Starting phenix.real_space_refine on Fri Mar 15 19:05:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f34_28831/03_2024/8f34_28831_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f34_28831/03_2024/8f34_28831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f34_28831/03_2024/8f34_28831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f34_28831/03_2024/8f34_28831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f34_28831/03_2024/8f34_28831_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f34_28831/03_2024/8f34_28831_updated.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 8180 2.51 5 N 2085 2.21 5 O 2250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 115": "OD1" <-> "OD2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "E PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 115": "OD1" <-> "OD2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D ASP 176": "OD1" <-> "OD2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 115": "OD1" <-> "OD2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ASP 176": "OD1" <-> "OD2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 115": "OD1" <-> "OD2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12545 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "B" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'3CN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.11, per 1000 atoms: 0.57 Number of scatterers: 12545 At special positions: 0 Unit cell: (88.038, 88.038, 122.859, 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 2250 8.00 N 2085 7.00 C 8180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.69 Conformation dependent library (CDL) restraints added in 2.3 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 20 sheets defined 27.4% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'E' and resid 63 through 69 Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 209 through 224 removed outlier: 3.945A pdb=" N VAL E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP E 224 " --> pdb=" O TRP E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 244 Processing helix chain 'E' and resid 261 through 285 Processing helix chain 'E' and resid 304 through 316 Processing helix chain 'D' and resid 63 through 69 Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 209 through 224 removed outlier: 3.944A pdb=" N VAL D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP D 224 " --> pdb=" O TRP D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 244 Processing helix chain 'D' and resid 261 through 285 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'C' and resid 63 through 69 Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 209 through 224 removed outlier: 3.945A pdb=" N VAL C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP C 224 " --> pdb=" O TRP C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 244 Processing helix chain 'C' and resid 261 through 285 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 209 through 224 removed outlier: 3.945A pdb=" N VAL B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N PHE B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N TRP B 224 " --> pdb=" O TRP B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 244 Processing helix chain 'B' and resid 261 through 285 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'A' and resid 63 through 69 Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 209 through 224 removed outlier: 3.945A pdb=" N VAL A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP A 224 " --> pdb=" O TRP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 244 Processing helix chain 'A' and resid 261 through 285 Processing helix chain 'A' and resid 304 through 316 Processing sheet with id= A, first strand: chain 'E' and resid 12 through 14 Processing sheet with id= B, first strand: chain 'E' and resid 145 through 148 removed outlier: 7.041A pdb=" N VAL E 16 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N TYR E 148 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE E 18 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 76 through 78 Processing sheet with id= D, first strand: chain 'E' and resid 166 through 174 Processing sheet with id= E, first strand: chain 'D' and resid 12 through 14 Processing sheet with id= F, first strand: chain 'D' and resid 145 through 148 removed outlier: 7.041A pdb=" N VAL D 16 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N TYR D 148 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE D 18 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 76 through 78 