Starting phenix.real_space_refine on Sat Aug 10 11:40:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3n_0136/08_2024/6h3n_0136.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3n_0136/08_2024/6h3n_0136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3n_0136/08_2024/6h3n_0136.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3n_0136/08_2024/6h3n_0136.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3n_0136/08_2024/6h3n_0136.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3n_0136/08_2024/6h3n_0136.cif" } resolution = 3.25 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= 0.002 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 S 45 5.16 5 C 9339 2.51 5 N 2730 2.21 5 O 2817 1.98 5 H 14388 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29319 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9773 Classifications: {'peptide': 627} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 591} Chain breaks: 1 Chain: "B" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9773 Classifications: {'peptide': 627} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 31, 'TRANS': 591} Chain breaks: 1 Chain: "C" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9773 Classifications: {'peptide': 627} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 591} Chain breaks: 1 Time building chain proxies: 13.17, per 1000 atoms: 0.45 Number of scatterers: 29319 At special positions: 0 Unit cell: (91.3, 93.5, 182.6, 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) S 45 16.00 O 2817 8.00 N 2730 7.00 C 9339 6.00 H 14388 1.00 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: 24.58 Conformation dependent library (CDL) restraints added in 2.9 seconds 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 14.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 151 through 163 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 264 through 281 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 625 through 635 Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 151 through 163 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 264 through 281 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 114 through 125 Processing helix chain 'C' and resid 151 through 163 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 264 through 281 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 625 through 637 155 hydrogen bonds defined for protein. 348 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: 9.15 Time building geometry restraints manager: 25.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 14367 1.13 - 1.30: 2550 1.30 - 1.47: 6356 1.47 - 1.64: 6331 1.64 - 1.81: 69 Bond restraints: 29673 Sorted by residual: bond pdb=" CD2 PHE B 152 " pdb=" HD2 PHE B 152 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" CZ2 TRP C 98 " pdb=" HZ2 TRP C 98 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" CD1 PHE A 127 " pdb=" HD1 PHE A 127 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" CZ3 TRP A 141 " pdb=" HZ3 TRP A 141 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" CD1 PHE C 392 " pdb=" HD1 PHE C 392 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.51e+01 ... (remaining 29668 not shown) Histogram of bond angle deviations from ideal: 95.63 - 103.30: 113 103.30 - 110.96: 30048 110.96 - 118.62: 8130 118.62 - 126.28: 14665 126.28 - 133.94: 357 Bond angle restraints: 53313 Sorted by residual: angle pdb=" C PRO A 638 " pdb=" N PRO A 639 " pdb=" CA PRO A 639 " ideal model delta sigma weight residual 119.66 127.34 -7.68 7.20e-01 1.93e+00 1.14e+02 angle pdb=" C PHE A 637 " pdb=" N PRO A 638 " pdb=" CA PRO A 638 " ideal model delta sigma weight residual 119.66 126.66 -7.00 7.20e-01 1.93e+00 9.46e+01 angle pdb=" C PHE B 637 " pdb=" N PRO B 638 " pdb=" CA PRO B 638 " ideal model delta sigma weight residual 119.66 126.49 -6.83 7.20e-01 1.93e+00 9.00e+01 angle pdb=" C GLY B 374 " pdb=" N PRO B 375 " pdb=" CA PRO B 375 " ideal model delta sigma weight residual 119.78 128.65 -8.87 1.03e+00 9.43e-01 7.41e+01 angle pdb=" C GLY C 374 " pdb=" N PRO C 375 " pdb=" CA PRO C 375 " ideal model delta sigma weight residual 119.78 128.62 -8.84 1.03e+00 9.43e-01 7.36e+01 ... (remaining 53308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 13210 16.78 - 33.57: 478 33.57 - 50.35: 194 50.35 - 67.14: 108 67.14 - 83.92: 26 Dihedral angle restraints: 14016 sinusoidal: 7665 harmonic: 6351 Sorted by residual: dihedral pdb=" CD2 HIS B 175 " pdb=" CG HIS B 175 " pdb=" ND1 HIS B 175 " pdb=" HD1 HIS B 175 " ideal model delta harmonic sigma weight residual 180.00 -147.20 -32.80 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CD2 HIS B 209 " pdb=" CG HIS B 209 " pdb=" ND1 HIS B 209 " pdb=" HD1 HIS B 209 " ideal model delta harmonic sigma weight residual 180.00 156.25 23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CD2 HIS B 71 " pdb=" CG HIS B 71 " pdb=" ND1 HIS B 71 " pdb=" HD1 HIS B 71 " ideal model delta harmonic sigma weight residual -180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 14013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1099 0.054 - 0.107: 738 0.107 - 0.161: 244 0.161 - 0.215: 54 0.215 - 0.268: 7 Chirality restraints: 