Starting phenix.real_space_refine on Sun Mar 10 23:59:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmt_34153/03_2024/8gmt_34153_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmt_34153/03_2024/8gmt_34153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmt_34153/03_2024/8gmt_34153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmt_34153/03_2024/8gmt_34153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmt_34153/03_2024/8gmt_34153_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmt_34153/03_2024/8gmt_34153_updated.pdb" } resolution = 3.31 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= 0.003 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 2 5.21 5 S 29 5.16 5 C 3854 2.51 5 N 1045 2.21 5 O 1230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 20": "OD1" <-> "OD2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F GLU 281": "OE1" <-> "OE2" Residue "F TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G GLU 156": "OE1" <-> "OE2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G GLU 266": "OE1" <-> "OE2" Residue "G TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 276": "OD1" <-> "OD2" Residue "G GLU 325": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6172 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 250 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 28} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 722 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "F" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2508 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "G" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2508 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 9, 'TRANS': 323} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.90, per 1000 atoms: 0.63 Number of scatterers: 6172 At special positions: 0 Unit cell: (99.96, 95.2, 105.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 P 12 15.00 Mg 2 11.99 O 1230 8.00 N 1045 7.00 C 3854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.5 seconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 11 sheets defined 36.3% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'F' and resid 2 through 21 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 33 through 35 No H-bonds generated for 'chain 'F' and resid 33 through 35' Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 72 through 86 removed outlier: 3.631A pdb=" N GLU F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 146 through 148 No H-bonds generated for 'chain 'F' and resid 146 through 148' Processing helix chain 'F' and resid 152 through 156 Processing helix chain 'F' and resid 166 through 185 removed outlier: 4.915A pdb=" N GLY F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 218 Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 302 through 311 Processing helix chain 'F' and resid 314 through 327 Processing helix chain 'G' and resid 2 through 21 Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 33 through 35 No H-bonds generated for 'chain 'G' and resid 33 through 35' Processing helix chain 'G' and resid 45 through 50 Processing helix chain 'G' and resid 72 through 86 removed outlier: 3.580A pdb=" N GLU G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 122 through 135 Processing helix chain 'G' and resid 146 through 148 No H-bonds generated for 'chain 'G' and resid 146 through 148' Processing helix chain 'G' and resid 152 through 156 Processing helix chain 'G' and resid 166 through 185 removed outlier: 4.775A pdb=" N GLY G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 218 Processing helix chain 'G' and resid 270 through 280 Processing helix chain 'G' and resid 301 through 311 Processing helix chain 'G' and resid 313 through 327 Processing sheet with id= A, first strand: chain 'B' and resid 15 through 18 Processing sheet with id= B, first strand: chain 'A' and resid 51 through 55 removed outlier: 3.617A pdb=" N HIS A 133 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP A 75 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL A 131 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 85 through 90 Processing sheet with id= D, first strand: chain 'F' and resid 257 through 263 removed outlier: 6.243A pdb=" N ARG F 222 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL F 221 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU F 189 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE F 64 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE F 191 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N GLY F 66 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASN F 193 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU F 115 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASP F 94 " --> pdb=" O LEU F 115 