Processing sheet with id= H, first strand: chain 'D' and resid 166 through 174 Processing sheet with id= I, first strand: chain 'C' and resid 12 through 14 Processing sheet with id= J, first strand: chain 'C' and resid 145 through 148 removed outlier: 7.041A pdb=" N VAL C 16 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N TYR C 148 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE C 18 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 76 through 78 Processing sheet with id= L, first strand: chain 'C' and resid 166 through 174 Processing sheet with id= M, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= N, first strand: chain 'B' and resid 145 through 148 removed outlier: 7.041A pdb=" N VAL B 16 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N TYR B 148 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE B 18 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 76 through 78 Processing sheet with id= P, first strand: chain 'B' and resid 166 through 174 Processing sheet with id= Q, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= R, first strand: chain 'A' and resid 145 through 148 removed outlier: 7.041A pdb=" N VAL A 16 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N TYR A 148 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 18 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 76 through 78 Processing sheet with id= T, first strand: chain 'A' and resid 166 through 174 530 hydrogen bonds defined for protein. 1560 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: 3.88 Time building geometry restraints manager: 5.07 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: 3892 1.34 - 1.46: 2331 1.46 - 1.57: 6607 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12880 Sorted by residual: bond pdb=" CA TRP C 160 " pdb=" C TRP C 160 " ideal model delta sigma weight residual 1.526 1.507 0.020 1.03e-02 9.43e+03 3.64e+00 bond pdb=" CA TRP E 160 " pdb=" C TRP E 160 " ideal model delta sigma weight residual 1.526 1.507 0.019 1.03e-02 9.43e+03 3.46e+00 bond pdb=" CA TRP A 160 " pdb=" C TRP A 160 " ideal model delta sigma weight residual 1.526 1.507 0.019 1.03e-02 9.43e+03 3.43e+00 bond pdb=" CA TRP B 160 " pdb=" C TRP B 160 " ideal model delta sigma weight residual 1.526 1.507 0.019 1.03e-02 9.43e+03 3.40e+00 bond pdb=" CA TRP D 160 " pdb=" C TRP D 160 " ideal model delta sigma weight residual 1.526 1.507 0.019 1.03e-02 9.43e+03 3.39e+00 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.77: 405 106.77 - 113.65: 6922 113.65 - 120.53: 5100 120.53 - 127.40: 4953 127.40 - 134.28: 165 Bond angle restraints: 17545 Sorted by residual: angle pdb=" C ASN B 60 " pdb=" N THR B 61 " pdb=" CA THR B 61 " ideal model delta sigma weight residual 121.54 130.85 -9.31 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C ASN E 60 " pdb=" N THR E 61 " pdb=" CA THR E 61 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C ASN C 60 " pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C ASN A 60 " pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta sigma weight residual 121.54 130.77 -9.23 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C ASN D 60 " pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.33e+01 ... (remaining 17540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6751 17.83 - 35.65: 644 35.65 - 53.48: 120 53.48 - 71.31: 10 71.31 - 89.13: 5 Dihedral angle restraints: 7530 sinusoidal: 3025 harmonic: 4505 Sorted by residual: dihedral pdb=" CA LEU B 118 " pdb=" C LEU B 118 " pdb=" N PHE B 119 " pdb=" CA PHE B 119 " ideal model delta harmonic sigma weight residual 180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU D 118 " pdb=" C LEU D 118 " pdb=" N PHE D 119 " pdb=" CA PHE D 119 " ideal model delta harmonic sigma weight residual -180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU A 118 " pdb=" C LEU A 118 " pdb=" N PHE A 119 " pdb=" CA PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 7527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1293 0.043 - 0.087: 396 0.087 - 0.130: 186 0.130 - 0.174: 59 0.174 - 0.217: 16 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CB ILE A 39 " pdb=" CA ILE A 39 " pdb=" CG1 ILE A 39 " pdb=" CG2 ILE A 39 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE D 39 " pdb=" CA ILE D 39 " pdb=" CG1 ILE D 39 " pdb=" CG2 ILE D 39 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE E 39 " pdb=" CA ILE E 39 " pdb=" CG1 ILE E 39 " pdb=" CG2 ILE E 39 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1947 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 176 