189 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 6.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 4802 1.40 - 1.58: 6748 1.58 - 1.75: 0 1.75 - 1.93: 126 1.93 - 2.10: 112 Bond restraints: 11788 Sorted by residual: bond pdb=" C3B HEC E 301 " pdb=" CAB HEC E 301 " ideal model delta sigma weight residual 1.544 1.562 -0.018 2.00e-02 2.50e+03 7.95e-01 bond pdb=" C3B HEC G 301 " pdb=" CAB HEC G 301 " ideal model delta sigma weight residual 1.544 1.562 -0.018 2.00e-02 2.50e+03 7.86e-01 bond pdb=" C3B HEC A 301 " pdb=" CAB HEC A 301 " ideal model delta sigma weight residual 1.544 1.562 -0.018 2.00e-02 2.50e+03 7.66e-01 bond pdb=" C3B HEC F 301 " pdb=" CAB HEC F 301 " ideal model delta sigma weight residual 1.544 1.561 -0.017 2.00e-02 2.50e+03 7.55e-01 bond pdb=" C3B HEC D 301 " pdb=" CAB HEC D 301 " ideal model delta sigma weight residual 1.544 1.561 -0.017 2.00e-02 2.50e+03 7.54e-01 ... (remaining 11783 not shown) Histogram of bond angle deviations from ideal: 87.42 - 105.70: 434 105.70 - 123.98: 14568 123.98 - 142.25: 1385 142.25 - 160.53: 0 160.53 - 178.81: 56 Bond angle restraints: 16443 Sorted by residual: angle pdb=" C ALA E 213 " pdb=" N PRO E 214 " pdb=" CD PRO E 214 " ideal model delta sigma weight residual 120.60 104.09 16.51 2.20e+00 2.07e-01 5.63e+01 angle pdb=" C ALA B 213 " pdb=" N PRO B 214 " pdb=" CD PRO B 214 " ideal model delta sigma weight residual 120.60 104.10 16.50 2.20e+00 2.07e-01 5.63e+01 angle pdb=" C ALA A 213 " pdb=" N PRO A 214 " pdb=" CD PRO A 214 " ideal model delta sigma weight residual 120.60 104.12 16.48 2.20e+00 2.07e-01 5.61e+01 angle pdb=" C ALA C 213 " pdb=" N PRO C 214 " pdb=" CD PRO C 214 " ideal model delta sigma weight residual 120.60 104.13 16.47 2.20e+00 2.07e-01 5.61e+01 angle pdb=" C ALA F 213 " pdb=" N PRO F 214 " pdb=" CD PRO F 214 " ideal model delta sigma weight residual 120.60 104.14 16.46 2.20e+00 2.07e-01 5.60e+01 ... (remaining 16438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 5733 17.11 - 34.23: 392 34.23 - 51.34: 84 51.34 - 68.46: 84 68.46 - 85.57: 42 Dihedral angle restraints: 6335 sinusoidal: 2415 harmonic: 3920 Sorted by residual: dihedral pdb=" CA ILE B 64 " pdb=" C ILE B 64 " pdb=" N PRO B 65 " pdb=" CA PRO B 65 " ideal model delta harmonic sigma weight residual -180.00 -143.17 -36.83 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" CA ILE E 64 " pdb=" C ILE E 64 " pdb=" N PRO E 65 " pdb=" CA PRO E 65 " ideal model delta harmonic sigma weight residual -180.00 -143.17 -36.83 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" CA ILE A 64 " pdb=" C ILE A 64 " pdb=" N PRO A 65 " pdb=" CA PRO A 65 " ideal model delta harmonic sigma weight residual 180.00 -143.18 -36.82 0 5.00e+00 4.00e-02 5.42e+01 ... (remaining 6332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1170 0.044 - 0.087: 387 0.087 - 0.131: 60 0.131 - 0.174: 7 0.174 - 0.218: 7 Chirality restraints: 1631 Sorted by residual: chirality pdb=" CA ILE D 64 " pdb=" N ILE D 64 " pdb=" C ILE D 64 " pdb=" CB ILE D 64 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ILE B 64 " pdb=" N ILE B 64 " pdb=" C ILE B 64 " pdb=" CB ILE B 64 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1628 not shown) Planarity restraints: 2065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA F 213 " -0.084 5.00e-02 4.00e+02 1.26e-01 2.52e+01 pdb=" N PRO F 214 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO F 214 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO F 214 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 213 " 0.083 5.00e-02 4.00e+02 1.26e-01 2.52e+01 pdb=" N PRO B 214 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO B 214 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO B 214 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 213 " -0.084 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO G 214 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO G 214 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO G 214 " -0.054 5.00e-02 4.00e+02 ... (remaining 2062 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 200 2.58 - 3.16: 9839 3.16 - 3.74: 17999 3.74 - 4.32: 23975 4.32 - 4.90: 37338 Nonbonded interactions: 89351 Sorted by model distance: nonbonded pdb=" NE2 HIS F 55 " pdb="FE HEC F 301 " model vdw 2.001 3.080 nonbonded pdb=" NE2 HIS B 55 " pdb="FE HEC B 301 " model vdw 2.001 3.080 nonbonded pdb=" NE2 HIS A 55 " pdb="FE HEC A 301 " model vdw 2.001 3.080 nonbonded pdb=" NE2 HIS D 55 " pdb="FE HEC D 301 " model vdw 2.001 3.080 nonbonded pdb=" NE2 HIS C 55 " pdb="FE HEC C 301 " model vdw 2.001 3.080 ... (remaining 89346 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' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 7.070 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 32.910 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11788 Z= 0.249 Angle : 0.957 16.507 16443 Z= 0.415 Chirality : 0.043 0.218 1631 Planarity : 0.010 0.126 2065 Dihedral : 16.802 85.571 3829 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 35.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -2.06 (0.20), residues: 1400 helix: 0.45 (0.39), residues: 154 sheet: -1.68 (0.45), residues: 70 loop : -1.77 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 67 HIS 0.012 0.002 HIS D 230 PHE 0.005 0.001 PHE D 215 TYR 0.002 0.001 TYR F 80 ARG 0.002 0.001 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.200 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: B 77 PHE cc_start: 0.7028 (m-10) cc_final: 0.6749 (m-10) REVERT: B 83 SER cc_start: 0.8054 (p) cc_final: 0.7792 (p) REVERT: B 148 ASP cc_start: 0.6455 (t70) cc_final: 0.6247 (t70) REVERT: B 174 ASN cc_start: 0.7817 (m-40) cc_final: 0.7553 (m-40) REVERT: C 83 SER cc_start: 0.7994 (p) cc_final: 0.7628 (p) REVERT: C 200 GLU cc_start: 0.8440 (tp30) cc_final: 0.8231 (tp30) REVERT: D 77 PHE cc_start: 0.7182 (m-10) cc_final: 0.6692 (m-10) REVERT: D 104 MET cc_start: 0.7909 (mtt) cc_final: 0.7666 (mtt) REVERT: D 174 ASN cc_start: 0.7891 (m-40) cc_final: 0.7549 (m-40) REVERT: D 231 LYS cc_start: 0.7641 (pptt) cc_final: 0.6608 (ttmt) REVERT: A 77 PHE cc_start: 0.7113 (m-10) cc_final: 0.6603 (m-10) REVERT: A 148 ASP cc_start: 0.6994 (t70) cc_final: 0.6753 (t70) REVERT: A 174 ASN cc_start: 0.7974 (m-40) cc_final: 0.7692 (m-40) REVERT: A 200 GLU cc_start: 0.8475 (tp30) cc_final: 0.8171 (tp30) REVERT: E 77 PHE cc_start: 0.7214 (m-10) cc_final: 0.6993 (m-10) REVERT: E 83 SER cc_start: 0.7852 (p) cc_final: 0.7632 (p) REVERT: E 150 PRO cc_start: 0.8906 (Cg_exo) cc_final: 0.8675 (Cg_endo) REVERT: F 67 TRP cc_start: 0.7281 (t-100) cc_final: 0.6095 (t-100) REVERT: F 77 PHE cc_start: 0.7228 (m-10) cc_final: 0.6962 (m-10) REVERT: F 102 PHE cc_start: 0.7363 (m-10) cc_final: 0.7147 (m-10) REVERT: F 104 MET cc_start: 0.8001 (mtt) cc_final: 0.7740 (mtt) REVERT: F 174 ASN cc_start: 0.7917 (m-40) cc_final: 0.7636 (m-40) REVERT: F 231 LYS cc_start: 0.7546 (pptt) cc_final: 0.6789 (ttmt) REVERT: G 67 TRP cc_start: 0.7500 (t-100) cc_final: 0.6966 (t-100) REVERT: G 83 SER cc_start: 0.7925 (p) cc_final: 0.7634 (p) REVERT: G 141 LEU cc_start: 0.8268 (tp) cc_final: 0.7986 (tp) REVERT: G 174 ASN cc_start: 0.8111 (m-40) cc_final: 0.7838 (m-40) REVERT: G 200 GLU cc_start: 0.8451 (tp30) cc_final: 0.8225 (tp30) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2196 time to fit residues: 83.7815 Evaluate side-chains 215 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.0170 chunk 106 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 0.0010 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 0.3980 chunk 109 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 0.0980 chunk 81 optimal weight: 0.0170 chunk 127 optimal weight: 0.7980 overall best weight: 0.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN C 152 ASN D 152 ASN A 152 ASN E 152 ASN F 152 ASN G 58 HIS G 152 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11788 Z= 0.247 Angle : 0.898 11.998 16443 Z= 0.330 Chirality : 0.041 0.202 1631 Planarity : 0.006 0.067 2065 Dihedral : 14.611 80.336 1659 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.21), residues: 1400 helix: 1.16 (0.40), residues: 147 sheet: -1.68 (0.50), residues: 70 loop : -1.55 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 67 HIS 0.006 0.001 HIS A 31 PHE 0.014 0.001 PHE E 215 TYR 0.012 0.001 TYR B 80 ARG 0.003 0.001 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: B 104 MET cc_start: 0.8102 (mtm) cc_final: 0.7893 (mtm) REVERT: B 231 LYS cc_start: 0.7931 (pptt) cc_final: 0.7108 (tttt) REVERT: C 77 PHE cc_start: 0.6990 (m-80) cc_final: 0.6774 (m-10) REVERT: C 83 SER cc_start: 0.7981 (p) cc_final: 0.7612 (p) REVERT: C 191 LYS cc_start: 0.8344 (tptp) cc_final: 0.8112 (tptp) REVERT: D 77 PHE cc_start: 0.7234 (m-80) cc_final: 0.6790 (m-10) REVERT: D 174 ASN cc_start: 0.7834 (m-40) cc_final: 0.7544 (m-40) REVERT: D 231 LYS cc_start: 0.7686 (pptt) cc_final: 0.6786 (ttmt) REVERT: A 77 PHE cc_start: 0.7119 (m-80) cc_final: 0.6606 (m-10) REVERT: A 148 ASP cc_start: 0.7092 (t70) cc_final: 0.6826 (t70) REVERT: A 174 ASN cc_start: 0.7849 (m-40) cc_final: 0.7646 (m-40) REVERT: A 231 LYS cc_start: 0.7836 (pptt) cc_final: 0.6894 (tttt) REVERT: F 47 THR cc_start: 0.6460 (t) cc_final: 0.6242 (t) REVERT: F 67 TRP cc_start: 0.6906 (t-100) cc_final: 0.6274 (t-100) REVERT: F 77 PHE cc_start: 0.7179 (m-80) cc_final: 0.6929 (m-10) REVERT: F 104 MET cc_start: 0.8014 (mtt) cc_final: 0.7745 (mtt) REVERT: F 174 ASN cc_start: 0.7856 (m-40) cc_final: 0.7630 (m-40) REVERT: F 231 LYS cc_start: 0.7543 (pptt) cc_final: 0.6777 (tttt) REVERT: G 67 TRP cc_start: 0.7498 (t-100) cc_final: 0.7003 (t-100) REVERT: G 83 SER cc_start: 0.7910 (p) cc_final: 0.7698 (p) REVERT: G 148 ASP cc_start: 0.7129 (t70) cc_final: 0.6834 (t70) REVERT: G 231 LYS cc_start: 0.6786 (pttp) cc_final: 0.6324 (ttmt) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2123 time to fit residues: 83.5275 Evaluate side-chains 211 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 6.9990 chunk 39 optimal weight: 0.0470 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN B 230 HIS C 152 ASN D 152 ASN A 152 ASN E 152 ASN F 152 ASN G 152 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11788 Z= 0.257 Angle : 0.906 14.495 16443 Z= 0.324 Chirality : 0.042 0.192 1631 Planarity : 0.004 0.040 2065 Dihedral : 14.480 86.956 1659 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -1.57 (0.22), residues: 1400 helix: 1.54 (0.43), residues: 147 sheet: -1.60 (0.50), residues: 70 loop : -1.49 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 67 HIS 0.015 0.002 HIS F 230 PHE 0.013 0.001 PHE E 215 TYR 0.013 0.002 TYR E 80 ARG 0.002 0.000 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.190 Fit side-chains revert: symmetry clash REVERT: B 128 MET cc_start: 0.6424 (tpt) cc_final: 0.5973 (tpp) REVERT: B 170 ASP cc_start: 0.6422 (t0) cc_final: 0.6001 (t0) REVERT: B 231 LYS cc_start: 0.7954 (pptt) cc_final: 0.7156 (tttt) REVERT: C 83 SER cc_start: 0.8020 (p) cc_final: 0.7572 (p) REVERT: D 77 PHE cc_start: 0.7260 (m-10) cc_final: 0.6919 (m-10) REVERT: D 128 MET cc_start: 0.6106 (tpt) cc_final: 0.5745 (tpp) REVERT: D 174 ASN cc_start: 0.7802 (m-40) cc_final: 0.7547 (m-40) REVERT: A 83 SER cc_start: 0.7982 (p) cc_final: 0.7728 (p) REVERT: A 148 ASP cc_start: 0.7378 (t70) cc_final: 0.7061 (t70) REVERT: A 231 LYS cc_start: 0.7955 (pptt) cc_final: 0.7096 (ttmt) REVERT: E 170 ASP cc_start: 0.6547 (t0) cc_final: 0.6214 (t0) REVERT: F 174 ASN cc_start: 0.7882 (m-40) cc_final: 0.7634 (m-40) REVERT: F 231 LYS cc_start: 0.8002 (pptt) cc_final: 0.6913 (tttt) REVERT: G 67 TRP cc_start: 0.7708 (t-100) cc_final: 0.7112 (t-100) REVERT: G 231 LYS cc_start: 0.6784 (pttp) cc_final: 0.6260 (tttt) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2295 time to fit residues: 87.8965 Evaluate side-chains 203 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN C 152 ASN D 152 ASN A 152 ASN E 152 ASN F 152 ASN G 152 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11788 Z= 0.240 Angle : 0.875 13.957 16443 Z= 0.314 Chirality : 0.042 0.212 1631 Planarity : 0.004 0.061 2065 Dihedral : 14.564 85.738 1659 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 6.49 % 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: -1.55 (0.21), residues: 1400 helix: 1.32 (0.42), residues: 147 sheet: -1.44 (0.52), residues: 70 loop : -1.45 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 67 HIS 0.013 0.001 HIS G 230 PHE 0.021 0.001 PHE B 102 TYR 0.010 0.002 TYR B 80 ARG 0.002 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.6142 (tpt) cc_final: 0.5625 (tpp) REVERT: B 231 LYS cc_start: 0.7879 (pptt) cc_final: 0.7185 (tttt) REVERT: C 83 SER cc_start: 0.7959 (p) cc_final: 0.7567 (p) REVERT: C 148 ASP cc_start: 0.7143 (t70) cc_final: 0.6921 (t70) REVERT: C 231 LYS cc_start: 0.7340 (pptt) cc_final: 0.7059 (pttm) REVERT: D 77 PHE cc_start: 0.7317 (m-10) cc_final: 0.7039 (m-10) REVERT: D 128 MET cc_start: 0.6186 (tpt) cc_final: 0.5700 (tpp) REVERT: D 135 ILE cc_start: 0.8539 (tp) cc_final: 0.8131 (tp) REVERT: D 174 ASN cc_start: 0.7706 (m-40) cc_final: 0.7443 (m-40) REVERT: A 148 ASP cc_start: 0.7277 (t70) cc_final: 0.6989 (t70) REVERT: A 231 LYS cc_start: 0.7514 (pptt) cc_final: 0.6943 (ttmt) REVERT: E 104 MET cc_start: 0.8004 (mtt) cc_final: 0.7801 (ttm) REVERT: E 148 ASP cc_start: 0.7157 (t70) cc_final: 0.6839 (t70) REVERT: E 206 LYS cc_start: 0.7791 (tttt) cc_final: 0.7584 (tptp) REVERT: F 174 ASN cc_start: 0.7924 (m-40) cc_final: 0.7717 (m-40) REVERT: F 231 LYS cc_start: 0.7608 (pptt) cc_final: 0.6830 (tttt) REVERT: G 67 TRP cc_start: 0.7869 (t-100) cc_final: 0.7377 (t-100) REVERT: G 83 SER cc_start: 0.7897 (p) cc_final: 0.7659 (p) REVERT: G 231 LYS cc_start: 0.6591 (pttp) cc_final: 0.6212 (ttmt) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2147 time to fit residues: 76.8552 Evaluate side-chains 204 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 0.0040 chunk 115 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 121 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN C 152 ASN D 152 ASN A 152 ASN E 152 ASN F 152 ASN G 152 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11788 Z= 0.211 Angle : 0.822 12.569 16443 Z= 0.298 Chirality : 0.041 0.210 1631 Planarity : 0.005 0.068 2065 Dihedral : 14.597 84.693 1659 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -1.45 (0.22), residues: 1400 helix: 1.52 (0.43), residues: 147 sheet: -1.59 (0.51), residues: 70 loop : -1.38 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 67 HIS 0.011 0.001 HIS C 230 PHE 0.017 0.001 PHE B 102 TYR 0.008 0.001 TYR B 80 ARG 0.003 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.6107 (tpt) cc_final: 0.5574 (tpp) REVERT: B 231 LYS cc_start: 0.7789 (pptt) cc_final: 0.7140 (tttt) REVERT: C 83 SER cc_start: 0.7908 (p) cc_final: 0.7585 (p) REVERT: C 148 ASP cc_start: 0.7080 (t70) cc_final: 0.6825 (t70) REVERT: C 191 LYS cc_start: 0.8469 (tptp) cc_final: 0.8255 (tptp) REVERT: C 231 LYS cc_start: 0.7409 (pptt) cc_final: 0.7050 (pttm) REVERT: D 77 PHE cc_start: 0.7251 (m-10) cc_final: 0.6942 (m-10) REVERT: D 128 MET cc_start: 0.6155 (tpt) cc_final: 0.5652 (tpp) REVERT: D 174 ASN cc_start: 0.7775 (m-40) cc_final: 0.7481 (m-40) REVERT: A 83 SER cc_start: 0.7993 (p) cc_final: 0.7728 (p) REVERT: A 148 ASP cc_start: 0.7220 (t70) cc_final: 0.6859 (t70) REVERT: A 174 ASN cc_start: 0.7901 (m-40) cc_final: 0.7671 (m-40) REVERT: A 231 LYS cc_start: 0.7312 (pptt) cc_final: 0.6850 (ttmt) REVERT: E 77 PHE cc_start: 0.7272 (m-10) cc_final: 0.6880 (m-10) REVERT: E 104 MET cc_start: 0.8071 (mtt) cc_final: 0.7842 (ttm) REVERT: E 148 ASP cc_start: 0.7124 (t70) cc_final: 0.6783 (t70) REVERT: E 170 ASP cc_start: 0.6422 (t0) cc_final: 0.6093 (t0) REVERT: F 104 MET cc_start: 0.8196 (mtt) cc_final: 0.7909 (mtt) REVERT: F 174 ASN cc_start: 0.7780 (m-40) cc_final: 0.7532 (m-40) REVERT: F 231 LYS cc_start: 0.7409 (pptt) cc_final: 0.6882 (tppt) REVERT: G 67 TRP cc_start: 0.7956 (t-100) cc_final: 0.7358 (t-100) REVERT: G 231 LYS cc_start: 0.6537 (pttp) cc_final: 0.5930 (ttmt) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2164 time to fit residues: 78.9930 Evaluate side-chains 200 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 20.0000 chunk 26 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN C 31 HIS C 152 ASN D 31 HIS D 152 ASN A 152 ASN E 152 ASN F 152 ASN G 31 HIS G 152 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11788 Z= 0.238 Angle : 0.874 14.056 16443 Z= 0.309 Chirality : 0.042 0.209 1631 Planarity : 0.005 0.061 2065 Dihedral : 14.709 84.881 1659 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 5.19 % 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: -1.46 (0.22), residues: 1400 helix: 1.47 (0.43), residues: 147 sheet: -1.59 (0.54), residues: 70 loop : -1.38 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 67 HIS 0.008 0.001 HIS D 230 PHE 0.009 0.001 PHE E 215 TYR 0.008 0.002 TYR G 80 ARG 0.003 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.5912 (tpt) cc_final: 0.5381 (tpp) REVERT: B 231 LYS cc_start: 0.7373 (pptt) cc_final: 0.6898 (tttt) REVERT: C 83 SER cc_start: 0.7874 (p) cc_final: 0.7570 (p) REVERT: C 231 LYS cc_start: 0.7163 (pptt) cc_final: 0.6896 (pttm) REVERT: D 77 PHE cc_start: 0.7327 (m-10) cc_final: 0.7055 (m-10) REVERT: D 128 MET cc_start: 0.6233 (tpt) cc_final: 0.5676 (tpp) REVERT: D 174 ASN cc_start: 0.7625 (m-40) cc_final: 0.7374 (m-40) REVERT: A 83 SER cc_start: 0.7912 (p) cc_final: 0.7697 (p) REVERT: A 148 ASP cc_start: 0.7343 (t70) cc_final: 0.7039 (t70) REVERT: E 77 PHE cc_start: 0.7350 (m-10) cc_final: 0.7087 (m-10) REVERT: E 148 ASP cc_start: 0.7166 (t70) cc_final: 0.6876 (t70) REVERT: F 104 MET cc_start: 0.8249 (mtt) cc_final: 0.8022 (mtt) REVERT: F 174 ASN cc_start: 0.7804 (m-40) cc_final: 0.7586 (m-40) REVERT: G 67 TRP cc_start: 0.8113 (t-100) cc_final: 0.7539 (t-100) REVERT: G 206 LYS cc_start: 0.7775 (tttt) cc_final: 0.7499 (tptt) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2213 time to fit residues: 77.0801 Evaluate side-chains 189 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.0370 chunk 77 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 82 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN C 31 HIS C 152 ASN D 31 HIS D 152 ASN A 31 HIS A 152 ASN E 31 HIS E 152 ASN F 152 ASN G 152 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11788 Z= 0.191 Angle : 0.816 11.907 16443 Z= 0.295 Chirality : 0.041 0.202 1631 Planarity : 0.005 0.053 2065 Dihedral : 14.711 82.410 1659 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 5.19 % 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: -1.43 (0.22), residues: 1400 helix: 1.53 (0.43), residues: 147 sheet: -1.66 (0.53), residues: 70 loop : -1.35 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 67 HIS 0.016 0.001 HIS C 230 PHE 0.009 0.001 PHE E 215 TYR 0.007 0.001 TYR B 80 ARG 0.006 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: B 85 MET cc_start: 0.7861 (mtp) cc_final: 0.7352 (mpp) REVERT: B 128 MET cc_start: 0.5935 (tpt) cc_final: 0.5418 (tpp) REVERT: B 231 LYS cc_start: 0.7336 (pptt) cc_final: 0.6917 (tttt) REVERT: C 83 SER cc_start: 0.8015 (p) cc_final: 0.7629 (p) REVERT: C 148 ASP cc_start: 0.7111 (t70) cc_final: 0.6841 (t70) REVERT: C 191 LYS cc_start: 0.8502 (tptp) cc_final: 0.8274 (tptp) REVERT: C 231 LYS cc_start: 0.7051 (pptt) cc_final: 0.6849 (pttm) REVERT: D 77 PHE cc_start: 0.7258 (m-10) cc_final: 0.6919 (m-10) REVERT: D 148 ASP cc_start: 0.7392 (t70) cc_final: 0.7086 (t70) REVERT: D 174 ASN cc_start: 0.7610 (m-40) cc_final: 0.7366 (m-40) REVERT: A 83 SER cc_start: 0.7876 (p) cc_final: 0.7658 (p) REVERT: A 148 ASP cc_start: 0.7239 (t70) cc_final: 0.6887 (t70) REVERT: A 170 ASP cc_start: 0.6438 (t0) cc_final: 0.6109 (t0) REVERT: A 174 ASN cc_start: 0.7812 (m-40) cc_final: 0.7573 (m-40) REVERT: E 148 ASP cc_start: 0.6980 (t70) cc_final: 0.6669 (t70) REVERT: E 170 ASP cc_start: 0.6470 (t0) cc_final: 0.6142 (t0) REVERT: F 104 MET cc_start: 0.8103 (mtt) cc_final: 0.7855 (mtt) REVERT: F 174 ASN cc_start: 0.7748 (m-40) cc_final: 0.7523 (m-40) REVERT: G 67 TRP cc_start: 0.8197 (t-100) cc_final: 0.7497 (t-100) REVERT: G 141 LEU cc_start: 0.8130 (tp) cc_final: 0.7924 (tp) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2231 time to fit residues: 78.3801 Evaluate side-chains 194 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 0.0070 chunk 106 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN C 31 HIS C 152 ASN D 62 GLN D 152 ASN A 31 HIS A 152 ASN E 31 HIS E 152 ASN F 152 ASN G 31 HIS G 152 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 11788 Z= 0.372 Angle : 1.073 17.825 16443 Z= 0.376 Chirality : 0.046 0.233 1631 Planarity : 0.005 0.066 2065 Dihedral : 15.353 88.365 1659 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 1.30 % 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: -1.85 (0.21), residues: 1400 helix: 0.73 (0.43), residues: 147 sheet: -1.83 (0.55), residues: 70 loop : -1.61 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 67 HIS 0.019 0.002 HIS C 230 PHE 0.016 0.001 PHE F 102 TYR 0.014 0.002 TYR G 80 ARG 0.006 0.001 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 MET cc_start: 0.8148 (mtm) cc_final: 0.7915 (ttp) REVERT: B 128 MET cc_start: 0.6264 (tpt) cc_final: 0.5666 (tpp) REVERT: C 83 SER cc_start: 0.7912 (p) cc_final: 0.7630 (p) REVERT: C 148 ASP cc_start: 0.7554 (t70) cc_final: 0.7306 (t70) REVERT: C 191 LYS cc_start: 0.8524 (tptp) cc_final: 0.8318 (tptp) REVERT: D 128 MET cc_start: 0.7093 (tpp) cc_final: 0.5909 (tpp) REVERT: D 170 ASP cc_start: 0.6324 (t0) cc_final: 0.5938 (t0) REVERT: D 174 ASN cc_start: 0.7715 (m-40) cc_final: 0.7458 (m-40) REVERT: A 83 SER cc_start: 0.7717 (p) cc_final: 0.7484 (p) REVERT: A 102 PHE cc_start: 0.7668 (m-10) cc_final: 0.7450 (m-10) REVERT: A 148 ASP cc_start: 0.7216 (t70) cc_final: 0.6993 (t70) REVERT: E 148 ASP cc_start: 0.7391 (t70) cc_final: 0.7156 (t70) REVERT: F 174 ASN cc_start: 0.7923 (m-40) cc_final: 0.7720 (m-40) REVERT: G 67 TRP cc_start: 0.8536 (t-100) cc_final: 0.7986 (t-100) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2312 time to fit residues: 75.3284 Evaluate side-chains 190 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 0.0770 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 132 optimal weight: 0.0980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN C 31 HIS C 152 ASN D 152 ASN A 31 HIS A 152 ASN E 31 HIS E 152 ASN F 152 ASN G 152 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11788 Z= 0.208 Angle : 0.850 14.589 16443 Z= 0.307 Chirality : 0.041 0.204 1631 Planarity : 0.005 0.048 2065 Dihedral : 15.063 80.368 1659 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 6.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.21), residues: 1400 helix: 1.06 (0.43), residues: 147 sheet: -1.76 (0.55), residues: 70 loop : -1.53 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 67 HIS 0.009 0.001 HIS C 230 PHE 0.017 0.001 PHE A 102 TYR 0.020 0.002 TYR G 80 ARG 0.004 0.001 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 PHE cc_start: 0.6756 (m-10) cc_final: 0.6222 (m-10) REVERT: B 128 MET cc_start: 0.5931 (tpt) cc_final: 0.5343 (tpp) REVERT: C 83 SER cc_start: 0.7899 (p) cc_final: 0.7611 (p) REVERT: C 148 ASP cc_start: 0.7330 (t70) cc_final: 0.7039 (t70) REVERT: C 170 ASP cc_start: 0.6562 (t0) cc_final: 0.6327 (t0) REVERT: D 128 MET cc_start: 0.6766 (tpp) cc_final: 0.5607 (tpp) REVERT: D 148 ASP cc_start: 0.7467 (t70) cc_final: 0.7243 (t70) REVERT: D 174 ASN cc_start: 0.7654 (m-40) cc_final: 0.7393 (m-40) REVERT: A 83 SER cc_start: 0.7918 (p) cc_final: 0.7669 (p) REVERT: A 148 ASP cc_start: 0.7290 (t70) cc_final: 0.6935 (t70) REVERT: A 170 ASP cc_start: 0.6529 (t0) cc_final: 0.6213 (t0) REVERT: A 174 ASN cc_start: 0.7662 (m-40) cc_final: 0.7381 (m-40) REVERT: E 148 ASP