Starting phenix.real_space_refine on Thu Jul 2 06:47:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyl_29585/07_2026/8fyl_29585.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyl_29585/07_2026/8fyl_29585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fyl_29585/07_2026/8fyl_29585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyl_29585/07_2026/8fyl_29585.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fyl_29585/07_2026/8fyl_29585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyl_29585/07_2026/8fyl_29585.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 54 5.16 5 C 4679 2.51 5 N 1239 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7330 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1891 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 232} Chain breaks: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2253 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 160 Unusual residues: {'J40': 1, 'Y01': 2, 'YG7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.76, per 1000 atoms: 0.24 Number of scatterers: 7330 At special positions: 0 Unit cell: (79.106, 101.555, 129.349, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 2 15.00 O 1356 8.00 N 1239 7.00 C 4679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 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: 0.63 Conformation dependent library (CDL) restraints added in 461.9 milliseconds 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1726 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 47.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.550A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.155A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 352 Processing helix chain 'B' and resid 6 through 26 removed outlier: 4.069A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.551A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.556A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 64 Processing helix chain 'R' and resid 69 through 89 Processing helix chain 'R' and resid 89 through 100 Processing helix chain 'R' and resid 105 through 140 Processing helix chain 'R' and resid 140 through 147 Processing helix chain 'R' and resid 149 through 169 removed outlier: 3.854A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 183 removed outlier: 4.029A pdb=" N ASP R 183 " --> pdb=" O GLU R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 228 removed outlier: 5.876A pdb=" N ILE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Proline residue: R 207 - end of helix Processing helix chain 'R' and resid 325 through 368 removed outlier: 3.780A pdb=" N LEU R 347 " --> pdb=" O THR R 343 " (cutoff:3.500A) Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 378 through 389 removed outlier: 4.257A pdb=" N GLY R 389 " --> pdb=" O ILE R 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 401 Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.771A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.858A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.636A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.683A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.740A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.629A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.873A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1140 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: 1.22 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1194 1.28 - 1.41: 1823 1.41 - 1.54: 4345 1.54 - 1.68: 38 1.68 - 1.81: 76 Bond restraints: 7476 Sorted by residual: bond pdb=" O4 J40 R 501 " pdb=" P4 J40 R 501 " ideal model delta sigma weight residual 1.702 1.619 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" O42 J40 R 501 " pdb=" P4 J40 R 501 " ideal model delta sigma weight residual 1.548 1.486 0.062 2.00e-02 2.50e+03 9.61e+00 bond pdb=" C VAL R 85 " pdb=" O VAL R 85 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.17e-02 7.31e+03 9.09e+00 bond pdb=" N ILE A 55 " pdb=" CA ILE A 55 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 8.90e+00 bond pdb=" N ILE A 56 " pdb=" CA ILE A 56 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 8.82e+00 ... (remaining 7471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 10086 3.56 - 7.12: 34 7.12 - 10.68: 6 10.68 - 14.24: 0 14.24 - 17.79: 1 Bond angle restraints: 10127 Sorted by residual: angle pdb=" O1 J40 R 501 " pdb=" P1 J40 R 501 " pdb=" O13 J40 R 501 " ideal model delta sigma weight residual 92.86 110.65 -17.79 3.00e+00 1.11e-01 3.52e+01 angle pdb=" N PRO R 170 " pdb=" CA PRO R 170 " pdb=" C PRO R 170 " ideal model delta sigma weight residual 110.70 115.34 -4.64 1.22e+00 6.72e-01 1.45e+01 angle pdb=" N VAL R 85 " pdb=" CA VAL R 85 " pdb=" C VAL R 85 " ideal model delta sigma weight residual 110.62 106.75 3.87 1.02e+00 9.61e-01 1.44e+01 angle pdb=" O4 J40 R 501 " pdb=" P4 J40 R 501 " pdb=" O42 J40 R 501 " ideal model delta sigma weight residual 103.19 113.41 -10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" CA PRO R 170 " pdb=" C PRO R 170 " pdb=" N PRO R 171 " ideal model delta sigma weight residual 117.93 121.89 -3.96 1.20e+00 6.94e-01 1.09e+01 ... (remaining 10122 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.59: 4371 24.59 - 49.18: 208 49.18 - 73.78: 18 73.78 - 98.37: 9 98.37 - 122.96: 4 Dihedral angle restraints: 4610 sinusoidal: 1950 harmonic: 2660 Sorted by residual: dihedral pdb=" N03 YG7 R 502 " pdb=" C08 YG7 R 502 " pdb=" C10 YG7 R 502 " pdb=" N04 YG7 R 502 " ideal model delta sinusoidal sigma weight residual -57.61 65.35 -122.96 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" C12 YG7 R 502 " pdb=" C13 YG7 R 502 " pdb=" C14 YG7 R 502 " pdb=" C16 YG7 R 502 " ideal model delta sinusoidal sigma weight residual -62.79 58.08 -120.87 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" C40 J40 R 501 " pdb=" C41 J40 R 501 " pdb=" C42 J40 R 501 " pdb=" C43 J40 R 501 " ideal model delta sinusoidal sigma weight residual 178.73 62.12 116.61 1 3.00e+01 1.11e-03 1.54e+01 ... (remaining 4607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 823 0.042 - 0.084: 240 0.084 - 0.126: 79 0.126 - 0.168: 11 0.168 - 0.210: 6 Chirality restraints: 1159 Sorted by residual: chirality pdb=" C8 J40 R 501 " pdb=" C7 J40 R 501 " pdb=" C9 J40 R 501 " pdb=" O16 J40 R 501 " both_signs ideal model delta sigma weight residual False -2.41 -2.62 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB THR B 223 " pdb=" CA THR B 223 " pdb=" OG1 THR B 223 " pdb=" CG2 THR B 223 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA VAL A 50 " pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CB VAL A 50 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.20e-01 ... (remaining 1156 not shown) Planarity restraints: 1264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 YG7 R 502 " 0.007 2.00e-02 2.50e+03 2.00e-02 1.10e+01 pdb=" C18 YG7 R 502 " 0.021 2.00e-02 2.50e+03 pdb=" C19 YG7 R 502 " 0.000 2.00e-02 2.50e+03 pdb=" C21 YG7 R 502 " 0.025 2.00e-02 2.50e+03 pdb=" C23 YG7 R 502 " 0.016 2.00e-02 2.50e+03 pdb=" C24 YG7 R 502 " 0.004 2.00e-02 2.50e+03 pdb=" C26 YG7 R 502 " 0.011 2.00e-02 2.50e+03 pdb=" C29 YG7 R 502 " -0.007 2.00e-02 2.50e+03 pdb=" C32 YG7 R 502 " -0.031 2.00e-02 2.50e+03 pdb=" N04 YG7 R 502 " -0.044 2.00e-02 2.50e+03 pdb=" O01 YG7 R 502 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 90 " -0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO R 91 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 91 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 91 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO G 55 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.020 5.00e-02 4.00e+02 ... (remaining 1261 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 497 2.74 - 3.28: 7052 3.28 - 3.82: 12039 3.82 - 4.36: 13967 4.36 - 4.90: 25184 Nonbonded interactions: 58739 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.196 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.254 3.040 nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 2.264 3.040 nonbonded pdb=" CD1 ILE A 49 " pdb=" SG CYS A 224 " model vdw 2.265 3.820 nonbonded pdb=" O THR A 181 " pdb=" OG1 THR A 182 " model vdw 2.273 3.040 ... (remaining 58734 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.240 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 7477 Z= 0.253 Angle : 0.653 17.794 10129 Z= 0.369 Chirality : 0.045 0.210 1159 Planarity : 0.003 0.049 1264 Dihedral : 14.110 122.961 2881 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.29), residues: 902 helix: 2.65 (0.27), residues: 398 sheet: 0.34 (0.39), residues: 188 loop : -0.80 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 148 TYR 0.008 0.001 TYR R 198 PHE 0.012 0.001 PHE B 222 TRP 0.019 0.001 TRP R 175 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.25 ( 7476) covalent geometry : angle 0.65339 / 0.37 (10127) SS BOND : bond 0.00048 / 0.03 ( 1) SS BOND : angle 0.24260 / 0.14 ( 2) hydrogen bonds : bond 0.15497 / 10.56 ( 397) hydrogen bonds : angle 5.87595 / 4.13 ( 1140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.256 Fit side-chains REVERT: A 18 MET cc_start: 0.6629 (ttm) cc_final: 0.6357 (ttm) REVERT: A 351 CYS cc_start: 0.7699 (t) cc_final: 0.7491 (t) REVERT: B 46 ARG cc_start: 0.6733 (mtp-110) cc_final: 0.6478 (mtp-110) REVERT: B 191 SER cc_start: 0.9030 (t) cc_final: 0.8759 (t) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.5272 time to fit residues: 46.9964 Evaluate side-chains 76 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 237 ASN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.087645 restraints weight = 8371.086| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.77 r_work: 0.2770 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7477 Z= 0.135 Angle : 0.538 10.529 10129 Z= 0.278 Chirality : 0.043 0.317 1159 Planarity : 0.003 0.045 1264 Dihedral : 9.990 95.782 1215 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.16 % Allowed : 6.05 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.29), residues: 902 helix: 2.82 (0.27), residues: 398 sheet: 0.38 (0.39), residues: 186 loop : -0.91 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 49 TYR 0.009 0.001 TYR R 198 PHE 0.011 0.001 PHE B 222 TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 7476) covalent geometry : angle 0.53780 / 0.28 (10127) SS BOND : bond 0.00112 / 0.06 ( 1) SS BOND : angle 0.21150 / 0.12 ( 2) hydrogen bonds : bond 0.04350 / 2.92 ( 397) hydrogen bonds : angle 4.37557 / 3.10 ( 1140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.266 Fit side-chains REVERT: A 18 MET cc_start: 0.6138 (ttm) cc_final: 0.5929 (ttm) REVERT: A 46 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6683 (ttmm) REVERT: A 351 CYS cc_start: 0.7280 (t) cc_final: 0.7055 (t) REVERT: B 46 ARG cc_start: 0.6426 (mtp-110) cc_final: 0.5843 (mtp-110) REVERT: B 191 SER cc_start: 0.9093 (t) cc_final: 0.8832 (t) REVERT: B 205 ASP cc_start: 0.8152 (p0) cc_final: 0.7911 (p0) REVERT: B 298 ASP cc_start: 0.8218 (t0) cc_final: 0.7660 (t70) outliers start: 9 outliers final: 2 residues processed: 94 average time/residue: 0.4981 time to fit residues: 49.6167 Evaluate side-chains 81 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 65 optimal weight: 0.2980 chunk 69 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 230 ASN B 237 ASN R 100 ASN R 146 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.087444 restraints weight = 8260.828| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.76 r_work: 0.2727 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7477 Z= 0.127 Angle : 0.515 10.338 10129 Z= 0.262 Chirality : 0.043 0.334 1159 Planarity : 0.003 0.043 1264 Dihedral : 9.414 80.858 1215 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.42 % Allowed : 9.01 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.29), residues: 902 helix: 2.98 (0.27), residues: 398 sheet: 0.27 (0.37), residues: 197 loop : -1.02 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 49 TYR 0.009 0.001 TYR R 198 PHE 0.010 0.001 PHE A 196 TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 7476) covalent geometry : angle 0.51537 / 0.26 (10127) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 0.17045 / 0.10 ( 2) hydrogen bonds : bond 0.04041 / 2.70 ( 397) hydrogen bonds : angle 4.14212 / 2.93 ( 1140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.215 Fit side-chains REVERT: A 351 CYS cc_start: 0.7331 (t) cc_final: 0.7064 (t) REVERT: B 46 ARG cc_start: 0.6578 (mtp-110) cc_final: 0.6247 (mtp-110) REVERT: B 59 TYR cc_start: 0.8992 (m-80) cc_final: 0.8731 (m-80) REVERT: B 191 SER cc_start: 0.9123 (t) cc_final: 0.8887 (t) REVERT: B 205 ASP cc_start: 0.8229 (p0) cc_final: 0.7983 (p0) REVERT: B 212 ASP cc_start: 0.7883 (t0) cc_final: 0.7678 (t0) REVERT: B 269 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7556 (pp) REVERT: B 298 ASP cc_start: 0.8309 (t0) cc_final: 0.7753 (t70) outliers start: 11 outliers final: 3 residues processed: 102 average time/residue: 0.4800 time to fit residues: 52.0857 Evaluate side-chains 88 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 87 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 237 ASN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.086264 restraints weight = 8462.952| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.76 r_work: 0.2704 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7477 Z= 0.148 Angle : 0.515 10.537 10129 Z= 0.264 Chirality : 0.043 0.350 1159 Planarity : 0.003 0.042 1264 Dihedral : 8.776 81.708 1215 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.80 % Allowed : 11.07 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.29), residues: 902 helix: 2.95 (0.27), residues: 399 sheet: 0.17 (0.36), residues: 196 loop : -1.09 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 137 TYR 0.011 0.001 TYR R 198 PHE 0.012 0.001 PHE A 196 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 7476) covalent geometry : angle 0.51533 / 0.26 (10127) SS BOND : bond 0.00110 / 0.06 ( 1) SS BOND : angle 0.19593 / 0.11 ( 2) hydrogen bonds : bond 0.04074 / 2.72 ( 397) hydrogen bonds : angle 4.15292 / 2.95 ( 1140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.268 Fit side-chains REVERT: A 46 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6704 (mtmm) REVERT: A 248 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6688 (mttm) REVERT: A 351 CYS cc_start: 0.7447 (t) cc_final: 0.7172 (t) REVERT: B 46 ARG cc_start: 0.6617 (mtp-110) cc_final: 0.6278 (mtp-110) REVERT: B 191 SER cc_start: 0.9125 (t) cc_final: 0.8876 (t) REVERT: B 212 ASP cc_start: 0.7945 (t0) cc_final: 0.7733 (t0) REVERT: B 298 ASP cc_start: 0.8363 (t0) cc_final: 0.7786 (t70) outliers start: 14 outliers final: 6 residues processed: 97 average time/residue: 0.4878 time to fit residues: 50.3563 Evaluate side-chains 92 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 356 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 39 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 237 ASN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.086862 restraints weight = 7941.870| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.75 r_work: 0.2627 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7477 Z= 0.138 Angle : 0.504 10.514 10129 Z= 0.258 Chirality : 0.043 0.348 1159 Planarity : 0.003 0.040 1264 Dihedral : 8.522 76.371 1215 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.67 % Allowed : 12.61 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.29), residues: 902 helix: 2.95 (0.26), residues: 399 sheet: 0.12 (0.36), residues: 197 loop : -1.04 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 176 TYR 0.010 0.001 TYR R 198 PHE 0.011 0.001 PHE A 196 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 7476) covalent geometry : angle 0.50422 / 0.26 (10127) SS BOND : bond 0.00107 / 0.06 ( 1) SS BOND : angle 0.19132 / 0.11 ( 2) hydrogen bonds : bond 0.03940 / 2.63 ( 397) hydrogen bonds : angle 4.10068 / 2.90 ( 1140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.271 Fit side-chains REVERT: A 248 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6872 (mttm) REVERT: A 351 CYS cc_start: 0.7404 (t) cc_final: 0.7123 (t) REVERT: B 46 ARG cc_start: 0.6580 (mtp-110) cc_final: 0.6261 (mtp-110) REVERT: B 191 SER cc_start: 0.9159 (t) cc_final: 0.8920 (t) REVERT: R 347 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7173 (mt) outliers start: 13 outliers final: 7 residues processed: 93 average time/residue: 0.5048 time to fit residues: 49.7487 Evaluate side-chains 85 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 347 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 0.0010 chunk 80 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 61 optimal weight: 0.1980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 237 ASN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.087858 restraints weight = 8410.269| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.79 r_work: 0.2730 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7477 Z= 0.116 Angle : 0.489 10.293 10129 Z= 0.250 Chirality : 0.042 0.336 1159 Planarity : 0.003 0.039 1264 Dihedral : 8.392 81.978 1215 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.93 % Allowed : 13.38 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.29), residues: 902 helix: 2.96 (0.26), residues: 400 sheet: 0.21 (0.36), residues: 196 loop : -1.00 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 152 TYR 0.009 0.001 TYR R 198 PHE 0.009 0.001 PHE A 196 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 7476) covalent geometry : angle 0.48860 / 0.25 (10127) SS BOND : bond 0.00092 / 0.05 ( 1) SS BOND : angle 0.14039 / 0.07 ( 2) hydrogen bonds : bond 0.03684 / 2.46 ( 397) hydrogen bonds : angle 4.04542 / 2.86 ( 1140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.310 Fit side-chains REVERT: A 46 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6847 (mtmm) REVERT: A 351 CYS cc_start: 0.7354 (t) cc_final: 0.7063 (t) REVERT: B 46 ARG cc_start: 0.6602 (mtp-110) cc_final: 0.6314 (mtp-110) REVERT: B 59 TYR cc_start: 0.8980 (m-80) cc_final: 0.8765 (m-80) REVERT: B 191 SER cc_start: 0.9154 (t) cc_final: 0.8925 (t) REVERT: B 298 ASP cc_start: 0.8662 (t70) cc_final: 0.7657 (t0) REVERT: R 169 ILE cc_start: 0.6736 (OUTLIER) cc_final: 0.6315 (tp) REVERT: R 347 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7271 (mt) outliers start: 15 outliers final: 6 residues processed: 99 average time/residue: 0.4873 time to fit residues: 51.3167 Evaluate side-chains 92 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 347 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 78 optimal weight: 0.0980 chunk 87 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 237 ASN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.131471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.088330 restraints weight = 8416.846| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.81 r_work: 0.2791 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7477 Z= 0.114 Angle : 0.487 9.754 10129 Z= 0.248 Chirality : 0.042 0.319 1159 Planarity : 0.003 0.040 1264 Dihedral : 8.235 72.888 1215 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.54 % Allowed : 14.93 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.29), residues: 902 helix: 2.99 (0.26), residues: 400 sheet: 0.18 (0.36), residues: 196 loop : -1.01 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 148 TYR 0.009 0.001 TYR R 198 PHE 0.009 0.001 PHE A 196 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 7476) covalent geometry : angle 0.48655 / 0.25 (10127) SS BOND : bond 0.00077 / 0.04 ( 1) SS BOND : angle 0.12979 / 0.07 ( 2) hydrogen bonds : bond 0.03586 / 2.40 ( 397) hydrogen bonds : angle 3.98028 / 2.82 ( 1140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.198 Fit side-chains REVERT: A 46 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6952 (mtmm) REVERT: A 248 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6907 (mttm) REVERT: A 351 CYS cc_start: 0.7361 (t) cc_final: 0.7073 (t) REVERT: B 46 ARG cc_start: 0.6620 (mtp-110) cc_final: 0.6155 (mtp-110) REVERT: B 175 GLN cc_start: 0.7655 (mm110) cc_final: 0.6950 (pt0) REVERT: B 191 SER cc_start: 0.9164 (t) cc_final: 0.8933 (t) REVERT: B 298 ASP cc_start: 0.8711 (t70) cc_final: 0.7614 (t0) REVERT: R 169 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6252 (tp) REVERT: R 347 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7305 (mt) outliers start: 12 outliers final: 5 residues processed: 101 average time/residue: 0.5018 time to fit residues: 53.8262 Evaluate side-chains 96 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 347 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 61 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 51 optimal weight: 0.3980 chunk 56 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 58 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 294 ASN B 237 ASN R 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.131986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.088739 restraints weight = 8391.321| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.81 r_work: 0.2800 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7477 Z= 0.109 Angle : 0.480 8.950 10129 Z= 0.246 Chirality : 0.042 0.293 1159 Planarity : 0.003 0.039 1264 Dihedral : 8.286 79.053 1215 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.54 % Allowed : 15.70 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.29), residues: 902 helix: 3.05 (0.26), residues: 401 sheet: 0.28 (0.36), residues: 193 loop : -1.04 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 148 TYR 0.008 0.001 TYR R 198 PHE 0.008 0.001 PHE A 196 TRP 0.012 0.001 TRP B 211 HIS 0.002 0.000 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 7476) covalent geometry : angle 0.48031 / 0.25 (10127) SS BOND : bond 0.00075 / 0.04 ( 1) SS BOND : angle 0.10957 / 0.06 ( 2) hydrogen bonds : bond 0.03503 / 2.33 ( 397) hydrogen bonds : angle 3.93956 / 2.79 ( 1140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.272 Fit side-chains REVERT: A 46 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6919 (mtmm) REVERT: A 248 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6915 (mttm) REVERT: A 351 CYS cc_start: 0.7351 (t) cc_final: 0.7054 (t) REVERT: B 46 ARG cc_start: 0.6566 (mtp-110) cc_final: 0.6118 (mtp-110) REVERT: B 175 GLN cc_start: 0.7649 (mm110) cc_final: 0.6957 (pt0) REVERT: B 191 SER cc_start: 0.9154 (t) cc_final: 0.8921 (t) REVERT: B 298 ASP cc_start: 0.8696 (t70) cc_final: 0.7586 (t0) REVERT: R 169 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6259 (tp) outliers start: 12 outliers final: 4 residues processed: 104 average time/residue: 0.4859 time to fit residues: 53.7951 Evaluate side-chains 93 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 237 ASN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.086238 restraints weight = 8310.178| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.78 r_work: 0.2710 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7477 Z= 0.153 Angle : 0.507 7.462 10129 Z= 0.263 Chirality : 0.043 0.244 1159 Planarity : 0.003 0.040 1264 Dihedral : 8.511 78.383 1215 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.42 % Allowed : 15.70 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.29), residues: 902 helix: 2.98 (0.26), residues: 400 sheet: 0.13 (0.35), residues: 200 loop : -0.98 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 148 TYR 0.010 0.001 TYR R 198 PHE 0.012 0.001 PHE A 196 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 ( 7476) covalent geometry : angle 0.50696 / 0.26 (10127) SS BOND : bond 0.00103 / 0.05 ( 1) SS BOND : angle 0.20773 / 0.12 ( 2) hydrogen bonds : bond 0.03958 / 2.63 ( 397) hydrogen bonds : angle 4.02662 / 2.85 ( 1140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.205 Fit side-chains REVERT: A 46 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6968 (mtmm) REVERT: A 248 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6922 (mttm) REVERT: A 351 CYS cc_start: 0.7502 (t) cc_final: 0.7226 (t) REVERT: B 46 ARG cc_start: 0.6602 (mtp-110) cc_final: 0.6242 (mtp-110) REVERT: B 175 GLN cc_start: 0.7663 (mm110) cc_final: 0.6945 (pt0) REVERT: B 191 SER cc_start: 0.9165 (t) cc_final: 0.8936 (t) REVERT: B 298 ASP cc_start: 0.8722 (t70) cc_final: 0.7553 (t0) REVERT: B 321 THR cc_start: 0.8400 (p) cc_final: 0.8114 (p) outliers start: 11 outliers final: 9 residues processed: 105 average time/residue: 0.4350 time to fit residues: 48.4868 Evaluate side-chains 96 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 363 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 58 optimal weight: 0.0670 chunk 49 optimal weight: 0.0040 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 57 optimal weight: 0.0040 chunk 2 optimal weight: 0.3980 chunk 87 optimal weight: 0.0670 chunk 68 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 51 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 overall best weight: 0.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 237 ASN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.135895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.092942 restraints weight = 8340.260| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.81 r_work: 0.2813 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7477 Z= 0.089 Angle : 0.465 7.974 10129 Z= 0.241 Chirality : 0.041 0.215 1159 Planarity : 0.003 0.039 1264 Dihedral : 8.223 71.239 1215 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.29 % Allowed : 16.73 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.29), residues: 902 helix: 3.02 (0.26), residues: 403 sheet: 0.49 (0.37), residues: 183 loop : -1.03 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 219 TYR 0.006 0.001 TYR R 198 PHE 0.007 0.001 PHE B 199 TRP 0.014 0.001 TRP B 211 HIS 0.002 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.09 ( 7476) covalent geometry : angle 0.46540 / 0.24 (10127) SS BOND : bond 0.00075 / 0.04 ( 1) SS BOND : angle 0.14309 / 0.07 ( 2) hydrogen bonds : bond 0.03051 / 2.00 ( 397) hydrogen bonds : angle 3.85766 / 2.73 ( 1140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.300 Fit side-chains REVERT: A 46 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6921 (mtmm) REVERT: A 248 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6861 (mttm) REVERT: A 351 CYS cc_start: 0.7271 (t) cc_final: 0.6925 (t) REVERT: B 46 ARG cc_start: 0.6730 (mtp-110) cc_final: 0.6261 (mtp-110) REVERT: B 191 SER cc_start: 0.9130 (t) cc_final: 0.8905 (t) REVERT: B 298 ASP cc_start: 0.8538 (t70) cc_final: 0.7531 (t0) REVERT: R 169 ILE cc_start: 0.6605 (OUTLIER) cc_final: 0.6189 (tp) outliers start: 10 outliers final: 3 residues processed: 98 average time/residue: 0.3675 time to fit residues: 38.6808 Evaluate side-chains 90 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN B 237 ASN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.086490 restraints weight = 8367.649| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.77 r_work: 0.2764 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7477 Z= 0.160 Angle : 0.516 8.430 10129 Z= 0.268 Chirality : 0.043 0.220 1159 Planarity : 0.003 0.040 1264 Dihedral : 8.395 74.050 1215 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.16 % Allowed : 16.99 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.29), residues: 902 helix: 3.04 (0.26), residues: 400 sheet: 0.15 (0.35), residues: 200 loop : -1.01 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 148 TYR 0.011 0.001 TYR R 215 PHE 0.012 0.001 PHE A 196 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 7476) covalent geometry : angle 0.51639 / 0.27 (10127) SS BOND : bond 0.00075 / 0.04 ( 1) SS BOND : angle 0.20157 / 0.12 ( 2) hydrogen bonds : bond 0.03952 / 2.61 ( 397) hydrogen bonds : angle 4.00601 / 2.84 ( 1140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1953.62 seconds wall clock time: 34 minutes 13.66 seconds (2053.66 seconds total)