Starting phenix.real_space_refine on Sat Apr 4 22:13:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9odo_70371/04_2026/9odo_70371.cif Found real_map, /net/cci-nas-00/data/ceres_data/9odo_70371/04_2026/9odo_70371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9odo_70371/04_2026/9odo_70371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9odo_70371/04_2026/9odo_70371.map" model { file = "/net/cci-nas-00/data/ceres_data/9odo_70371/04_2026/9odo_70371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9odo_70371/04_2026/9odo_70371.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 17 5.16 5 C 2922 2.51 5 N 826 2.21 5 O 818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4586 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2116 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PTRANS': 4, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 632 Unresolved non-hydrogen angles: 787 Unresolved non-hydrogen dihedrals: 493 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLU:plan': 27, 'ASP:plan': 24, 'ARG:plan': 14, 'GLN:plan1': 12, 'PHE:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 358 Chain: "B" Number of atoms: 2149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2149 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 429 Unresolved non-hydrogen angles: 535 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 23, 'GLN:plan1': 10, 'ARG:plan': 14, 'ASN:plan1': 11, 'HIS:plan': 1, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 252 Chain: "G" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 289 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.12, per 1000 atoms: 0.24 Number of scatterers: 4586 At special positions: 0 Unit cell: (70.2837, 93.7116, 91.1085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 3 15.00 O 818 8.00 N 826 7.00 C 2922 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: 0.39 Conformation dependent library (CDL) restraints added in 303.7 milliseconds 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1372 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 9 sheets defined 35.6% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.703A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 91 removed outlier: 4.556A pdb=" N ALA A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.508A pdb=" N ALA A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 133 removed outlier: 3.625A pdb=" N ALA A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.686A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.590A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.243A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.011A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 328 through 349 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 11 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.520A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 226 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.543A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.682A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.220A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.364A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.012A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.737A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 284 through 285 229 hydrogen bonds defined for protein. 654 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: 0.66 Time building geometry restraints manager: 0.52 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: 1561 1.34 - 1.46: 846 1.46 - 1.57: 2239 1.57 - 1.69: 5 1.69 - 1.81: 26 Bond restraints: 4677 Sorted by residual: bond pdb=" CA GLY B 306 " pdb=" C GLY B 306 " ideal model delta sigma weight residual 1.518 1.505 0.014 1.02e-02 9.61e+03 1.87e+00 bond pdb=" C GLY B 319 " pdb=" N VAL B 320 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.97e-02 2.58e+03 8.52e-01 bond pdb=" N TYR A 69 " pdb=" CA TYR A 69 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.32e-02 5.74e+03 7.58e-01 bond pdb=" CA GLY B 202 " pdb=" C GLY B 202 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 7.04e-01 bond pdb=" C2' GTP A 401 " pdb=" C3' GTP A 401 " ideal model delta sigma weight residual 1.524 1.510 0.014 2.00e-02 2.50e+03 4.73e-01 ... (remaining 4672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 6133 1.12 - 2.24: 250 2.24 - 3.36: 53 3.36 - 4.48: 9 4.48 - 5.60: 3 Bond angle restraints: 6448 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.71 110.66 3.05 9.50e-01 1.11e+00 1.03e+01 angle pdb=" N GLY B 282 " pdb=" CA GLY B 282 " pdb=" C GLY B 282 " ideal model delta sigma weight residual 115.72 111.03 4.69 1.51e+00 4.39e-01 9.67e+00 angle pdb=" N TYR B 289 " pdb=" CA TYR B 289 " pdb=" C TYR B 289 " ideal model delta sigma weight residual 110.24 113.71 -3.47 1.30e+00 5.92e-01 7.11e+00 angle pdb=" CA GLY B 282 " pdb=" C GLY B 282 " pdb=" N ARG B 283 " ideal model delta sigma weight residual 118.55 116.11 2.44 1.10e+00 8.26e-01 4.91e+00 angle pdb=" CA TYR A 230 " pdb=" CB TYR A 230 " pdb=" CG TYR A 230 " ideal model delta sigma weight residual 113.90 117.85 -3.95 1.80e+00 3.09e-01 4.82e+00 ... (remaining 6443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 2592 34.41 - 68.81: 56 68.81 - 103.22: 2 103.22 - 137.63: 1 137.63 - 172.03: 1 Dihedral angle restraints: 2652 sinusoidal: 538 harmonic: 2114 Sorted by residual: dihedral pdb=" O5' GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PA GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual -85.88 86.16 -172.03 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -12.74 117.33 1 2.00e+01 2.50e-03 3.50e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual -68.92 -165.29 96.37 1 2.00e+01 2.50e-03 2.67e+01 ... (remaining 2649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 454 0.027 - 0.054: 192 0.054 - 0.082: 84 0.082 - 0.109: 39 0.109 - 0.136: 12 Chirality restraints: 781 Sorted by residual: chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE B 269 " pdb=" N ILE B 269 " pdb=" C ILE B 269 " pdb=" CB ILE B 269 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 778 not shown) Planarity restraints: 844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.05e-01 pdb=" N PRO B 194 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 74 " 0.002 2.00e-02 2.50e+03 6.34e-03 8.05e-01 pdb=" CG TYR A 74 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 74 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 74 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 74 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 74 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 74 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 74 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.014 5.00e-02 4.00e+02 2.11e-02 7.10e-01 pdb=" N PRO B 236 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.012 5.00e-02 4.00e+02 ... (remaining 841 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1626 2.83 - 3.35: 3896 3.35 - 3.87: 6838 3.87 - 4.38: 6867 4.38 - 4.90: 12859 Nonbonded interactions: 32086 Sorted by model distance: nonbonded pdb=" OG SER A 44 " pdb=" NZ LYS A 46 " model vdw 2.316 3.120 nonbonded pdb=" O LEU A 249 " pdb=" OG SER A 252 " model vdw 2.333 3.040 nonbonded pdb=" NH1 ARG B 49 " pdb=" O SER B 84 " model vdw 2.383 3.120 nonbonded pdb=" O2' GTP A 401 " pdb=" O3' GTP A 401 " model vdw 2.426 2.432 nonbonded pdb=" OG SER A 206 " pdb=" O GLY B 162 " model vdw 2.440 3.040 ... (remaining 32081 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: 1.500 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4677 Z= 0.148 Angle : 0.556 5.603 6448 Z= 0.328 Chirality : 0.041 0.136 781 Planarity : 0.002 0.024 844 Dihedral : 15.096 172.033 1280 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.81 % Allowed : 25.91 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.33), residues: 717 helix: 3.00 (0.34), residues: 247 sheet: -1.50 (0.40), residues: 175 loop : -1.52 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 15 TYR 0.013 0.002 TYR A 74 PHE 0.009 0.001 PHE B 292 TRP 0.008 0.001 TRP B 339 HIS 0.001 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4677) covalent geometry : angle 0.55593 ( 6448) hydrogen bonds : bond 0.14949 ( 229) hydrogen bonds : angle 4.83065 ( 654) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.185 Fit side-chains REVERT: B 74 SER cc_start: 0.8456 (t) cc_final: 0.8026 (p) REVERT: B 80 ILE cc_start: 0.9009 (mt) cc_final: 0.8766 (mt) REVERT: B 228 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7908 (m-30) outliers start: 2 outliers final: 0 residues processed: 81 average time/residue: 0.0852 time to fit residues: 8.5458 Evaluate side-chains 49 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.121581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.095587 restraints weight = 10698.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.094304 restraints weight = 8862.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.095701 restraints weight = 7234.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.096164 restraints weight = 5366.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.096332 restraints weight = 4980.292| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4677 Z= 0.286 Angle : 0.658 7.940 6448 Z= 0.357 Chirality : 0.046 0.158 781 Planarity : 0.004 0.025 844 Dihedral : 10.218 159.967 770 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 8.10 % Allowed : 23.89 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.33), residues: 717 helix: 2.68 (0.34), residues: 249 sheet: -1.72 (0.40), residues: 178 loop : -1.76 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 178 TYR 0.017 0.002 TYR B 111 PHE 0.021 0.003 PHE B 241 TRP 0.016 0.003 TRP B 297 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00640 ( 4677) covalent geometry : angle 0.65755 ( 6448) hydrogen bonds : bond 0.04179 ( 229) hydrogen bonds : angle 4.31989 ( 654) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.154 Fit side-chains REVERT: A 131 TRP cc_start: 0.7675 (t-100) cc_final: 0.7415 (t-100) REVERT: B 74 SER cc_start: 0.8936 (t) cc_final: 0.8706 (p) REVERT: B 160 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.9115 (m) REVERT: B 262 MET cc_start: 0.8636 (ppp) cc_final: 0.8027 (ppp) outliers start: 20 outliers final: 10 residues processed: 67 average time/residue: 0.0697 time to fit residues: 6.0256 Evaluate side-chains 52 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 37 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 63 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.124150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096060 restraints weight = 10577.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097533 restraints weight = 6471.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.098124 restraints weight = 5107.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098186 restraints weight = 4547.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.098289 restraints weight = 4384.333| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4677 Z= 0.111 Angle : 0.504 7.120 6448 Z= 0.268 Chirality : 0.041 0.137 781 Planarity : 0.003 0.033 844 Dihedral : 9.700 152.712 768 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.26 % Allowed : 28.74 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.34), residues: 717 helix: 2.99 (0.34), residues: 248 sheet: -1.52 (0.40), residues: 180 loop : -1.61 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 178 TYR 0.009 0.001 TYR A 296 PHE 0.013 0.001 PHE A 336 TRP 0.007 0.001 TRP B 99 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 4677) covalent geometry : angle 0.50442 ( 6448) hydrogen bonds : bond 0.03054 ( 229) hydrogen bonds : angle 3.59945 ( 654) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.180 Fit side-chains REVERT: A 131 TRP cc_start: 0.7891 (t-100) cc_final: 0.7575 (t-100) REVERT: B 262 MET cc_start: 0.8098 (ppp) cc_final: 0.7724 (ppp) outliers start: 13 outliers final: 7 residues processed: 58 average time/residue: 0.0680 time to fit residues: 5.1384 Evaluate side-chains 52 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 63 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.125742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.098504 restraints weight = 10584.