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" CG ASP D 176 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP D 176 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP D 176 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 176 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" CG ASP A 176 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP A 176 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 176 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 176 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" CG ASP B 176 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP B 176 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP B 176 " -0.014 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4144 2.85 - 3.36: 10933 3.36 - 3.87: 21234 3.87 - 4.39: 24668 4.39 - 4.90: 42404 Nonbonded interactions: 103383 Sorted by model distance: nonbonded pdb=" O SER C 221 " pdb=" OG SER C 221 " model vdw 2.333 2.440 nonbonded pdb=" O SER B 221 " pdb=" OG SER B 221 " model vdw 2.334 2.440 nonbonded pdb=" O SER E 221 " pdb=" OG SER E 221 " model vdw 2.334 2.440 nonbonded pdb=" O SER D 221 " pdb=" OG SER D 221 " model vdw 2.335 2.440 nonbonded pdb=" O SER A 221 " pdb=" OG SER A 221 " model vdw 2.335 2.440 ... (remaining 103378 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' } 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: 1.140 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: 5.470 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 35.450 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 : 0.005 0.050 12880 Z= 0.295 Angle : 0.770 9.307 17545 Z= 0.417 Chirality : 0.056 0.217 1950 Planarity : 0.005 0.046 2235 Dihedral : 14.077 89.134 4620 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1525 helix: 0.24 (0.23), residues: 500 sheet: 1.44 (0.25), residues: 460 loop : -3.01 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 206 HIS 0.002 0.001 HIS C 177 PHE 0.028 0.002 PHE C 116 TYR 0.022 0.002 TYR D 248 ARG 0.002 0.000 ARG D 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.408 Fit side-chains REVERT: B 176 ASP cc_start: 0.7075 (t0) cc_final: 0.6855 (t0) REVERT: A 158 ASP cc_start: 0.6033 (p0) cc_final: 0.5282 (m-30) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2523 time to fit residues: 58.2457 Evaluate side-chains 145 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 5.9990 chunk 113 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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: 0.7773 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12880 Z= 0.320 Angle : 0.637 8.903 17545 Z= 0.323 Chirality : 0.049 0.138 1950 Planarity : 0.004 0.036 2235 Dihedral : 5.066 34.193 1690 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.58 % Allowed : 7.93 % Favored : 91.49 % 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: -0.36 (0.23), residues: 1525 helix: 0.92 (0.24), residues: 500 sheet: 1.71 (0.26), residues: 430 loop : -2.95 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 206 HIS 0.004 0.001 HIS A 284 PHE 0.021 0.002 PHE C 116 TYR 0.022 0.002 TYR C 248 ARG 0.002 0.001 ARG C 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 1.490 Fit side-chains REVERT: E 230 GLU cc_start: 0.5160 (mt-10) cc_final: 0.4528 (mm-30) REVERT: D 230 GLU cc_start: 0.5116 (mt-10) cc_final: 0.4462 (mm-30) REVERT: C 115 ASP cc_start: 0.7133 (t70) cc_final: 0.6540 (t70) REVERT: C 230 GLU cc_start: 0.5136 (mt-10) cc_final: 0.4523 (mm-30) REVERT: A 115 ASP cc_start: 0.7037 (t70) cc_final: 0.6532 (t70) REVERT: A 238 LEU cc_start: 0.7991 (mt) cc_final: 0.7762 (mt) outliers start: 8 outliers final: 8 residues processed: 161 average time/residue: 0.2385 time to fit residues: 56.3592 Evaluate side-chains 149 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 60 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 92 optimal weight: 0.0570 chunk 37 optimal weight: 0.0010 chunk 136 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 135 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 overall best weight: 0.4504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12880 Z= 0.125 Angle : 0.465 5.668 17545 Z= 0.238 Chirality : 0.043 0.122 1950 Planarity : 0.003 0.031 2235 Dihedral : 4.183 17.711 1690 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.51 % Allowed : 11.78 % Favored : 87.71 % 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: 0.06 (0.23), residues: 1525 helix: 1.42 (0.24), residues: 500 sheet: 1.80 (0.27), residues: 430 loop : -2.73 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 206 HIS 0.003 0.001 HIS D 284 PHE 0.013 0.001 