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER F 117 " --> pdb=" O ASP F 94 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 195 through 197 Processing sheet with id= F, first strand: chain 'F' and resid 285 through 287 removed outlier: 3.795A pdb=" N GLY F 299 " --> pdb=" O TYR F 291 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR F 293 " --> pdb=" O LYS F 297 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS F 297 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 229 through 233 removed outlier: 6.569A pdb=" N GLU F 233 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 257 through 263 removed outlier: 6.321A pdb=" N ARG G 222 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL G 221 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU G 189 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE G 64 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE G 191 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N GLY G 66 " --> pdb=" O PHE G 191 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASN G 193 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU G 115 " --> pdb=" O PHE G 92 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP G 94 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER G 117 " --> pdb=" O ASP G 94 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 195 through 197 Processing sheet with id= J, first strand: chain 'G' and resid 285 through 287 removed outlier: 6.454A pdb=" N TYR G 293 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS G 297 " --> pdb=" O TYR G 293 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 229 through 233 removed outlier: 6.643A pdb=" N GLU G 233 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL G 237 " --> pdb=" O GLU G 233 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 2059 1.36 - 1.51: 1517 1.51 - 1.65: 2635 1.65 - 1.80: 32 1.80 - 1.95: 17 Bond restraints: 6260 Sorted by residual: bond pdb=" CA SER G 145 " pdb=" CB SER G 145 " ideal model delta sigma weight residual 1.532 1.498 0.033 1.36e-02 5.41e+03 5.98e+00 bond pdb=" N ASP G 94 " pdb=" CA ASP G 94 " ideal model delta sigma weight residual 1.462 1.490 -0.028 1.26e-02 6.30e+03 4.97e+00 bond pdb=" N SER G 145 " pdb=" CA SER G 145 " ideal model delta sigma weight residual 1.461 1.487 -0.027 1.38e-02 5.25e+03 3.73e+00 bond pdb=" CG LEU F 309 " pdb=" CD2 LEU F 309 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" C ASP G 94 " pdb=" O ASP G 94 " ideal model delta sigma weight residual 1.233 1.247 -0.014 1.26e-02 6.30e+03 1.18e+00 ... (remaining 6255 not shown) Histogram of bond angle deviations from ideal: 100.15 - 107.00: 195 107.00 - 113.85: 3592 113.85 - 120.70: 2593 120.70 - 127.55: 2064 127.55 - 134.41: 37 Bond angle restraints: 8481 Sorted by residual: angle pdb=" CA SER G 145 " pdb=" C SER G 145 " pdb=" O SER G 145 " ideal model delta sigma weight residual 122.45 118.14 4.31 1.30e+00 5.92e-01 1.10e+01 angle pdb=" C ASN F 312 " pdb=" CA ASN F 312 " pdb=" CB ASN F 312 " ideal model delta sigma weight residual 110.02 114.72 -4.70 1.50e+00 4.44e-01 9.82e+00 angle pdb=" C ASP B 32 " pdb=" N TYR B 33 " pdb=" CA TYR B 33 " ideal model delta sigma weight residual 123.34 118.15 5.19 1.80e+00 3.09e-01 8.33e+00 angle pdb=" C TRP F 308 " pdb=" CA TRP F 308 " pdb=" CB TRP F 308 " ideal model delta sigma weight residual 110.88 106.39 4.49 1.57e+00 4.06e-01 8.17e+00 angle pdb=" N ILE A 132 " pdb=" CA ILE A 132 " pdb=" C ILE A 132 " ideal model delta sigma weight residual 112.96 110.25 2.71 1.00e+00 1.00e+00 7.35e+00 ... (remaining 8476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.35: 3542 29.35 - 58.69: 245 58.69 - 88.04: 17 88.04 - 117.39: 0 117.39 - 146.74: 2 Dihedral angle restraints: 3806 sinusoidal: 1557 harmonic: 2249 Sorted by residual: dihedral pdb=" O1A AGS G 402 " pdb=" O3A AGS G 402 " pdb=" PA AGS G 402 " pdb=" PB AGS G 402 " ideal model delta sinusoidal sigma weight residual -67.73 79.01 -146.74 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" O1A AGS F 402 " pdb=" O3A AGS F 402 " pdb=" PA AGS F 402 " pdb=" PB AGS F 402 " ideal model delta sinusoidal sigma weight residual -67.73 75.30 -143.03 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" CA VAL B 34 " pdb=" C VAL B 34 " pdb=" N GLU B 35 " pdb=" CA GLU B 35 " ideal model delta harmonic sigma weight residual -180.00 -161.68 -18.32 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 690 0.036 - 0.072: 198 0.072 - 0.108: 75 0.108 - 0.144: 24 0.144 - 0.180: 2 Chirality restraints: 989 Sorted by residual: chirality pdb=" CA SER G 145 " pdb=" N SER G 145 " pdb=" C SER G 145 " pdb=" CB SER G 145 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CB THR G 208 " pdb=" CA THR G 208 " pdb=" OG1 THR G 208 " pdb=" CG2 THR G 208 