Starting phenix.real_space_refine on Thu Jan 18 04:39:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmq_16121/01_2024/8bmq_16121_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmq_16121/01_2024/8bmq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmq_16121/01_2024/8bmq_16121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmq_16121/01_2024/8bmq_16121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmq_16121/01_2024/8bmq_16121_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmq_16121/01_2024/8bmq_16121_updated.pdb" } 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 Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 104": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 4.93, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.4 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... running ksdssp... Secondary structure from input PDB file: 42 helices and 6 sheets defined 53.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 79 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 108 through 113 removed outlier: 3.747A pdb=" N ARG A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 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) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 146 through 159 Processing helix chain 'A' and resid 176 through 193 Processing helix chain 'A' and resid 206 through 209 removed outlier: 3.763A pdb=" N GLY A 209 " --> pdb=" O GLU A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'A' and resid 227 through 230 No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 268 through 280 Processing helix chain 'B' and resid 46 through 52 removed outlier: 3.564A pdb=" N HIS B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 103 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 118 through 131 Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 148 through 158 removed outlier: 3.798A pdb=" N ARG B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 194 removed outlier: 3.931A pdb=" N ALA B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 248 through 259 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 270 through 280 Processing helix chain 'C' and resid 13 through 30 Processing helix chain 'C' and resid 44 through 53 Processing helix chain 'C' and resid 57 through 74 removed outlier: 4.406A pdb=" N ALA C 62 " --> pdb=" O TRP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 100 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 107 through 120 Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 138 through 144 Processing helix chain 'C' and resid 146 through 171 Proline residue: C 153 - end of helix 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) Processing helix chain 'D' and resid 15 through 18 Processing helix chain 'D' and resid 21 through 36 removed outlier: 3.923A pdb=" N PHE D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 62 through 86 Proline residue: D 71 - end of helix removed outlier: 5.019A pdb=" N TRP D 74 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N MET D 75 " --> pdb=" O PRO D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 128 removed outlier: 3.793A pdb=" N ARG D 115 " --> pdb=" O TYR D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 149 removed outlier: 4.174A pdb=" N THR D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Proline residue: D 145 - end of helix removed outlier: 4.697A pdb=" N LEU D 148 " --> pdb=" O THR D 144 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE D 149 " --> pdb=" O PRO D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 184 Proline residue: D 168 - end of helix Processing helix chain 'D' and resid 192 through 225 removed outlier: 4.338A pdb=" N VAL D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Proline residue: D 202 - end of helix Proline residue: D 206 - end of helix Processing helix chain 'D' and resid 244 through 261 Proline residue: D 248 - end of helix removed outlier: 3.705A pdb=" N LEU D 253 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU D 255 " --> pdb=" O CYS D 252 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 67 through 69 removed outlier: 6.709A pdb=" N ILE A 30 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE A 5 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N PHE A 28 " --> pdb=" O ILE A 5 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 212 through 216 Processing sheet with id= C, first strand: chain 'B' and resid 69 through 72 removed outlier: 3.704A pdb=" N PHE B 28 " --> pdb=" O PHE B 5 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 26 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 36 through 40 removed outlier: 6.432A pdb=" N ASP B 214 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL B 39 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU B 216 " --> pdb=" O VAL B 39 " (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= E, first strand: chain 'B' and resid 166 through 170 removed outlier: 6.021A pdb=" N THR B 197 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU B 169 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE B 199 " --> pdb=" O LEU B 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 33 through 35 347 hydrogen bonds defined for protein. 993 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 3.24 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: 97.43 - 104.79: 139 104.79 - 112.14: 4068 112.14 - 119.49: 2722 119.49 - 126.84: 3724 126.84 - 134.19: 128 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: 554 2.73 - 3.27: 7998 3.27 - 3.82: 12381 3.82 - 4.36: 14434 4.36 - 4.90: 25483 Nonbonded interactions: 60850 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 2.520 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 2.440 nonbonded pdb=" OH TYR D 30 " pdb=" OG1 THR D 256 " model vdw 2.253 2.440 ... (remaining 60845 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.600 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.440 Find NCS groups from input model: 0.270 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.980 ------------------------------------------------------------------------------- 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= 0.425 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 fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.855 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: 0.2139 time to fit residues: 34.0496 Evaluate side-chains 95 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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: 0.6980 chunk 40 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7949 Z= 0.163 Angle : 0.502 8.936 10781 Z= 0.246 Chirality : 0.042 0.193 1243 Planarity : 0.004 0.039 1336 Dihedral : 9.651 56.554 1107 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.24 % Allowed : 8.86 % Favored : 90.90 % 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: 0.32 (0.28), residues: 975 helix: 1.07 (0.23), residues: 550 sheet: -0.37 (0.62), residues: 70 loop : -0.96 (0.33), 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 0.010 0.001 PHE B 188 TYR 0.017 0.001 TYR D 54 ARG 0.004 0.000 ARG D 263 *********************** 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 102 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.908 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 101 average time/residue: 0.1809 time to fit residues: 25.8552 Evaluate side-chains 96 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 48 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7949 Z= 0.268 Angle : 0.553 9.221 10781 Z= 0.273 Chirality : 0.043 0.172 1243 Planarity : 0.004 0.044 1336 Dihedral : 7.791 59.081 1107 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.44 % Allowed : 10.66 % Favored : 87.90 % 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 (0.28), residues: 975 helix: 1.00 (0.23), residues: 543 sheet: -0.38 (0.64), residues: 70 loop : -1.07 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 276 HIS 0.003 0.001 HIS B 52 PHE 0.015 0.001 PHE D 86 TYR 0.021 0.002 TYR D 54 ARG 0.004 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 114 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 ILE cc_start: 0.8591 (tp) cc_final: 0.8235 (tp) outliers start: 12 outliers final: 10 residues processed: 109 average time/residue: 0.2161 time to fit residues: 32.8849 Evaluate side-chains 107 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR 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 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 190 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.0983 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= 0.165 Angle : 0.472 8.485 10781 Z= 0.235 Chirality : 0.041 0.164 1243 Planarity : 0.004 0.043 1336 Dihedral : 7.053 62.050 1107 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.08 % Allowed : 12.93 % Favored : 85.99 % 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: 0.41 (0.28), residues: 975 helix: 1.15 (0.23), residues: 550 sheet: -0.17 (0.64), residues: 70 loop : -0.98 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 276 HIS 0.002 0.001 HIS A 10 PHE 0.015 0.001 PHE D 86 TYR 0.015 0.001 TYR D 17 ARG 0.002 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 103 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: B 66 ILE cc_start: 0.8524 (tp) cc_final: 0.8153 (tp) REVERT: C 100 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7264 (pp) outliers start: 9 outliers final: 7 residues processed: 100 average time/residue: 0.2249 time to fit residues: 31.9836 Evaluate side-chains 101 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 52 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 79 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7949 Z= 0.152 Angle : 0.460 7.999 10781 Z= 0.230 Chirality : 0.040 0.157 1243 Planarity : 0.004 0.046 1336 Dihedral : 6.705 61.829 1107 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.44 % Allowed : 13.41 % Favored : 85.15 % 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: 0.57 (0.28), residues: 975 helix: 1.28 (0.23), residues: 550 sheet: -0.04 (0.65), residues: 70 loop : -0.92 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 276 HIS 0.002 0.001 HIS B 242 PHE 0.015 0.001 PHE D 86 TYR 0.012 0.001 TYR D 17 ARG 0.002 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 109 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: B 66 ILE cc_start: 0.8533 (tp) cc_final: 0.8176 (tp) REVERT: C 100 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7256 (pp) outliers start: 12 outliers final: 7 residues processed: 105 average time/residue: 0.1798 time to fit residues: 26.8127 Evaluate side-chains 104 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain C residue 100 LEU 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 190 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.0030 chunk 89 optimal weight: 0.9980 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1067 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= 0.247 Angle : 0.515 8.721 10781 Z= 0.257 Chirality : 0.042 0.153 1243 Planarity : 0.004 0.047 1336 Dihedral : 6.695 60.324 1107 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.80 % Allowed : 13.77 % Favored : 84.43 % 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: 0.41 (0.28), residues: 975 helix: 1.19 (0.23), residues: 543 sheet: -0.22 (0.63), residues: 70 loop : -0.99 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 276 HIS 0.003 0.001 HIS B 242 PHE 0.018 0.001 PHE D 86 TYR 0.021 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 fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8175 (tp) REVERT: C 100 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7257 (pp) REVERT: D 190 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7184 (m-30) outliers start: 15 outliers final: 11 residues processed: 106 average time/residue: 0.1988 time to fit residues: 28.9836 Evaluate side-chains 112 