PHE E 116 TYR 0.011 0.001 TYR E 248 ARG 0.001 0.000 ARG E 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 1.397 Fit side-chains REVERT: E 176 ASP cc_start: 0.7079 (t0) cc_final: 0.6859 (t0) REVERT: D 54 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6809 (mttm) REVERT: D 59 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7754 (tp30) REVERT: D 151 ASN cc_start: 0.7723 (m110) cc_final: 0.7406 (m-40) REVERT: D 230 GLU cc_start: 0.5011 (mt-10) cc_final: 0.4442 (mm-30) REVERT: C 115 ASP cc_start: 0.6822 (t70) cc_final: 0.6404 (t70) REVERT: C 174 ARG cc_start: 0.7410 (mmt180) cc_final: 0.7138 (ttm170) REVERT: B 59 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7753 (mm-30) REVERT: B 230 GLU cc_start: 0.5059 (mt-10) cc_final: 0.4557 (mm-30) REVERT: B 265 MET cc_start: 0.8050 (ttm) cc_final: 0.7836 (ttt) REVERT: A 115 ASP cc_start: 0.6674 (t70) cc_final: 0.6325 (t70) outliers start: 7 outliers final: 1 residues processed: 151 average time/residue: 0.2051 time to fit residues: 47.6147 Evaluate side-chains 145 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain B residue 150 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN D 151 ASN C 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 12880 Z= 0.473 Angle : 0.727 10.213 17545 Z= 0.370 Chirality : 0.052 0.199 1950 Planarity : 0.004 0.034 2235 Dihedral : 5.225 29.121 1690 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.45 % Allowed : 15.42 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1525 helix: 0.97 (0.24), residues: 495 sheet: 1.59 (0.26), residues: 425 loop : -2.94 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 206 HIS 0.004 0.001 HIS D 284 PHE 0.020 0.002 PHE C 116 TYR 0.026 0.003 TYR C 248 ARG 0.003 0.001 ARG E 286 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.443 Fit side-chains REVERT: E 31 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7352 (mt0) REVERT: E 161 TRP cc_start: 0.7503 (m-10) cc_final: 0.7287 (m-10) REVERT: E 163 ARG cc_start: 0.6944 (mmt180) cc_final: 0.6613 (mmt180) REVERT: D 151 ASN cc_start: 0.7831 (m-40) cc_final: 0.7594 (m-40) REVERT: D 230 GLU cc_start: 0.5192 (mt-10) cc_final: 0.4575 (mm-30) REVERT: C 174 ARG cc_start: 0.7451 (mmt180) cc_final: 0.7133 (ttm170) REVERT: A 31 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7151 (mt0) REVERT: A 115 ASP cc_start: 0.7247 (t70) cc_final: 0.6845 (t70) REVERT: A 151 ASN cc_start: 0.8006 (m110) cc_final: 0.7724 (m-40) outliers start: 20 outliers final: 16 residues processed: 169 average time/residue: 0.2808 time to fit residues: 66.1077 Evaluate side-chains 159 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 168 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 123 optimal weight: 0.3980 chunk 100 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN C 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12880 Z= 0.205 Angle : 0.540 7.563 17545 Z= 0.273 Chirality : 0.045 0.137 1950 Planarity : 0.003 0.035 2235 Dihedral : 4.521 17.942 1690 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.96 % Allowed : 15.93 % Favored : 82.11 % 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: -0.13 (0.23), residues: 1525 helix: 1.23 (0.24), residues: 500 sheet: 1.58 (0.26), residues: 430 loop : -2.70 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 206 HIS 0.004 0.001 HIS C 284 PHE 0.014 0.001 PHE E 116 TYR 0.017 0.001 TYR A 248 ARG 0.001 0.000 ARG E 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 147 time to evaluate : 1.462 Fit side-chains REVERT: D 151 ASN cc_start: 0.7743 (m-40) cc_final: 0.7462 (m-40) REVERT: D 230 GLU cc_start: 0.5125 (mt-10) cc_final: 0.4398 (mm-30) REVERT: C 174 ARG cc_start: 0.7417 (mmt180) cc_final: 0.7101 (ttm170) REVERT: C 233 GLN cc_start: 0.6935 (tp40) cc_final: 0.6699 (mt0) REVERT: A 151 ASN cc_start: 0.7907 (m110) cc_final: 0.7593 (m-40) outliers start: 27 outliers final: 21 residues processed: 170 average time/residue: 0.2641 time to fit residues: 64.3714 Evaluate side-chains 164 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN C 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12880 Z= 0.305 Angle : 0.604 8.559 17545 Z= 0.306 Chirality : 0.047 0.162 1950 Planarity : 0.003 0.036 2235 Dihedral : 4.666 19.806 1690 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.69 % Allowed : 16.29 % Favored : 81.02 % 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: -0.30 (0.23), residues: 1525 helix: 1.08 (0.24), residues: 500 sheet: 1.50 (0.26), residues: 430 loop : -2.80 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 206 HIS 0.003 0.001 HIS D 284 PHE 