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA ILE A 87 " pdb=" N ILE A 87 " pdb=" C ILE A 87 " pdb=" CB ILE A 87 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 986 not shown) Planarity restraints: 1069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 308 " 0.012 2.00e-02 2.50e+03 2.46e-02 1.51e+01 pdb=" CG TRP F 308 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP F 308 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP F 308 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 308 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP F 308 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 308 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 308 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 308 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP F 308 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 312 " -0.056 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO F 313 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO F 313 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 313 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 312 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C ASN F 312 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN F 312 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO F 313 " -0.011 2.00e-02 2.50e+03 ... (remaining 1066 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 57 2.58 - 3.16: 4776 3.16 - 3.74: 9592 3.74 - 4.32: 13441 4.32 - 4.90: 22527 Nonbonded interactions: 50393 Sorted by model distance: nonbonded pdb=" OG1 THR G 73 " pdb="MG MG G 401 " model vdw 1.995 2.170 nonbonded pdb=" O CYS B 24 " pdb=" OG SER A 60 " model vdw 2.202 2.440 nonbonded pdb=" OG SER F 44 " pdb=" OE2 GLU F 273 " model vdw 2.209 2.440 nonbonded pdb=" O GLN F 300 " pdb=" ND2 ASN F 304 " model vdw 2.243 2.520 nonbonded pdb=" O1B AGS G 402 " pdb=" O2G AGS G 402 " model vdw 2.247 2.440 ... (remaining 50388 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 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.620 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.700 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.490 ------------------------------------------------------------------------------- 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 : 0.003 0.039 6260 Z= 0.184 Angle : 0.519 6.667 8481 Z= 0.308 Chirality : 0.043 0.180 989 Planarity : 0.004 0.085 1069 Dihedral : 18.125 146.736 2366 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.32 % Allowed : 17.19 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.30), residues: 788 helix: 1.55 (0.30), residues: 317 sheet: 1.53 (0.42), residues: 132 loop : -0.52 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.005 TRP F 308 HIS 0.002 0.001 HIS G 97 PHE 0.008 0.001 PHE A 128 TYR 0.026 0.001 TYR B 33 ARG 0.008 0.000 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.635 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 64 average time/residue: 0.1956 time to fit residues: 16.7262 Evaluate side-chains 61 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 150 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 0.1980 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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: 0.7785 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6260 Z= 0.276 Angle : 0.501 5.445 8481 Z= 0.273 Chirality : 0.045 0.147 989 Planarity : 0.004 0.065 1069 Dihedral : 13.043 142.768 937 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.00 % Allowed : 16.09 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.29), residues: 788 helix: 1.43 (0.30), residues: 317 sheet: 1.23 (0.40), residues: 143 loop : -0.55 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP F 308 HIS 0.002 0.001 HIS G 97 PHE 0.008 0.001 PHE F 255 TYR 0.011 0.001 TYR A 52 ARG 0.005 0.001 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.687 Fit side-chains REVERT: G 164 MET cc_start: 0.4834 (ptm) cc_final: 0.4229 (ptm) outliers start: 19 outliers final: 13 residues processed: 71 average time/residue: 0.1675 time to fit residues: 16.4316 Evaluate side-chains 74 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 6260 Z= 0.371 Angle : 0.554 5.651 8481 Z= 0.299 Chirality : 0.048 0.167 989 Planarity : 0.004 0.058 1069 Dihedral : 13.113 141.402 937 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.63 % Allowed : 16.72 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.29), residues: 788 helix: 1.25 (0.30), residues: 305 sheet: 0.91 (0.40), residues: 147 loop : -0.88 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP F 308 HIS 0.004 0.001 HIS G 97 PHE 0.011 0.002 PHE F 255 TYR 0.011 0.002 TYR A 52 ARG 0.006 0.001 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 60 time to evaluate : 0.553 Fit side-chains REVERT: F 