Starting phenix.real_space_refine on Fri Dec 27 17:53:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gmt_34153/12_2024/8gmt_34153.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmt_34153/12_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/cci-nas-00/data/ceres_data/8gmt_34153/12_2024/8gmt_34153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmt_34153/12_2024/8gmt_34153.map" model { file = "/net/cci-nas-00/data/ceres_data/8gmt_34153/12_2024/8gmt_34153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmt_34153/12_2024/8gmt_34153.cif" } 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. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.42, per 1000 atoms: 0.72 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 - 3.00 Amino acid : True - 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: 1.75 Conformation dependent library (CDL) restraints added in 875.4 milliseconds 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... Secondary structure from input PDB file: 30 helices and 10 sheets defined 42.8% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'F' and resid 2 through 22 Processing helix chain 'F' and resid 30 through 36 removed outlier: 5.791A pdb=" N ARG F 33 " --> pdb=" O GLY F 30 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER F 34 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 52 Processing helix chain 'F' and resid 71 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 100 through 107 Processing helix chain 'F' and resid 121 through 136 removed outlier: 3.598A pdb=" N GLY F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 151 through 157 Processing helix chain 'F' and resid 165 through 186 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 213 through 219 Processing helix chain 'F' and resid 269 through 281 Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 313 through 328 Processing helix chain 'G' and resid 2 through 22 Processing helix chain 'G' and resid 28 through 36 removed outlier: 3.520A pdb=" N ASP G 32 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG G 33 " --> pdb=" O GLY G 30 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER G 34 " --> pdb=" O GLU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 51 Processing helix chain 'G' and resid 71 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 100 through 107 Processing helix chain 'G' and resid 121 through 136 removed outlier: 3.530A pdb=" N GLY G 136 " --> pdb=" O LEU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 149 Processing helix chain 'G' and resid 151 through 157 Processing helix chain 'G' and resid 165 through 186 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 213 through 219 Processing helix chain 'G' and resid 269 through 281 Processing helix chain 'G' and resid 301 through 312 Processing helix chain 'G' and resid 312 through 328 removed outlier: 3.535A pdb=" N LEU G 328 " --> pdb=" O ARG G 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 15 through 18 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 23 removed outlier: 6.082A pdb=" N VAL B 22 " --> pdb=" O SER A 57 " (cutoff:3.500A) 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) removed outlier: 5.979A pdb=" N ILE A 87 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL A 130 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE A 85 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 26 through 28 removed outlier: 6.438A pdb=" N ILE G 141 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE G 192 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL G 143 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N GLN G 194 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 26 through 28 removed outlier: 6.438A pdb=" N ILE G 141 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE G 192 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL G 143 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N GLN G 194 " --> pdb=" O VAL G 143 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL G 62 " --> pdb=" O PHE G 191 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASN G 193 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE G 64 " --> pdb=" O ASN G 193 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE G 195 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY G 66 " --> pdb=" O ILE G 195 " (cutoff:3.500A) removed outlier: 9.550A pdb=" N MET G 197 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE G 61 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LEU G 223 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU G 63 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE G 225 " --> pdb=" O GLU G 63 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR G 65 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ARG G 227 " --> pdb=" O TYR G 65 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG G 222 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU G 241 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ALA G 230 " --> pdb=" O GLY G 239 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY G 239 " --> pdb=" O ALA G 230 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS G 232 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL G 237 " --> pdb=" O LYS G 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AA6, first strand: chain 'F' and resid 115 through 117 Processing sheet with id=AA7, first strand: chain 'F' and resid 115 through 117 removed outlier: 6.428A pdb=" N VAL F 62 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ASN F 193 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE F 64 " --> pdb=" O ASN F 193 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE F 195 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLY F 66 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N MET F 197 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE F 61 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU F 223 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU F 63 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE F 225 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR F 65 " --> pdb=" O ILE F 225 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ARG F 227 " --> pdb=" O TYR F 65 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL F 221 " --> pdb=" O ASN F 249 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN F 249 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU F 223 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL F 247 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE F 225 " --> pdb=" O LYS F 245 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS F 245 " --> pdb=" O ILE F 225 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ARG F 227 " --> pdb=" O ARG F 243 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG F 243 " --> pdb=" O ARG F 227 " (cutoff:3.500A) 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=AA8, first strand: chain 'F' and resid 285 through 287 removed outlier: 7.096A pdb=" N TYR F 291 " --> pdb=" O ILE F 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 39 through 40 Processing sheet with id=AB1, first strand: chain 'G' and resid 285 through 287 removed outlier: 6.994A pdb=" N TYR G 291 " --> pdb=" O ILE G 298 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.81 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: 0.00 - 1.33: 8253 1.33 - 2.67: 189 2.67 - 4.00: 28 4.00 - 5.33: 10 5.33 - 6.67: 1 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: 53 2.58 - 3.16: 4740 3.16 - 3.74: 9527 3.74 - 4.32: 13337 4.32 - 4.90: 22512 Nonbonded interactions: 50169 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 3.040 nonbonded pdb=" OG SER F 44 " pdb=" OE2 GLU F 273 " model vdw 2.209 3.040 nonbonded pdb=" O GLN F 300 " pdb=" ND2 ASN F 304 " model vdw 2.243 3.120 nonbonded pdb=" O1B AGS G 402 " pdb=" O2G AGS G 402 " model vdw 2.247 3.040 ... (remaining 50164 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '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: 0.460 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.330 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.890 ------------------------------------------------------------------------------- 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= 0.188 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 to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.618 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 64 average time/residue: 0.1882 time to fit residues: 16.2067 Evaluate side-chains 61 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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: 7.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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: 0.7829 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 6260 Z= 0.446 Angle : 0.627 5.377 8481 Z= 0.338 Chirality : 0.050 0.174 989 Planarity : 0.005 0.067 1069 Dihedral : 13.098 147.856 937 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.47 % Allowed : 15.77 % Favored : 80.76 % 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: 1.28 (0.29), residues: 305 sheet: 0.78 (0.40), residues: 143 loop : -0.60 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP F 308 HIS 0.003 0.001 HIS G 97 PHE 0.014 0.002 PHE F 217 TYR 0.012 0.002 TYR A 52 ARG 0.005 0.001 ARG F 169 *********************** 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 83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.666 Fit side-chains REVERT: G 164 MET cc_start: 0.4904 (ptm) cc_final: 0.4276 (ptm) outliers start: 22 outliers final: 16 residues processed: 75 average time/residue: 0.1714 time to fit residues: 17.7313 Evaluate side-chains 75 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 152 LYS Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 102 ILE 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6260 Z= 0.248 Angle : 0.500 4.717 8481 Z= 0.274 Chirality : 0.045 0.178 989 Planarity : 0.004 0.054 1069 Dihedral : 12.866 145.122 937 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.52 % Allowed : 17.82 % 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: 0.53 (0.29), residues: 788 helix: 1.20 (0.29), residues: 317 sheet: 0.73 (0.41), residues: 143 loop : -0.61 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 308 HIS 0.002 0.001 HIS G 97 PHE 0.009 0.001 PHE F 217 TYR 0.009 0.001 TYR A 52 ARG 0.005 0.000 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 79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.766 Fit side-chains REVERT: G 164 MET cc_start: 0.4808 (ptm) cc_final: 0.4149 (ptm) outliers start: 16 outliers final: 16 residues processed: 73 average time/residue: 0.1695 time to fit residues: 17.1456 Evaluate side-chains 76 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 233 GLU 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 145 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 37 optimal weight: 0.0770 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6260 Z= 0.232 Angle : 0.481 4.660 8481 Z= 0.262 Chirality : 0.045 0.158 989 Planarity : 0.003 0.051 1069 Dihedral : 12.708 143.349 937 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.42 % Allowed : 16.88 % 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: 0.59 (0.30), residues: 788 helix: 1.31 (0.30), residues: 317 sheet: 0.69 (0.41), residues: 143 loop : -0.61 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP F 308 HIS 0.002 0.001 HIS G 97 PHE 0.009 0.001 PHE F 217 TYR 0.012 0.001 TYR F 293 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 90 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.662 Fit side-chains REVERT: F 161 ASP cc_start: 0.7780 (m-30) cc_final: 0.7417 (m-30) REVERT: F 259 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: G 159 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8004 (mm) REVERT: G 164 MET cc_start: 0.4814 (ptm) cc_final: 0.4121 (ptm) outliers start: 28 outliers final: 22 residues processed: 83 average time/residue: 0.1936 time to fit residues: 21.8713 Evaluate side-chains 85 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 202 MET Chi-restraints excluded: chain F residue 233 GLU 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6260 Z= 0.204 Angle : 0.467 4.480 8481 Z= 0.255 Chirality : 0.044 0.156 989 Planarity : 0.003 0.046 1069 Dihedral : 12.627 140.751 937 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.26 % Allowed : 16.88 % 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: 0.65 (0.30), residues: 788 helix: 1.37 (0.30), residues: 317 sheet: 0.72 (0.41), residues: 143 loop : -0.59 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 308 HIS 0.002 0.001 HIS G 97 PHE 0.008 0.001 PHE F 203 TYR 0.008 0.001 TYR A 52 ARG 0.005 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 90 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.709 Fit side-chains REVERT: F 161 ASP cc_start: 0.7762 (m-30) cc_final: 0.7403 (m-30) REVERT: F 259 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: G 159 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7955 (mm) REVERT: G 164 MET cc_start: 0.4798 (ptm) cc_final: 0.4139 (ptm) outliers start: 27 outliers final: 18 residues processed: 83 average time/residue: 0.1870 time to fit residues: 20.9146 Evaluate side-chains 78 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 111 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 233 GLU 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 G residue 102 ILE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.7801 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6260 Z= 0.242 Angle : 0.486 4.632 8481 Z= 0.264 Chirality : 0.045 0.206 989 Planarity : 0.003 0.052 1069 Dihedral : 12.719 141.382 936 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.10 % Allowed : 17.82 % Favored : 78.08 % 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: 0.69 (0.30), residues: 788 helix: 1.58 (0.30), residues: 305 sheet: 0.67 (0.42), residues: 143 loop : -0.66 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP F 308 HIS 0.002 0.001 HIS G 97 PHE 0.009 0.001 PHE F 203 TYR 0.010 0.001 TYR F 293 ARG 0.007 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 88 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.693 Fit side-chains REVERT: B 33 TYR cc_start: 0.4847 (OUTLIER) cc_final: 0.4455 (p90) REVERT: F 259 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: G 159 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7984 (mm) REVERT: G 164 MET cc_start: 0.4417 (ptm) cc_final: 0.3997 (ptm) outliers start: 26 outliers final: 18 residues processed: 82 average time/residue: 0.1617 time to fit residues: 18.3653 Evaluate side-chains 79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 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 233 GLU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain G residue 102 ILE 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 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: 8.9990 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6260 Z= 0.227 Angle : 0.474 4.398 8481 Z= 0.259 Chirality : 0.045 0.217 989 Planarity : 0.003 0.049 1069 Dihedral : 12.759 140.795 936 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.63 % Allowed : 18.30 % Favored : 78.08 % 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: 0.62 (0.30), residues: 788 helix: 1.34 (0.30), residues: 317 sheet: 0.95 (0.42), residues: 139 loop : -0.72 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP F 308 HIS 0.002 0.001 HIS G 97 PHE 0.010 0.001 PHE F 203 TYR 0.008 0.001 TYR A 52 ARG 0.007 0.001 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 87 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.634 Fit side-chains REVERT: B 33 TYR cc_start: 0.4671 (OUTLIER) cc_final: 0.4314 (p90) REVERT: F 259 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: G 159 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7970 (mm) REVERT: G 164 MET cc_start: 0.4412 (ptm) cc_final: 0.3702 (ptm) outliers start: 23 outliers final: 18 residues processed: 81 average time/residue: 0.1645 time to fit residues: 18.5916 Evaluate side-chains 81 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 233 GLU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain G residue 102 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.0770 chunk 47 optimal weight: 0.0870 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 40.0000 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 0.0010 overall best weight: 0.3322 ------------------------------------------------------------------------------- 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: 0.7745 moved from start: 0.1918 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= 0.129 Angle : 0.435 4.131 8481 Z= 0.240 Chirality : 0.043 0.180 989 Planarity : 0.003 0.048 1069 Dihedral : 12.473 136.514 936 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.37 % Allowed : 19.40 % Favored : 78.23 % 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: 0.81 (0.30), residues: 788 helix: 1.53 (0.30), residues: 317 sheet: 0.78 (0.42), residues: 143 loop : -0.53 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP F 308 HIS 0.002 0.000 HIS G 97 PHE 0.009 0.001 PHE F 203 TYR 0.008 0.001 TYR F 271 ARG 0.008 0.000 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 82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.718 Fit side-chains REVERT: F 19 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7954 (mmpt) REVERT: F 161 ASP cc_start: 0.7712 (m-30) cc_final: 0.7320 (m-30) REVERT: F 259 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: G 164 MET cc_start: 0.4822 (ptm) cc_final: 0.4146 (ptm) outliers start: 15 outliers final: 10 residues processed: 78 average time/residue: 0.1795 time to fit residues: 18.8521 Evaluate side-chains 76 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain G residue 145 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 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: 4.9990 chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 0.2980 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6260 Z= 0.309 Angle : 0.513 4.750 8481 Z= 0.276 Chirality : 0.047 0.221 989 Planarity : 0.004 0.048 1069 Dihedral : 12.911 143.090 936 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.05 % Allowed : 20.03 % Favored : 77.92 % 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: 0.72 (0.30), residues: 788 helix: 1.61 (0.30), residues: 305 sheet: 0.84 (0.43), residues: 137 loop : -0.69 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP F 308 HIS 0.003 0.001 HIS G 97 PHE 0.012 0.002 PHE G 203 TYR 0.009 0.001 TYR A 52 ARG 0.008 0.001 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 74 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.701 Fit side-chains REVERT: F 259 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: G 164 MET cc_start: 0.4474 (ptm) cc_final: 0.4021 (ptm) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.1712 time to fit residues: 16.9860 Evaluate side-chains 73 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 145 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 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: 0.7848 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 6260 Z= 0.403 Angle : 0.570 5.138 8481 Z= 0.305 Chirality : 0.049 0.244 989 Planarity : 0.004 0.049 1069 Dihedral : 13.154 143.411 936 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.05 % Allowed : 19.87 % Favored : 78.08 % 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: 0.28 (0.29), residues: 788 helix: 1.21 (0.29), residues: 305 sheet: 0.61 (0.42), residues: 137 loop : -0.91 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP F 308 HIS 0.004 0.001 HIS G 97 PHE 0.012 0.002 PHE B 15 TYR 0.010 0.001 TYR A 52 ARG 0.009 0.001 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 74 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.691 Fit side-chains REVERT: A 66 ILE cc_start: 0.6463 (mt) cc_final: 0.6170 (mt) REVERT: F 259 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: G 202 MET cc_start: 0.6512 (mtp) cc_final: 0.6205 (mmt) outliers start: 13 outliers final: 11 residues processed: 72 average time/residue: 0.1723 time to fit residues: 17.0878 Evaluate side-chains 71 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 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 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 210 THR Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.1980 chunk 25 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** ** G 118 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 = 0.3790 r_free = 0.3790 target = 0.166042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.115221 restraints weight = 6911.836| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.83 r_work: 0.3048 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6260 Z= 0.216 Angle : 0.493 9.113 8481 Z= 0.267 Chirality : 0.045 0.189 989 Planarity : 0.003 0.048 1069 Dihedral : 12.923 139.998 936 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.89 % Allowed : 19.87 % Favored : 78.23 % 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 (0.30), residues: 788 helix: 1.44 (0.30), residues: 305 sheet: 0.69 (0.42), residues: 137 loop : -0.74 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP F 308 HIS 0.002 0.001 HIS F 97 PHE 0.011 0.002 PHE B 15 TYR 0.008 0.001 TYR A 52 ARG 0.009 0.001 ARG G 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1404.71 seconds wall clock time: 27 minutes 12.02 seconds (1632.02 seconds total)