Starting phenix.real_space_refine on Wed Mar 12 12:45:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bmq_16121/03_2025/8bmq_16121.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bmq_16121/03_2025/8bmq_16121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bmq_16121/03_2025/8bmq_16121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bmq_16121/03_2025/8bmq_16121.map" model { file = "/net/cci-nas-00/data/ceres_data/8bmq_16121/03_2025/8bmq_16121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bmq_16121/03_2025/8bmq_16121.cif" } resolution = 3.6 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= 0.010 sd= 0.098 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 6 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 5044 2.51 5 N 1283 2.21 5 O 1414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7784 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2137 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain breaks: 1 Chain: "B" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2162 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1321 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "D" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2101 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.21, per 1000 atoms: 0.67 Number of scatterers: 7784 At special positions: 0 Unit cell: (79.716, 83.804, 128.772, 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 36 16.00 P 6 15.00 Mg 1 11.99 O 1414 8.00 N 1283 7.00 C 5044 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: 2.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1820 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 5 sheets defined 61.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.793A pdb=" N ASN A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 85 removed outlier: 4.215A pdb=" N GLU A 84 " --> pdb=" O TRP A 80 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.904A pdb=" N LYS A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.217A pdb=" N VAL A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 194 Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.763A pdb=" N GLY A 209 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.822A pdb=" N PHE A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.912A pdb=" N LEU A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 267 through 281 removed outlier: 3.883A pdb=" N LEU A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.509A pdb=" N LEU B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.938A pdb=" N ASP B 82 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.800A pdb=" N LEU B 98 " --> pdb=" O GLU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.119A pdb=" N GLY B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Proline residue: B 111 - end of helix removed outlier: 3.959A pdb=" N PHE B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 132 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.724A pdb=" N LEU B 146 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.798A pdb=" N ARG B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 235 through 242 removed outlier: 3.900A pdb=" N LEU B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 260 removed outlier: 3.616A pdb=" N ALA B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 281 Processing helix chain 'C' and resid 12 through 30 Processing helix chain 'C' and resid 43 through 54 removed outlier: 3.974A pdb=" N GLY C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 75 removed outlier: 4.406A pdb=" N ALA C 62 " --> pdb=" O TRP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 101 removed outlier: 3.894A pdb=" N THR C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY C 92 " --> pdb=" O THR C 88 " (cutoff:3.500A) Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 106 through 121 Processing helix chain 'C' and resid 125 through 135 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.538A pdb=" N ARG C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 152 Processing helix chain 'C' and resid 152 through 172 removed outlier: 4.720A pdb=" N VAL C 158 " --> pdb=" O TRP C 154 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP C 161 " --> pdb=" O MET C 157 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 Processing helix chain 'D' and resid 20 through 37 removed outlier: 3.923A pdb=" N PHE D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU D 37 " --> pdb=" O ILE D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 59 removed outlier: 3.554A pdb=" N GLY D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 70 removed outlier: 4.217A pdb=" N PHE D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 87 Processing helix chain 'D' and resid 102 through 129 removed outlier: 3.793A pdb=" N ARG D 115 " --> pdb=" O TYR D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 144 through 150 Processing helix chain 'D' and resid 152 through 185 removed outlier: 4.019A pdb=" N ILE