cc_start: 0.7211 (t70) cc_final: 0.6865 (t70) REVERT: F 174 ASN cc_start: 0.7862 (m-40) cc_final: 0.7604 (m-40) REVERT: G 67 TRP cc_start: 0.8598 (t-100) cc_final: 0.7910 (t-100) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2268 time to fit residues: 76.6937 Evaluate side-chains 191 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 8.9990 chunk 63 optimal weight: 0.0970 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 128 optimal weight: 20.0000 chunk 111 optimal weight: 0.0010 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN C 31 HIS C 152 ASN D 152 ASN A 31 HIS A 152 ASN E 31 HIS E 152 ASN F 31 HIS F 152 ASN G 31 HIS G 152 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11788 Z= 0.260 Angle : 0.908 15.992 16443 Z= 0.326 Chirality : 0.043 0.212 1631 Planarity : 0.005 0.050 2065 Dihedral : 14.833 82.225 1659 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -1.81 (0.21), residues: 1400 helix: 0.91 (0.42), residues: 147 sheet: -2.07 (0.53), residues: 70 loop : -1.57 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 67 HIS 0.011 0.001 HIS C 230 PHE 0.014 0.001 PHE F 102 TYR 0.022 0.002 TYR G 80 ARG 0.005 0.000 ARG E 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 MET cc_start: 0.8131 (ttp) cc_final: 0.7842 (ttm) REVERT: B 128 MET cc_start: 0.5996 (tpt) cc_final: 0.5474 (tpp) REVERT: C 83 SER cc_start: 0.7978 (p) cc_final: 0.7622 (p) REVERT: D 128 MET cc_start: 0.6840 (tpp) cc_final: 0.5670 (tpp) REVERT: D 148 ASP cc_start: 0.7528 (t70) cc_final: 0.7321 (t70) REVERT: D 170 ASP cc_start: 0.6097 (t0) cc_final: 0.5571 (t0) REVERT: D 174 ASN cc_start: 0.7667 (m-40) cc_final: 0.7387 (m-40) REVERT: A 83 SER cc_start: 0.7825 (p) cc_final: 0.7566 (p) REVERT: A 148 ASP cc_start: 0.7379 (t70) cc_final: 0.7017 (t70) REVERT: A 174 ASN cc_start: 0.7655 (m-40) cc_final: 0.7422 (m-40) REVERT: E 148 ASP cc_start: 0.7418 (t70) cc_final: 0.6877 (t70) REVERT: G 67 TRP cc_start: 0.8673 (t-100) cc_final: 0.7932 (t-100) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2206 time to fit residues: 75.4723 Evaluate side-chains 191 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 0.0050 chunk 114 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN C 31 HIS C 152 ASN D 152 ASN A 31 HIS A 152 ASN E 31 HIS E 152 ASN F 31 HIS F 152 ASN G 31 HIS G 152 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.174957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.137107 restraints weight = 18917.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.141716 restraints weight = 14078.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.145139 restraints weight = 11334.406| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11788 Z= 0.312 Angle : 0.941 16.755 16443 Z= 0.339 Chirality : 0.044 0.220 1631 Planarity : 0.005 0.051 2065 Dihedral : 14.890 86.369 1659 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 2.60 % 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: -1.88 (0.21), residues: 1400 helix: 0.79 (0.43), residues: 147 sheet: -1.98 (0.55), residues: 70 loop : -1.63 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 67 HIS 0.012 0.001 HIS C 230 PHE 0.025 0.001 PHE C 102 TYR 0.024 0.002 TYR G 80 ARG 0.005 0.001 ARG E 69 =============================================================================== Job complete usr+sys time: 2573.72 seconds wall clock time: 47 minutes 50.65 seconds (2870.65 seconds total)