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 66 ILE 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 118 MET Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7949 Z= 0.168 Angle : 0.474 8.116 10781 Z= 0.236 Chirality : 0.041 0.155 1243 Planarity : 0.004 0.048 1336 Dihedral : 6.542 59.640 1107 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.80 % Allowed : 14.25 % Favored : 83.95 % 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: 0.57 (0.28), residues: 975 helix: 1.28 (0.23), residues: 549 sheet: -0.07 (0.64), residues: 70 loop : -0.92 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 276 HIS 0.002 0.001 HIS A 10 PHE 0.018 0.001 PHE D 86 TYR 0.014 0.001 TYR D 17 ARG 0.001 0.000 ARG D 225 *********************** 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 111 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: B 66 ILE cc_start: 0.8547 (tp) cc_final: 0.8016 (tp) REVERT: C 100 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7283 (pp) outliers start: 15 outliers final: 10 residues processed: 104 average time/residue: 0.1790 time to fit residues: 26.6230 Evaluate side-chains 102 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 277 GLN 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 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7949 Z= 0.299 Angle : 0.552 8.874 10781 Z= 0.272 Chirality : 0.043 0.146 1243 Planarity : 0.004 0.048 1336 Dihedral : 6.648 59.799 1107 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.92 % Allowed : 14.97 % Favored : 83.11 % 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: 0.30 (0.27), residues: 975 helix: 1.11 (0.23), residues: 543 sheet: -0.40 (0.62), residues: 70 loop : -1.03 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 276 HIS 0.003 0.001 HIS B 52 PHE 0.020 0.001 PHE D 86 TYR 0.019 0.002 TYR D 54 ARG 0.002 0.000 ARG D 184 *********************** 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 110 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8297 (tp) REVERT: C 100 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7288 (pp) REVERT: C 157 MET cc_start: 0.6941 (mtp) cc_final: 0.6732 (mtm) outliers start: 16 outliers final: 14 residues processed: 102 average time/residue: 0.1909 time to fit residues: 27.1672 Evaluate side-chains 110 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 66 ILE 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 58 THR 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 118 MET Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7949 Z= 0.231 Angle : 0.515 8.589 10781 Z= 0.256 Chirality : 0.042 0.152 1243 Planarity : 0.004 0.048 1336 Dihedral : 6.577 59.706 1107 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.16 % Allowed : 14.61 % Favored : 83.23 % 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: 0.35 (0.28), residues: 975 helix: 1.11 (0.23), residues: 549 sheet: -0.34 (0.62), residues: 70 loop : -0.98 (0.33), residues: 356 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 0.020 0.001 PHE D 86 TYR 0.017 0.001 TYR D 54 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 111 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8291 (tp) REVERT: C 100 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7299 (pp) REVERT: C 157 MET cc_start: 0.6911 (mtp) cc_final: 0.6693 (mtm) outliers start: 18 outliers final: 14 residues processed: 101 average time/residue: 0.1895 time to fit residues: 26.7919 Evaluate side-chains 110 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 66 ILE 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 58 THR 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 118 MET Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 0.0670 chunk 95 optimal weight: 0.7980 chunk 88 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7949 Z= 0.144 Angle : 0.470 7.890 10781 Z= 0.235 Chirality : 0.040 0.154 1243 Planarity : 0.004 0.048 1336 Dihedral : 6.341 59.400 1107 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.32 % Allowed : 15.45 % Favored : 83.23 % 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: 0.61 (0.28), residues: 975 helix: 1.33 (0.23), residues: 549 sheet: -0.09 (0.64), residues: 70 loop : -0.90 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 276 HIS 0.002 0.001 HIS A 10 PHE 0.018 0.001 PHE D 86 TYR 0.012 0.001 TYR D 54 ARG 0.001 0.000 ARG D 225 ********************** 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 105 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: B 66 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8237 (tp) REVERT: C 100 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7326 (pp) REVERT: D 196 ARG cc_start: 0.6839 (ttp-170) cc_final: 0.6429 (mtp180) outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 0.2005 time to fit residues: 27.8930 Evaluate side-chains 104 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 66 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 HIS D 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.165526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.148929 restraints weight = 9431.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.148147 restraints weight = 8165.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.148248 restraints weight = 7980.789| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7949 Z= 0.202 Angle : 0.492 8.181 10781 Z= 0.244 Chirality : 0.041 0.152 1243 Planarity : 0.004 0.048 1336 Dihedral : 6.326 59.217 1107 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.68 % Allowed : 15.33 % Favored : 82.99 % 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: 0.57 (0.28), residues: 975 helix: 1.29 (0.23), residues: 549 sheet: -0.18 (0.63), residues: 70 loop : -0.90 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 276 HIS 0.002 0.001 HIS B 52 PHE 0.019 0.001 PHE D 86 TYR 0.014 0.001 TYR D 17 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: 1595.37 seconds wall clock time: 30 minutes 6.88 seconds (1806.88 seconds total)