2142 Sorted by residual: chirality pdb=" CA TRP C 96 " pdb=" N TRP C 96 " pdb=" C TRP C 96 " pdb=" CB TRP C 96 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ARG C 502 " pdb=" N ARG C 502 " pdb=" C ARG C 502 " pdb=" CB ARG C 502 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA TRP A 96 " pdb=" N TRP A 96 " pdb=" C TRP A 96 " pdb=" CB TRP A 96 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2139 not shown) Planarity restraints: 4569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 175 " -0.096 2.00e-02 2.50e+03 1.18e-01 3.12e+02 pdb=" CG HIS B 175 " -0.076 2.00e-02 2.50e+03 pdb=" ND1 HIS B 175 " -0.120 2.00e-02 2.50e+03 pdb=" CD2 HIS B 175 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 HIS B 175 " -0.057 2.00e-02 2.50e+03 pdb=" NE2 HIS B 175 " 0.035 2.00e-02 2.50e+03 pdb=" HD1 HIS B 175 " 0.274 2.00e-02 2.50e+03 pdb=" HD2 HIS B 175 " 0.095 2.00e-02 2.50e+03 pdb=" HE1 HIS B 175 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 209 " -0.088 2.00e-02 2.50e+03 9.05e-02 1.84e+02 pdb=" CG HIS B 209 " -0.050 2.00e-02 2.50e+03 pdb=" ND1 HIS B 209 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 HIS B 209 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 HIS B 209 " -0.048 2.00e-02 2.50e+03 pdb=" NE2 HIS B 209 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS B 209 " 0.210 2.00e-02 2.50e+03 pdb=" HD2 HIS B 209 " 0.074 2.00e-02 2.50e+03 pdb=" HE1 HIS B 209 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 209 " -0.086 2.00e-02 2.50e+03 8.71e-02 1.71e+02 pdb=" CG HIS A 209 " -0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS A 209 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 HIS A 209 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 HIS A 209 " -0.045 2.00e-02 2.50e+03 pdb=" NE2 HIS A 209 " 0.022 2.00e-02 2.50e+03 pdb=" HD1 HIS A 209 " 0.202 2.00e-02 2.50e+03 pdb=" HD2 HIS A 209 " 0.071 2.00e-02 2.50e+03 pdb=" HE1 HIS A 209 " -0.066 2.00e-02 2.50e+03 ... (remaining 4566 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 3911 2.19 - 2.79: 57698 2.79 - 3.39: 81498 3.39 - 4.00: 117025 4.00 - 4.60: 172218 Nonbonded interactions: 432350 Sorted by model distance: nonbonded pdb=" O TRP C 98 " pdb=" HG1 THR C 101 " model vdw 1.587 2.450 nonbonded pdb=" O TRP B 98 " pdb=" HG1 THR B 101 " model vdw 1.591 2.450 nonbonded pdb=" O TRP A 98 " pdb=" HG1 THR A 101 " model vdw 1.593 2.450 nonbonded pdb=" OE1 GLU B 494 " pdb=" H GLU B 494 " model vdw 1.597 2.450 nonbonded pdb=" OE1 GLU C 402 " pdb=" H GLU C 402 " model vdw 1.598 2.450 ... (remaining 432345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.450 Extract box with map and model: 1.120 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 92.580 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.015 0.067 15285 Z= 0.986 Angle : 1.517 16.538 20715 Z= 1.030 Chirality : 0.074 0.268 2142 Planarity : 0.010 0.162 2796 Dihedral : 10.777 83.921 5700 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.70 % Allowed : 4.65 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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: -0.43 (0.18), residues: 1869 helix: 0.60 (0.36), residues: 192 sheet: 0.31 (0.21), residues: 528 loop : -0.72 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.006 TRP B 414 HIS 0.007 0.002 HIS B 186 PHE 0.019 0.004 PHE A 33 TYR 0.056 0.007 TYR A 138 ARG 0.009 0.001 ARG C 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 2.103 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 SER cc_start: 0.7932 (t) cc_final: 0.7208 (t) REVERT: A 132 ASP cc_start: 0.7244 (t0) cc_final: 0.6972 (p0) REVERT: A 246 ARG cc_start: 0.7439 (mmt180) cc_final: 0.7094 (mmp-170) REVERT: A 280 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7363 (tm-30) REVERT: A 356 LEU cc_start: 0.8802 (mt) cc_final: 0.8410 (mm) REVERT: B 33 PHE cc_start: 0.5004 (m-10) cc_final: 0.4736 (m-10) REVERT: B 80 VAL cc_start: 0.7290 (m) cc_final: 0.7046 (m) REVERT: B 378 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8045 (mm-30) REVERT: C 280 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7154 (tm-30) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.8078 time to fit residues: 475.3225 Evaluate side-chains 215 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 168 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 510 ASN B 454 GLN B 510 ASN C 510 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15285 Z= 0.261 Angle : 0.585 5.670 20715 Z= 0.318 Chirality : 0.046 0.148 2142 Planarity : 0.006 0.049 2796 Dihedral : 4.722 19.161 2109 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.71 % Allowed : 8.24 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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: -0.08 (0.19), residues: 1869 helix: 1.52 (0.37), residues: 189 sheet: -0.12 (0.21), residues: 513 loop : -0.22 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 96 HIS 0.006 0.001 HIS C 209 PHE 0.017 0.002 PHE A 154 TYR 0.013 0.002 TYR A 322 ARG 0.006 0.001 ARG B 302 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 236 time to evaluate : 2.198 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6704 (mt-10) REVERT: A 132 ASP cc_start: 0.7294 (t0) cc_final: 0.7037 (p0) REVERT: A 246 ARG cc_start: 0.7616 (mmt180) cc_final: 0.6924 (mmm160) REVERT: A 280 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7428 (tm-30) REVERT: A 356 LEU cc_start: 0.8708 (mt) cc_final: 0.8303 (mm) REVERT: A 636 MET cc_start: 0.8455 (mmp) cc_final: 0.8199 (tpp) REVERT: C 280 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7265 (tm-30) REVERT: C 488 GLU cc_start: 0.7992 (tp30) cc_final: 0.7659 (tp30) outliers start: 27 outliers final: 22 residues processed: 254 average time/residue: 0.7201 time to fit residues: 259.1776 Evaluate side-chains 208 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 186 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 527 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.0770 chunk 52 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 169 optimal weight: 1.9990 chunk 182 optimal weight: 0.0020 chunk 150 optimal weight: 0.0270 chunk 167 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 135 optimal weight: 0.7980 overall best weight: 0.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 368 GLN C 368 GLN ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15285 Z= 0.131 Angle : 0.492 6.463 20715 Z= 0.258 Chirality : 0.045 0.150 2142 Planarity : 0.004 0.042 2796 Dihedral : 4.375 18.405 2109 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.76 % Allowed : 9.76 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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: 0.16 (0.19), residues: 1869 helix: 2.15 (0.39), residues: 192 sheet: -0.32 (0.21), residues: 513 loop : 0.05 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 96 HIS 0.005 0.001 HIS B 175 PHE 0.015 0.001 PHE B 70 TYR 0.010 0.001 TYR A 322 ARG 0.010 0.000 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 200 time to evaluate : 2.533 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7295 (t0) cc_final: 0.7024 (p0) REVERT: A 246 ARG cc_start: 0.7629 (mmt180) cc_final: 0.6903 (mmm160) REVERT: A 356 LEU cc_start: 0.8706 (mt) cc_final: 0.8300 (mm) REVERT: C 280 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7278 (tm-30) REVERT: C 488 GLU cc_start: 0.7915 (tp30) cc_final: 0.7654 (tp30) outliers start: 12 outliers final: 9 residues processed: 210 average time/residue: 0.6578 time to fit residues: 198.7486 Evaluate side-chains 178 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 612 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 GLN B 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15285 Z= 0.244 Angle : 0.500 6.853 20715 Z= 0.260 Chirality : 0.044 0.144 2142 Planarity : 0.004 0.070 2796 Dihedral : 4.340 17.662 2109 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.20 % Allowed : 11.15 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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: 0.01 (0.19), residues: 1869 helix: 2.14 (0.38), residues: 192 sheet: -0.41 (0.21), residues: 543 loop : -0.06 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.005 0.001 HIS C 209 PHE 0.017 0.001 PHE A 592 TYR 0.012 0.001 TYR B 143 ARG 0.005 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 2.237 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7416 (t0) cc_final: 0.7200 (p0) REVERT: A 356 LEU cc_start: 0.8792 (mt) cc_final: 0.8486 (mm) REVERT: C 280 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7304 (tm-30) outliers start: 19 outliers final: 16 residues processed: 188 average time/residue: 0.6268 time to fit residues: 174.1010 Evaluate side-chains 178 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 264 GLN C 243 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15285 Z= 0.282 Angle : 0.497 6.153 20715 Z= 0.260 Chirality : 0.044 0.146 2142 Planarity : 0.004 0.039 2796 Dihedral : 4.376 18.181 2109 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.33 % Allowed : 11.53 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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 (0.19), residues: 1869 helix: 2.07 (0.38), residues: 192 sheet: -0.82 (0.21), residues: 519 loop : -0.17 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 96 HIS 0.005 0.001 HIS C 209 PHE 0.013 0.001 PHE A 592 TYR 0.011 0.001 TYR C 143 ARG 0.005 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 1.484 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: 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 27 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6650 (mt-10) REVERT: B 246 ARG cc_start: 0.7876 (mmt180) cc_final: 0.7353 (mmm160) REVERT: B 379 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8014 (tp30) REVERT: C 280 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7365 (tm-30) outliers start: 21 outliers final: 14 residues processed: 179 average time/residue: 0.4082 time to fit residues: 108.7673 Evaluate side-chains 168 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.0870 chunk 161 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 179 optimal weight: 0.4980 chunk 149 optimal weight: 0.3980 chunk 83 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN C 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4491 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: