Starting phenix.real_space_refine on Thu Mar 21 03:37:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3n_0136/03_2024/6h3n_0136.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3n_0136/03_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_0136/03_2024/6h3n_0136.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3n_0136/03_2024/6h3n_0136.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3n_0136/03_2024/6h3n_0136.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3n_0136/03_2024/6h3n_0136.pdb" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.00, per 1000 atoms: 0.41 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: 24.29 Conformation dependent library (CDL) restraints added in 3.7 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: 1.97 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: 9.21 Time building geometry restraints manager: 25.13 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 1.850 nonbonded pdb=" O TRP B 98 " pdb=" HG1 THR B 101 " model vdw 1.591 1.850 nonbonded pdb=" O TRP A 98 " pdb=" HG1 THR A 101 " model vdw 1.593 1.850 nonbonded pdb=" OE1 GLU B 494 " pdb=" H GLU B 494 " model vdw 1.597 1.850 nonbonded pdb=" OE1 GLU C 402 " pdb=" H GLU C 402 " model vdw 1.598 1.850 ... (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 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: 2.360 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: 0.480 Extract box with map and model: 10.920 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 89.890 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.520 ------------------------------------------------------------------------------- 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 : 2.408 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: 0.8131 time to fit residues: 477.0508 Evaluate side-chains 215 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 2.339 ------------------------------------------------------------------------------- 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: 0.9990 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 168 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7830 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15285 Z= 0.227 Angle : 0.555 5.619 20715 Z= 0.298 Chirality : 0.045 0.143 2142 Planarity : 0.005 0.047 2796 Dihedral : 4.633 17.859 2109 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.71 % Allowed : 8.17 % Favored : 90.11 % 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: 0.03 (0.19), residues: 1869 helix: 1.49 (0.37), residues: 189 sheet: 0.20 (0.21), residues: 528 loop : -0.27 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 96 HIS 0.008 0.001 HIS C 209 PHE 0.017 0.002 PHE A 154 TYR 0.014 0.001 TYR C 229 ARG 0.006 0.000 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 266 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 239 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: 0.6937 (mt-10) cc_final: 0.6660 (mt-10) REVERT: A 132 ASP cc_start: 0.7343 (t0) cc_final: 0.7134 (p0) REVERT: A 246 ARG cc_start: 0.7479 (mmt180) cc_final: 0.6912 (mmm160) REVERT: A 356 LEU cc_start: 0.8716 (mt) cc_final: 0.8311 (mm) REVERT: A 636 MET cc_start: 0.8456 (mmp) cc_final: 0.8204 (tpp) REVERT: B 378 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8085 (mm-30) REVERT: C 280 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7269 (tm-30) REVERT: C 488 GLU cc_start: 0.7986 (tp30) cc_final: 0.7695 (tp30) outliers start: 27 outliers final: 22 residues processed: 258 average time/residue: 0.7022 time to fit residues: 255.3015 Evaluate side-chains 204 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 2.353 ------------------------------------------------------------------------------- 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 441 ASP 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 A residue 543 ASN Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 310 ASP 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 543 ASN 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 527 ASP Chi-restraints excluded: chain C residue 612 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 15285 Z= 0.316 Angle : 0.546 7.469 20715 Z= 0.288 Chirality : 0.044 0.141 2142 Planarity : 0.005 0.083 2796 Dihedral : 4.516 16.599 2109 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.34 % Allowed : 9.44 % Favored : 88.21 % 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: -0.15 (0.19), residues: 1869 helix: 1.70 (0.38), residues: 192 sheet: -0.02 (0.21), residues: 531 loop : -0.41 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 96 HIS 0.007 0.001 HIS C 209 PHE 0.014 0.002 PHE A 154 TYR 0.014 0.001 TYR A 143 ARG 0.013 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 223 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 186 time to evaluate : 2.572 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: B 46 LEU cc_start: 0.7888 (tp) cc_final: 0.7640 (tt) REVERT: C 280 GLN cc_start: 0.7580 (mm-40) cc_final: 0.7312 (tm-30) REVERT: C 488 GLU cc_start: 0.8078 (tp30) cc_final: 0.7843 (tp30) REVERT: C 636 MET cc_start: 0.8396 (mmp) cc_final: 0.8156 (mmm) outliers start: 37 outliers final: 29 residues processed: 213 average time/residue: 0.6305 time to fit residues: 196.1810 Evaluate side-chains 195 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 310 ASP 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 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 543 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 161 GLN B 326 GLN C 264 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15285 Z= 0.351 Angle : 0.530 6.173 20715 Z= 0.278 Chirality : 0.044 0.142 2142 Planarity : 0.004 0.060 2796 Dihedral : 4.641 18.428 2109 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.66 % Allowed : 10.39 % Favored : 86.95 % 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: -0.38 (0.19), residues: 1869 helix: 1.72 (0.38), residues: 192 sheet: -0.39 (0.21), residues: 546 loop : -0.48 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 96 HIS 0.007 0.001 HIS C 499 PHE 0.018 0.002 PHE A 592 TYR 0.011 0.001 TYR B 143 ARG 0.005 0.001 ARG B 308 *********************** 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 208 