D 156 " --> pdb=" O ASN D 152 " (cutoff:3.500A) Proline residue: D 168 - end of helix Processing helix chain 'D' and resid 191 through 199 removed outlier: 4.136A pdb=" N LYS D 195 " --> pdb=" O GLY D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 226 Proline residue: D 206 - end of helix Processing helix chain 'D' and resid 245 through 262 removed outlier: 3.856A pdb=" N VAL D 249 " --> pdb=" O ASP D 245 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR D 256 " --> pdb=" O CYS D 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.301A pdb=" N ILE A 165 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE A 200 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 167 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 213 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLN A 224 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 215 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 26 through 30 removed outlier: 5.238A pdb=" N LEU B 26 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 28 " --> pdb=" O PHE B 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 90 removed outlier: 7.008A pdb=" N ALA B 90 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE B 167 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL B 201 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU B 169 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE B 36 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 225 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU B 219 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 33 through 35 421 hydrogen bonds defined for protein. 1185 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: 1.94 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2451 1.34 - 1.46: 1198 1.46 - 1.57: 4220 1.57 - 1.69: 12 1.69 - 1.81: 68 Bond restraints: 7949 Sorted by residual: bond pdb=" O3A ANP A 301 " pdb=" PB ANP A 301 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" O3A ANP B 301 " pdb=" PB ANP B 301 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" N3B ANP A 301 " pdb=" PG ANP A 301 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" N3B ANP B 301 " pdb=" PG ANP B 301 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" O5' ANP A 301 " pdb=" PA ANP A 301 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 7944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 10729 3.84 - 7.68: 42 7.68 - 11.52: 8 11.52 - 15.36: 0 15.36 - 19.20: 2 Bond angle restraints: 10781 Sorted by residual: angle pdb=" PB ANP A 301 " pdb=" N3B ANP A 301 " pdb=" PG ANP A 301 " ideal model delta sigma weight residual 126.95 107.75 19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" PB ANP B 301 " pdb=" N3B ANP B 301 " pdb=" PG ANP B 301 " ideal model delta sigma weight residual 126.95 107.82 19.13 3.00e+00 1.11e-01 4.06e+01 angle pdb=" O1B ANP B 301 " pdb=" PB ANP B 301 " pdb=" O2B ANP B 301 " ideal model delta sigma weight residual 120.08 109.00 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" C LEU A 174 " pdb=" N ASP A 175 " pdb=" CA ASP A 175 " ideal model delta sigma weight residual 120.65 125.64 -4.99 1.36e+00 5.41e-01 1.35e+01 angle pdb=" O1B ANP A 301 " pdb=" PB ANP A 301 " pdb=" O2B ANP A 301 " ideal model delta sigma weight residual 120.08 109.21 10.87 3.00e+00 1.11e-01 1.31e+01 ... (remaining 10776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4255 17.69 - 35.39: 383 35.39 - 53.08: 72 53.08 - 70.78: 31 70.78 - 88.47: 14 Dihedral angle restraints: 4755 sinusoidal: 1931 harmonic: 2824 Sorted by residual: dihedral pdb=" CA SER A 103 " pdb=" C SER A 103 " pdb=" N ASP A 104 " pdb=" CA ASP A 104 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP A 211 " pdb=" CB ASP A 211 " pdb=" CG ASP A 211 " pdb=" OD1 ASP A 211 " ideal model delta sinusoidal sigma weight residual -30.00 -85.09 55.09 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA THR B 197 " pdb=" C THR B 197 " pdb=" N VAL B 198 " pdb=" CA VAL B 198 " ideal model delta harmonic sigma weight residual -180.00 -164.03 -15.97 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 4752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1027 0.056 - 0.113: 190 0.113 - 0.169: 23 0.169 - 0.226: 1 0.226 - 0.282: 2 Chirality restraints: 1243 Sorted by residual: chirality pdb=" C3' ANP B 301 " pdb=" C2' ANP B 301 " pdb=" C4' ANP B 301 " pdb=" O3' ANP B 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C3' ANP A 301 " pdb=" C2' ANP A 301 " pdb=" C4' ANP A 301 " pdb=" O3' ANP A 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE B 21 " pdb=" CA ILE B 21 " pdb=" CG1 ILE B 21 " pdb=" CG2 ILE B 21 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1240 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 47 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C GLY C 47 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY C 47 " 0.011 2.00e-02 2.50e+03 pdb=" N SER C 48 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 92 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO C 93 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 198 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C VAL B 198 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL B 198 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE B 199 " -0.009 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 545 2.73 - 3.27: 7949 3.27 - 3.82: 12315 3.82 - 4.36: 14288 4.36 - 4.90: 25457 Nonbonded interactions: 60554 Sorted by model distance: nonbonded pdb=" O1B ANP B 301 " pdb=" O2G ANP B 301 " model vdw 2.190 3.040 nonbonded pdb=" OD1 ASN D 40 " pdb=" N TRP D 41 " model vdw 2.203 3.120 nonbonded pdb=" OD1 ASP B 170 " pdb="MG MG B 302 " model vdw 2.251 2.170 nonbonded pdb=" O PRO B 164 " pdb=" OH TYR B 191 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR D 30 " pdb=" OG1 THR D 256 " model vdw 2.253 3.040 ... (remaining 60549 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 group one per residue 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: 1.540 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.760 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.006 0.146 7949 Z= 0.387 Angle : 0.756 19.200 10781 Z= 0.355 Chirality : 0.046 0.282 1243 Planarity : 0.004 0.041 1336 Dihedral : 15.483 88.472 2935 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.27), residues: 975 helix: 0.76 (0.23), residues: 547 sheet: -0.74 (0.60), residues: 70 loop : -1.07 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 58 HIS 0.005 0.001 HIS A 202 PHE 0.020 0.002 PHE D 86 TYR 0.027 0.002 TYR D 54 ARG 0.006 0.000 ARG D 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.839 Fit side-chains REVERT: B 82 ASP cc_start: 0.5799 (m-30) cc_final: 0.5558 (m-30) REVERT: C 157 MET cc_start: 0.7164 (mtm) cc_final: 0.6944 (mtp) REVERT: D 126 MET cc_start: 0.8272 (tpp) cc_final: 0.8029 (tpp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1878 time to fit residues: 29.2453 Evaluate side-chains 95 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.164626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145726 restraints weight = 9325.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145752 restraints weight = 8498.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146265 restraints weight = 7952.999| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7949 Z= 0.250 Angle : 0.567 10.405 10781 Z= 0.284 Chirality : 0.044 0.197 1243 Planarity : 0.004 0.045 1336 Dihedral : 9.945 57.011 1107 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.60 % Allowed : 9.58 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.28), residues: 975 helix: 1.08 (0.23), residues: 550 sheet: -0.67 (0.62), residues: 70 loop : -0.96 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 276 HIS 0.004 0.001 HIS B 242 PHE 0.011 0.001 PHE B 188 TYR 0.020 0.002 TYR D 54 ARG 0.004 0.000 ARG A 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.982 Fit side-chains REVERT: D 126 MET cc_start: 0.8420 (tpp) cc_final: 0.8126 (tpp) outliers start: 5 outliers final: 5 residues processed: 101 average time/residue: 0.2447 time to fit residues: 35.1740 Evaluate side-chains 100 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.165788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144158 restraints weight = 9699.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143961 restraints weight = 8605.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145722 restraints weight = 7958.564| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7949 Z= 0.249 Angle : 0.546 10.020 10781 Z= 0.273 Chirality : 0.043 0.173 1243 Planarity : 0.004 0.052 1336 Dihedral : 7.884 59.823 1107 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.68 % Allowed : 11.14 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.28), residues: 975 helix: 1.12 (0.23), residues: 557 sheet: -0.65 (0.63), residues: 70 loop : -0.93 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 276 HIS 0.004 0.001 HIS B 242 PHE 0.013 0.001 PHE D 86 TYR 0.018 0.002 TYR D 54 ARG 0.003 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: B 66 ILE cc_start: 0.8628 (tp) cc_final: 0.8252 (tp) REVERT: D 126 MET cc_start: 0.8422 (tpp) cc_final: 0.8173 (tpp) outliers start: 14 outliers final: 11 residues processed: 107 average time/residue: 0.2092 time to fit residues: 31.7342 Evaluate side-chains 106 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.165315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147743 restraints weight = 9396.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147431 restraints weight = 9022.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147680 restraints weight = 8446.675| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7949 Z= 0.215 Angle : 0.516 9.741 10781 Z= 0.260 Chirality : 0.042 0.164 1243 Planarity : 0.004 0.056 1336 Dihedral : 7.087 62.112 1107 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.56 % Allowed : 13.53 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.28), residues: 975 helix: 1.24 (0.23), residues: 557 sheet: -0.61 (0.63), residues: 70 loop : -0.93 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 276 HIS 0.003 0.001 HIS B 242 PHE 0.014 0.001 PHE D 86 TYR 0.017 0.002 TYR D 17 ARG 0.003 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: B 66 ILE cc_start: 0.8539 (tp) cc_final: 0.8173 (tp) REVERT: C 100 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7249 (pp) REVERT: D 190 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.7021 (m-30) outliers start: 13 outliers final: 9 residues processed: 104 average time/residue: 0.1720 time to fit residues: 25.3504 Evaluate side-chains 105 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 152 ASN ** 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 = 0.3772 r_free = 0.3772 target = 0.148456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117963 restraints weight = 10739.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121298 restraints weight = 7091.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.123553 restraints weight = 5349.023| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7949 Z= 0.369 Angle : 0.613 10.492 10781 Z= 0.309 Chirality : 0.045 0.165 1243 Planarity : 0.005 0.057 1336 Dihedral : 7.084 61.255 1107 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.16 % Allowed : 13.77 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.27), residues: 975 helix: 1.06 (0.23), residues: 550 sheet: -0.90 (0.60), residues: 70 loop : -1.10 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 276 HIS 0.004 0.001 HIS B 52 PHE 0.017 0.002 PHE D 86 TYR 0.022 0.002 TYR D 54 ARG 0.004 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 100 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7125 (pp) outliers start: 18 outliers final: 14 residues processed: 118 average time/residue: 0.1839 time to fit residues: 30.3115 Evaluate side-chains 112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 86 optimal weight: 0.1980 chunk 47 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.165573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146473 restraints weight = 9409.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146677 restraints weight = 8683.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.147173 restraints weight = 8183.992| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7949 Z= 0.176 Angle : 0.508 9.590 10781 Z= 0.257 Chirality : 0.042 0.163 1243 Planarity : 0.004 0.058 1336 Dihedral : 6.803 61.151 1107 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.80 % Allowed : 15.69 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 975 helix: 1.34 (0.23), residues: 554 sheet: -0.73 (0.61), residues: 70 loop : -0.96 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 276 HIS 0.002 0.001 HIS B 242 PHE 0.015 0.001 PHE D 86 TYR 0.020 0.002 TYR B 12 ARG 0.002 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: B 66 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8155 (tp) REVERT: C 100 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7262 (pp) REVERT: D 196 ARG cc_start: 0.6776 (ttp-170) cc_final: 0.6412 (mtp180) outliers start: 15 outliers final: 10 residues processed: 109 average time/residue: 0.1704 time to fit residues: 26.6056 Evaluate side-chains 107 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 175 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.153115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121846 restraints weight = 10852.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125310 restraints weight = 7007.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127672 restraints weight = 5243.995| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7949 Z= 0.303 Angle : 0.567 9.959 10781 Z= 0.285 Chirality : 0.044 0.163 1243 Planarity : 0.004 0.058 1336 Dihedral : 6.792 60.076 1107 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.63 % Allowed : 16.05 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.28), residues: 975 helix: 1.21 (0.23), residues: 556 sheet: -0.88 (0.60), residues: 70 loop : -0.99 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 276 HIS 0.003 0.001 HIS A 10 PHE 0.018 0.001 PHE D 86 TYR 0.021 0.002 TYR D 17 ARG 0.002 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: B 66 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8108 (tp) REVERT: C 100 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7210 (pp) outliers start: 22 outliers final: 17 residues processed: 114 average time/residue: 0.1818 time to fit residues: 29.0956 Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 257 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.153954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122779 restraints weight = 10879.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126327 restraints weight = 6988.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.128749 restraints weight = 5198.519| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7949 Z= 0.252 Angle : 0.545 10.088 10781 Z= 0.275 Chirality : 0.043 0.157 1243 Planarity : 0.004 0.058 1336 Dihedral : 6.733 59.528 1107 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.40 % Allowed : 16.41 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.27), residues: 975 helix: 1.24 (0.23), residues: 556 sheet: -0.88 (0.60), residues: 70 loop : -0.98 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 276 HIS 0.003 0.001 HIS B 52 PHE 0.019 0.001 PHE D 86 TYR 0.020 0.002 TYR D 17 ARG 0.002 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 277 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: B 66 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8097 (tp) REVERT: C 100 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7239 (pp) REVERT: D 196 ARG cc_start: 0.6513 (ttp-170) cc_final: 0.5721 (ttm110) outliers start: 20 outliers final: 16 residues processed: 112 average time/residue: 0.1800 time to fit residues: 28.3491 Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 175 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.165747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.146893 restraints weight = 9536.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.147196 restraints weight = 8529.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147587 restraints weight = 7732.307| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7949 Z= 0.195 Angle : 0.516 9.293 10781 Z= 0.260 Chirality : 0.042 0.159 1243 Planarity : 0.004 0.058 1336 Dihedral : 6.591 58.812 1107 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.80 % Allowed : 17.37 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 975 helix: 1.39 (0.23), residues: 556 sheet: -0.75 (0.61), residues: 70 loop : -0.90 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 276 HIS 0.002 0.001 HIS B 52 PHE 0.018 0.001 PHE D 86 TYR 0.018 0.001 TYR D 17 ARG 0.002 0.000 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 277 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8070 (mp10) REVERT: B 66 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8144 (tp) REVERT: C 100 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7312 (pp) REVERT: D 196 ARG cc_start: 0.6790 (ttp-170) cc_final: 0.6411 (mtp180) outliers start: 15 outliers final: 12 residues processed: 109 average time/residue: 0.1854 time to fit residues: 28.5978 Evaluate side-chains 113 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 258 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.152467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121157 restraints weight = 10862.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124619 restraints weight = 7061.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126988 restraints weight = 5291.126| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7949 Z= 0.328 Angle : 0.595 10.535 10781 Z= 0.299 Chirality : 0.044 0.155 1243 Planarity : 0.004 0.058 1336 Dihedral : 6.714 58.302 1107 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.75 % Allowed : 16.65 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.27), residues: 975 helix: 1.20 (0.23), residues: 556 sheet: -0.94 (0.60), residues: 70 loop : -1.00 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 276 HIS 0.003 0.001 HIS B 52 PHE 0.021 0.002 PHE D 86 TYR 0.018 0.002 TYR D 54 ARG 0.003 0.000 ARG D 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 277 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: B 66 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8119 (tp) REVERT: C 100 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7225 (pp) REVERT: D 196 ARG cc_start: 0.6543 (ttp-170) cc_final: 0.5864 (ttm110) outliers start: 23 outliers final: 18 residues processed: 117 average time/residue: 0.1798 time to fit residues: 29.4725 Evaluate side-chains 120 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 257 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.164186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145228 restraints weight = 9553.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145324 restraints weight = 8496.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145881 restraints weight = 7899.602| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7949 Z= 0.232 Angle : 0.541 9.746 10781 Z= 0.273 Chirality : 0.042 0.158 1243 Planarity : 0.004 0.059 1336 Dihedral : 6.642 58.294 1107 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.28 % Allowed : 17.13 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.28), residues: 975 helix: 1.31 (0.23), residues: 556 sheet: -0.83 (0.60), residues: 70 loop : -0.94 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 276 HIS 0.003 0.001 HIS B 52 PHE 0.019 0.001 PHE D 86 TYR 0.015 0.001 TYR D 54 ARG 0.002 0.000 ARG D 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2169.48 seconds wall clock time: 39 minutes 7.85 seconds (2347.85 seconds total)