161 ASP cc_start: 0.7863 (m-30) cc_final: 0.7574 (m-30) REVERT: G 164 MET cc_start: 0.4268 (ptm) cc_final: 0.3669 (ptm) outliers start: 23 outliers final: 20 residues processed: 75 average time/residue: 0.1663 time to fit residues: 17.1987 Evaluate side-chains 80 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 236 ASN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 30.0000 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6260 Z= 0.218 Angle : 0.465 5.071 8481 Z= 0.255 Chirality : 0.044 0.168 989 Planarity : 0.003 0.054 1069 Dihedral : 12.916 136.708 937 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.15 % Allowed : 17.98 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.29), residues: 788 helix: 1.20 (0.30), residues: 317 sheet: 0.98 (0.40), residues: 143 loop : -0.73 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP F 308 HIS 0.003 0.001 HIS G 97 PHE 0.016 0.001 PHE G 270 TYR 0.008 0.001 TYR A 52 ARG 0.005 0.000 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 0.733 Fit side-chains REVERT: G 159 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8021 (mm) REVERT: G 164 MET cc_start: 0.4256 (ptm) cc_final: 0.3583 (ptm) outliers start: 20 outliers final: 17 residues processed: 76 average time/residue: 0.1713 time to fit residues: 17.8294 Evaluate side-chains 76 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.0070 chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6260 Z= 0.128 Angle : 0.420 4.609 8481 Z= 0.233 Chirality : 0.042 0.153 989 Planarity : 0.003 0.048 1069 Dihedral : 12.259 126.391 937 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.52 % Allowed : 18.45 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.30), residues: 788 helix: 1.47 (0.30), residues: 317 sheet: 1.40 (0.44), residues: 129 loop : -0.59 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP F 308 HIS 0.002 0.000 HIS G 97 PHE 0.015 0.001 PHE G 270 TYR 0.007 0.001 TYR F 271 ARG 0.006 0.000 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.697 Fit side-chains REVERT: A 61 MET cc_start: 0.6419 (OUTLIER) cc_final: 0.4902 (mpp) REVERT: F 161 ASP cc_start: 0.7695 (m-30) cc_final: 0.7434 (m-30) REVERT: G 164 MET cc_start: 0.4834 (ptm) cc_final: 0.4122 (ptm) outliers start: 16 outliers final: 11 residues processed: 80 average time/residue: 0.1769 time to fit residues: 19.1175 Evaluate side-chains 73 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 242 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 0.0000 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 overall best weight: 2.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6260 Z= 0.358 Angle : 0.532 5.531 8481 Z= 0.285 Chirality : 0.048 0.209 989 Planarity : 0.004 0.049 1069 Dihedral : 12.812 137.254 936 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.26 % Allowed : 16.56 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.29), residues: 788 helix: 1.43 (0.30), residues: 305 sheet: 1.10 (0.41), residues: 137 loop : -0.85 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP F 308 HIS 0.003 0.001 HIS G 97 PHE 0.014 0.002 PHE G 270 TYR 0.010 0.001 TYR A 52 ARG 0.008 0.001 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 58 time to evaluate : 0.642 Fit side-chains REVERT: B 33 TYR cc_start: 0.4816 (OUTLIER) cc_final: 0.4433 (p90) REVERT: A 61 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.4944 (mpp) REVERT: G 159 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8035 (mm) REVERT: G 164 MET cc_start: 0.4361 (ptm) cc_final: 0.3913 (ptm) outliers start: 27 outliers final: 20 residues processed: 80 average time/residue: 0.1687 time to fit residues: 18.5428 Evaluate side-chains 79 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 56 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 242 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6260 Z= 0.222 Angle : 0.461 4.930 8481 Z= 0.252 Chirality : 0.045 0.226 989 Planarity : 0.003 0.048 1069 Dihedral : 12.545 131.501 936 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.15 % Allowed : 17.98 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.29), residues: 788 helix: 1.25 (0.30), residues: 317 sheet: 1.10 (0.42), residues: 137 loop : -0.78 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP F 308 HIS 0.003 0.001 HIS G 97 PHE 0.013 0.001 PHE G 270 TYR 0.008 0.001 TYR A 52 ARG 0.007 0.000 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.687 Fit side-chains REVERT: A 61 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.4868 (mpp) REVERT: F 259 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: G 164 MET cc_start: 0.4377 (ptm) cc_final: 0.3714 (ptm) outliers start: 20 outliers final: 13 residues processed: 75 average time/residue: 0.1847 time to fit residues: 18.7513 Evaluate side-chains 72 