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 166 time to evaluate : 2.620 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: B 379 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7953 (tp30) REVERT: C 280 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7391 (tm-30) REVERT: C 636 MET cc_start: 0.8474 (mmp) cc_final: 0.8255 (mmm) outliers start: 42 outliers final: 32 residues processed: 194 average time/residue: 0.6208 time to fit residues: 182.4194 Evaluate side-chains 189 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 441 ASP 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 A residue 554 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 310 ASP 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 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 543 ASN Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 527 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.7974 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15285 Z= 0.195 Angle : 0.473 5.964 20715 Z= 0.244 Chirality : 0.043 0.147 2142 Planarity : 0.003 0.036 2796 Dihedral : 4.339 18.364 2109 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.96 % Allowed : 11.60 % Favored : 86.44 % 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: -0.14 (0.19), residues: 1869 helix: 2.00 (0.38), residues: 192 sheet: -0.17 (0.22), residues: 531 loop : -0.38 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 96 HIS 0.005 0.001 HIS C 209 PHE 0.014 0.001 PHE A 592 TYR 0.008 0.001 TYR B 143 ARG 0.003 0.000 ARG A 187 *********************** 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 191 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 2.532 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: A 153 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7414 (t0) REVERT: B 379 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7962 (tp30) REVERT: C 79 GLN cc_start: 0.7576 (tm-30) cc_final: 0.7265 (tm-30) REVERT: C 280 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7503 (tm-30) REVERT: C 636 MET cc_start: 0.8403 (mmp) cc_final: 0.8189 (mmm) outliers start: 31 outliers final: 25 residues processed: 179 average time/residue: 0.5569 time to fit residues: 150.8144 Evaluate side-chains 177 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 310 ASP 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 B residue 478 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 543 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15285 Z= 0.225 Angle : 0.467 6.045 20715 Z= 0.240 Chirality : 0.043 0.144 2142 Planarity : 0.004 0.038 2796 Dihedral : 4.247 18.073 2109 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.22 % Allowed : 11.60 % Favored : 86.19 % 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: -0.11 (0.20), residues: 1869 helix: 2.11 (0.38), residues: 192 sheet: -0.16 (0.22), residues: 531 loop : -0.37 (0.19), residues: 1146 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 0.015 0.001 PHE B 33 TYR 0.008 0.001 TYR B 497 ARG 0.003 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 6 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 186 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 2.898 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: A 153 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7476 (t0) REVERT: A 607 ARG cc_start: 0.5887 (ttt90) cc_final: 0.5122 (tpt90) REVERT: B 379 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8039 (tp30) REVERT: B 483 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.8017 (m110) REVERT: C 280 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7524 (tm-30) outliers start: 35 outliers final: 30 residues processed: 176 average time/residue: 0.5735 time to fit residues: 151.2918 Evaluate side-chains 177 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 144 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 404 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 A residue 543 ASN Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 310 ASP 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 441 ASP Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 543 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.8012 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15285 Z= 0.242 Angle : 0.475 6.084 20715 Z= 0.245 Chirality : 0.043 0.140 2142 Planarity : 0.004 0.034 2796 Dihedral : 4.218 18.146 2109 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.60 % Allowed : 11.09 % Favored : 86.31 % 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: -0.15 (0.20), residues: 1869 helix: 2.17 (0.38), residues: 192 sheet: -0.20 (0.22), residues: 531 loop : -0.40 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 96 HIS 0.005 0.001 HIS C 209 PHE 0.016 0.001 PHE A 592 TYR 0.008 0.001 TYR A 497 ARG 0.003 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 7 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: 41 poor density : 147 time to evaluate : 2.218 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: A 153 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7508 (t0) REVERT: A 607 ARG cc_start: 0.6050 (ttt90) cc_final: 0.4697 (tpt90) REVERT: B 27 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.7037 (mm-30) REVERT: B 379 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8019 (tp30) REVERT: B 483 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.8055 (m110) REVERT: C 280 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7479 (tm-30) REVERT: C 636 MET cc_start: 0.8356 (mmp) cc_final: 0.8130 (tpp) outliers start: 41 outliers final: 34 residues processed: 174 average time/residue: 0.5636 time to fit residues: 147.7558 Evaluate side-chains 181 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 143 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 310 ASP 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 441 ASP Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 543 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 113 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15285 Z= 0.219 Angle : 0.465 6.043 20715 Z= 0.239 Chirality : 0.043 0.138 2142 Planarity : 0.003 0.033 2796 Dihedral : 4.152 18.257 2109 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.41 % Allowed : 11.41 % Favored : 86.19 % 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: -0.14 (0.20), residues: 1869 helix: 2.23 (0.38), residues: 192 sheet: -0.13 (0.22), residues: 525 loop : -0.44 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 96 HIS 0.005 0.001 HIS B 499 PHE 0.014 0.001 PHE A 592 TYR 0.008 0.001 TYR B 497 ARG 0.003 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 8 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 182 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 144 time to evaluate : 1.913 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: A 153 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7393 (t0) REVERT: A 519 ASP cc_start: 0.8286 (t0) cc_final: 0.7852 (m-30) REVERT: A 607 ARG cc_start: 0.6110 (ttt90) cc_final: 0.4662 (tpt90) REVERT: B 379 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8118 (tp30) REVERT: B 483 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.8043 (m110) REVERT: C 280 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7580 (tm-30) REVERT: C 636 MET cc_start: 0.8426 (mmp) cc_final: 0.8180 (tpp) outliers start: 38 outliers final: 30 residues processed: 167 average time/residue: 0.5802 time to fit residues: 146.0823 Evaluate side-chains 174 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 310 ASP 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 441 ASP Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 543 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.0270 chunk 171 optimal weight: 1.9990 chunk 156 optimal weight: 0.2980 chunk 167 optimal weight: 0.2980 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 0.0170 chunk 131 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 150 optimal weight: 0.5980 chunk 158 optimal weight: 0.6980 chunk 166 optimal weight: 0.5980 overall best weight: 0.2476 ------------------------------------------------------------------------------- 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: 0.7974 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15285 Z= 0.125 Angle : 0.449 5.900 20715 Z= 0.226 Chirality : 0.044 0.145 2142 Planarity : 0.003 0.029 2796 Dihedral : 3.916 18.062 2109 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.39 % Allowed : 12.42 % Favored : 86.19 % 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: 0.15 (0.20), residues: 1869 helix: 2.56 (0.39), residues: 192 sheet: 0.07 (0.23), residues: 519 loop : -0.27 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 96 HIS 0.005 0.001 HIS B 499 PHE 0.017 0.001 PHE A 592 TYR 0.007 0.001 TYR C 497 ARG 0.002 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 9 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 175 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 2.578 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: A 153 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7304 (t0) REVERT: A 519 ASP cc_start: 0.8137 (t0) cc_final: 0.7870 (m-30) REVERT: A 607 ARG cc_start: 0.6093 (ttt90) cc_final: 0.4599 (tpt90) REVERT: B 379 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8144 (tp30) REVERT: B 632 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8326 (mt0) REVERT: C 280 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7585 (tm-30) outliers start: 22 outliers final: 17 residues processed: 166 average time/residue: 0.5710 time to fit residues: 142.4828 Evaluate side-chains 165 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain B residue 160 GLU 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 469 MET Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 543 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 170 optimal weight: 0.0970 chunk 147 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 526 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15285 Z= 0.168 Angle : 0.457 7.815 20715 Z= 0.228 Chirality : 0.043 0.141 2142 Planarity : 0.003 0.035 2796 Dihedral : 3.909 17.549 2109 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.20 % Allowed : 12.93 % Favored : 85.87 % 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: 0.15 (0.20), residues: 1869 helix: 2.62 (0.39), residues: 192 sheet: 0.21 (0.23), residues: 489 loop : -0.35 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 96 HIS 0.004 0.001 HIS B 499 PHE 0.016 0.001 PHE A 592 TYR 0.008 0.001 TYR A 253 ARG 0.003 0.000 ARG B 187 ********************** REFINEMENT MACRO_CYCLE 10 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 169 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 150 time to evaluate : 2.371 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: A 153 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7371 (t0) REVERT: A 519 ASP cc_start: 0.8085 (t0) cc_final: 0.7843 (m-30) REVERT: A 607 ARG cc_start: 0.6119 (ttt90) cc_final: 0.4656 (tpt90) REVERT: B 379 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8161 (tp30) REVERT: C 280 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7592 (tm-30) REVERT: C 636 MET cc_start: 0.8402 (tpp) cc_final: 0.8036 (tpp) outliers start: 19 outliers final: 16 residues processed: 160 average time/residue: 0.5770 time to fit residues: 139.3737 Evaluate side-chains 161 residues out of total 1578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain B residue 160 GLU 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 469 MET Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN C 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.133223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102118 restraints weight = 51821.333| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.35 r_work: 0.3376 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15285 Z= 0.333 Angle : 0.511 7.562 20715 Z= 0.264 Chirality : 0.043 0.137 2142 Planarity : 0.004 0.045 2796 Dihedral : 4.224 18.273 2109 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.90 % Allowed : 12.29 % Favored : 85.80 % 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: -0.29 (0.20), residues: 1869 helix: 2.29 (0.39), residues: 192 sheet: -0.20 (0.23), residues: 510 loop : -0.60 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 96 HIS 0.007 0.001 HIS C 499 PHE 0.022 0.002 PHE A 592 TYR 0.010 0.001 TYR B 306 ARG 0.004 0.001 ARG B 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6807.71 seconds wall clock time: 120 minutes 26.66 seconds (7226.66 seconds total)