0.015 0.002 PHE B 116 TYR 0.018 0.002 TYR C 248 ARG 0.002 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 147 time to evaluate : 1.640 Fit side-chains REVERT: E 230 GLU cc_start: 0.5700 (OUTLIER) cc_final: 0.4727 (mm-30) REVERT: D 31 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.6716 (mt0) REVERT: D 117 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.5654 (mtt180) REVERT: D 151 ASN cc_start: 0.7785 (m-40) cc_final: 0.7485 (m-40) REVERT: D 230 GLU cc_start: 0.4977 (mt-10) cc_final: 0.4314 (mm-30) REVERT: C 31 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7124 (mt0) REVERT: C 174 ARG cc_start: 0.7416 (mmt180) cc_final: 0.7118 (ttm170) REVERT: B 31 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7337 (mt0) REVERT: A 151 ASN cc_start: 0.8034 (m110) cc_final: 0.7720 (m-40) outliers start: 37 outliers final: 25 residues processed: 181 average time/residue: 0.2553 time to fit residues: 66.1241 Evaluate side-chains 174 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 0.0050 chunk 66 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN C 151 ASN C 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12880 Z= 0.320 Angle : 0.616 8.662 17545 Z= 0.313 Chirality : 0.048 0.169 1950 Planarity : 0.003 0.036 2235 Dihedral : 4.747 19.946 1690 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.05 % Allowed : 16.95 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.23), residues: 1525 helix: 1.01 (0.24), residues: 500 sheet: 1.41 (0.26), residues: 430 loop : -2.77 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 206 HIS 0.003 0.001 HIS D 284 PHE 0.015 0.002 PHE E 116 TYR 0.019 0.002 TYR C 248 ARG 0.003 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 146 time to evaluate : 1.337 Fit side-chains REVERT: E 31 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: D 31 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.6708 (mt0) REVERT: D 117 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.5663 (mtt180) REVERT: D 150 GLU cc_start: 0.5960 (pt0) cc_final: 0.5666 (pt0) REVERT: D 151 ASN cc_start: 0.7842 (m-40) cc_final: 0.7539 (m-40) REVERT: D 230 GLU cc_start: 0.5056 (mt-10) cc_final: 0.4411 (mm-30) REVERT: C 31 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7127 (mt0) REVERT: C 174 ARG cc_start: 0.7401 (mmt180) cc_final: 0.7091 (ttm170) REVERT: B 117 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.5656 (mtt180) REVERT: A 31 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7200 (mt0) REVERT: A 151 ASN cc_start: 0.8030 (m110) cc_final: 0.7742 (m-40) outliers start: 42 outliers final: 28 residues processed: 184 average time/residue: 0.2522 time to fit residues: 66.1315 Evaluate side-chains 178 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 316 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 91 optimal weight: 0.0870 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN C 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12880 Z= 0.145 Angle : 0.488 6.128 17545 Z= 0.246 Chirality : 0.044 0.128 1950 Planarity : 0.003 0.036 2235 Dihedral : 4.147 14.528 1690 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.11 % Allowed : 18.25 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.23), residues: 1525 helix: 1.39 (0.25), residues: 500 sheet: 1.56 (0.26), residues: 430 loop : -2.65 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 206 HIS 0.003 0.001 HIS A 284 PHE 0.011 0.001 PHE B 116 TYR 0.009 0.001 TYR A 248 ARG 0.001 0.000 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 1.549 Fit side-chains REVERT: E 49 LYS cc_start: 0.7032 (tppt) cc_final: 0.6159 (tptt) REVERT: D 117 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.4983 (mtt180) REVERT: D 230 GLU cc_start: 0.5058 (mt-10) cc_final: 0.4399 (mm-30) REVERT: C 49 LYS cc_start: 0.7000 (tppt) cc_final: 0.6128 (tptt) REVERT: C 117 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.4962 (mtt180) REVERT: C 174 ARG cc_start: 0.7366 (mmt180) cc_final: 0.7089 (ttm170) REVERT: B 49 LYS cc_start: 0.7009 (tppt) cc_final: 0.6141 (tptt) REVERT: B 117 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.5258 (mtt180) REVERT: A 117 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.5936 (mpt180) REVERT: A 151 ASN cc_start: 0.7952 (m110) cc_final: 0.7602 (m-40) outliers start: 29 outliers final: 23 residues processed: 179 average time/residue: 0.2833 time to fit residues: 70.5518 Evaluate side-chains 176 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN E 284 HIS C 151 ASN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12880 Z= 0.350 Angle : 0.640 8.887 17545 