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 242 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 6260 Z= 0.401 Angle : 0.567 5.758 8481 Z= 0.302 Chirality : 0.049 0.244 989 Planarity : 0.004 0.049 1069 Dihedral : 13.148 140.918 936 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.42 % Allowed : 16.72 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 788 helix: 1.14 (0.29), residues: 303 sheet: 0.89 (0.41), residues: 143 loop : -1.11 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP F 308 HIS 0.004 0.001 HIS G 97 PHE 0.012 0.002 PHE G 270 TYR 0.011 0.002 TYR A 52 ARG 0.008 0.001 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 58 time to evaluate : 0.714 Fit side-chains REVERT: B 33 TYR cc_start: 0.4500 (OUTLIER) cc_final: 0.4214 (p90) REVERT: F 259 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: G 159 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.7986 (mm) REVERT: G 164 MET cc_start: 0.4474 (ptm) cc_final: 0.4010 (ptm) outliers start: 28 outliers final: 21 residues processed: 82 average time/residue: 0.1560 time to fit residues: 18.1201 Evaluate side-chains 80 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 56 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 242 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6260 Z= 0.223 Angle : 0.473 5.516 8481 Z= 0.257 Chirality : 0.045 0.190 989 Planarity : 0.003 0.050 1069 Dihedral : 12.723 132.222 936 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.10 % Allowed : 17.03 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.29), residues: 788 helix: 1.15 (0.30), residues: 315 sheet: 1.02 (0.42), residues: 139 loop : -0.96 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP F 308 HIS 0.002 0.001 HIS F 97 PHE 0.021 0.002 PHE G 270 TYR 0.007 0.001 TYR A 52 ARG 0.008 0.000 ARG G 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 58 time to evaluate : 0.734 Fit side-chains REVERT: B 33 TYR cc_start: 0.4067 (OUTLIER) cc_final: 0.3742 (p90) REVERT: A 61 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.4951 (mpp) REVERT: F 259 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: G 159 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7977 (mm) REVERT: G 164 MET cc_start: 0.4403 (ptm) cc_final: 0.3970 (ptm) outliers start: 26 outliers final: 20 residues processed: 79 average time/residue: 0.1584 time to fit residues: 17.3899 Evaluate side-chains 81 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 57 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 242 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6260 Z= 0.154 Angle : 0.439 5.114 8481 Z= 0.239 Chirality : 0.043 0.155 989 Planarity : 0.003 0.051 1069 Dihedral : 12.129 122.006 936 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.00 % Allowed : 18.14 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.30), residues: 788 helix: 1.42 (0.30), residues: 315 sheet: 0.94 (0.42), residues: 145 loop : -0.74 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP F 308 HIS 0.001 0.001 HIS G 97 PHE 0.018 0.001 PHE G 270 TYR 0.007 0.001 TYR G 65 ARG 0.009 0.000 ARG G 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.730 Fit side-chains REVERT: A 61 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.4786 (mpp) REVERT: F 19 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7876 (mmpt) REVERT: F 259 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: G 164 MET cc_start: 0.4478 (ptm) cc_final: 0.3781 (ptm) outliers start: 19 outliers final: 15 residues processed: 80 average time/residue: 0.1677 time to fit residues: 18.5674 Evaluate side-chains 80 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 240 SER Chi-restraints excluded: chain G residue 242 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 11 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.0570 chunk 41 optimal weight: 9.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.168134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119678 restraints weight = 6875.415| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.88 r_work: 0.3049 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6260 Z= 0.155 Angle : 0.431 5.306 8481 Z= 0.235 Chirality : 0.043 0.149 989 Planarity : 0.003 0.049 1069 Dihedral : 12.013 118.315 936 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.68 % Allowed : 18.61 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.30), residues: 788 helix: 1.50 (0.30), residues: 315 sheet: 1.05 (0.45), residues: 137 loop : -0.71 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP F 308 HIS 0.002 0.001 HIS G 97 PHE 0.019 0.001 PHE G 270 TYR 0.006 0.001 TYR G 65 ARG 0.008 0.000 ARG G 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1498.74 seconds wall clock time: 27 minutes 54.79 seconds (1674.79 seconds total)