Z= 0.324 Chirality : 0.049 0.172 1950 Planarity : 0.004 0.036 2235 Dihedral : 4.685 20.275 1690 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.40 % Allowed : 18.76 % Favored : 78.84 % 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: -0.27 (0.23), residues: 1525 helix: 1.11 (0.24), residues: 500 sheet: 1.31 (0.27), residues: 420 loop : -2.54 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 206 HIS 0.003 0.001 HIS E 284 PHE 0.016 0.002 PHE B 116 TYR 0.020 0.002 TYR E 258 ARG 0.002 0.000 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 1.368 Fit side-chains REVERT: E 31 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7362 (mp10) REVERT: D 117 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.5609 (mtt180) REVERT: D 151 ASN cc_start: 0.7854 (m110) cc_final: 0.7542 (m-40) REVERT: D 230 GLU cc_start: 0.5121 (mt-10) cc_final: 0.4474 (mm-30) REVERT: C 49 LYS cc_start: 0.6977 (tppt) cc_final: 0.6096 (tptt) REVERT: C 117 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.5522 (mtt180) REVERT: B 49 LYS cc_start: 0.6974 (tppt) cc_final: 0.6121 (tptt) REVERT: B 117 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.5661 (mtt180) REVERT: A 117 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.5617 (mtt180) REVERT: A 151 ASN cc_start: 0.8043 (m110) cc_final: 0.7769 (m-40) outliers start: 33 outliers final: 24 residues processed: 177 average time/residue: 0.2785 time to fit residues: 68.3773 Evaluate side-chains 179 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 94 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 36 optimal weight: 0.0070 overall best weight: 1.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN E 284 HIS C 151 ASN A 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12880 Z= 0.191 Angle : 0.535 7.593 17545 Z= 0.269 Chirality : 0.045 0.137 1950 Planarity : 0.003 0.036 2235 Dihedral : 4.368 17.273 1690 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.04 % Allowed : 19.20 % Favored : 78.76 % 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: -0.11 (0.23), residues: 1525 helix: 1.32 (0.25), residues: 500 sheet: 1.29 (0.27), residues: 425 loop : -2.47 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 206 HIS 0.003 0.001 HIS A 284 PHE 0.014 0.001 PHE C 236 TYR 0.014 0.001 TYR A 248 ARG 0.001 0.000 ARG C 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 1.495 Fit side-chains REVERT: E 49 LYS cc_start: 0.6985 (tppt) cc_final: 0.6129 (tptt) REVERT: D 117 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.5337 (mtt180) REVERT: D 151 ASN cc_start: 0.7788 (m110) cc_final: 0.7454 (m-40) REVERT: D 230 GLU cc_start: 0.5025 (mt-10) cc_final: 0.4429 (mm-30) REVERT: C 31 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7095 (mt0) REVERT: C 49 LYS cc_start: 0.7007 (tppt) cc_final: 0.6117 (tptt) REVERT: C 117 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.5218 (mtt180) REVERT: B 117 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.5400 (mtt180) REVERT: A 117 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6020 (mpt180) REVERT: A 151 ASN cc_start: 0.7989 (m110) cc_final: 0.7718 (m-40) outliers start: 28 outliers final: 22 residues processed: 172 average time/residue: 0.2869 time to fit residues: 68.2929 Evaluate side-chains 173 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 117 ARG Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 316 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 119 optimal weight: 0.3980 chunk 49 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 104 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN E 284 HIS C 151 ASN A 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.147783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.115530 restraints weight = 13991.191| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.56 r_work: 0.3058 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12880 Z= 0.353 Angle : 0.646 9.366 17545 Z= 0.327 Chirality : 0.049 0.174 1950 Planarity : 0.004 0.036 2235 Dihedral : 4.759 20.327 1690 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.62 % Allowed : 18.84 % Favored : 78.55 % 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: -0.33 (0.23), residues: 1525 helix: 1.11 (0.24), residues: 495 sheet: 1.34 (0.26), residues: 415 loop : -2.62 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 206 HIS 0.003 0.001 HIS D 284 PHE 0.016 0.002 PHE D 116 TYR 0.019 0.002 TYR A 248 ARG 0.004 0.001 ARG E 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2606.72 seconds wall clock time: 50 minutes 2.01 seconds (3002.01 seconds total)