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099047 restraints weight = 6999.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.100193 restraints weight = 5555.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.100476 restraints weight = 4703.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.100518 restraints weight = 4573.982| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4677 Z= 0.082 Angle : 0.471 6.884 6448 Z= 0.246 Chirality : 0.040 0.128 781 Planarity : 0.002 0.023 844 Dihedral : 9.422 150.889 768 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.45 % Allowed : 29.55 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.34), residues: 717 helix: 3.09 (0.34), residues: 248 sheet: -1.26 (0.41), residues: 172 loop : -1.59 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 178 TYR 0.008 0.001 TYR A 296 PHE 0.014 0.001 PHE A 336 TRP 0.010 0.001 TRP B 82 HIS 0.001 0.000 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00166 ( 4677) covalent geometry : angle 0.47146 ( 6448) hydrogen bonds : bond 0.02613 ( 229) hydrogen bonds : angle 3.30371 ( 654) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.169 Fit side-chains REVERT: A 131 TRP cc_start: 0.7862 (t-100) cc_final: 0.7612 (t-100) outliers start: 11 outliers final: 7 residues processed: 53 average time/residue: 0.0575 time to fit residues: 4.0141 Evaluate side-chains 51 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 40.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.123725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.096247 restraints weight = 10771.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096204 restraints weight = 7231.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.097362 restraints weight = 6095.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.097741 restraints weight = 4987.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.097811 restraints weight = 4679.303| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4677 Z= 0.113 Angle : 0.490 6.999 6448 Z= 0.256 Chirality : 0.041 0.131 781 Planarity : 0.002 0.019 844 Dihedral : 9.492 153.039 768 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.64 % Allowed : 29.96 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.34), residues: 717 helix: 3.13 (0.34), residues: 251 sheet: -1.33 (0.41), residues: 173 loop : -1.61 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 178 TYR 0.008 0.001 TYR A 296 PHE 0.013 0.001 PHE A 336 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 4677) covalent geometry : angle 0.48994 ( 6448) hydrogen bonds : bond 0.02780 ( 229) hydrogen bonds : angle 3.28574 ( 654) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.173 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 53 average time/residue: 0.0728 time to fit residues: 5.0121 Evaluate side-chains 50 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 64 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.125016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.096437 restraints weight = 10840.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.097353 restraints weight = 6686.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.098060 restraints weight = 5723.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098302 restraints weight = 4826.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098454 restraints weight = 4580.582| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4677 Z= 0.082 Angle : 0.462 6.924 6448 Z= 0.240 Chirality : 0.040 0.128 781 Planarity : 0.002 0.024 844 Dihedral : 9.296 150.965 768 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.24 % Allowed : 30.77 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.34), residues: 717 helix: 3.21 (0.33), residues: 250 sheet: -1.13 (0.42), residues: 172 loop : -1.64 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 178 TYR 0.007 0.001 TYR B 264 PHE 0.011 0.001 PHE A 274 TRP 0.012 0.001 TRP B 82 HIS 0.001 0.000 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00171 ( 4677) covalent geometry : angle 0.46188 ( 6448) hydrogen bonds : bond 0.02445 ( 229) hydrogen bonds : angle 3.13366 ( 654) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.169 Fit side-chains REVERT: A 131 TRP cc_start: 0.7946 (t-100) cc_final: 0.7679 (t-100) outliers start: 8 outliers final: 7 residues processed: 52 average time/residue: 0.0737 time to fit residues: 4.9938 Evaluate side-chains 50 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 9 optimal weight: 40.0000 chunk 8 optimal weight: 30.0000 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 0.0670 chunk 13 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 overall best weight: 2.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.119829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.089424 restraints weight = 10882.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.091424 restraints weight = 7192.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.092734 restraints weight = 5547.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.093345 restraints weight = 4689.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094295 restraints weight = 4259.502| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4677 Z= 0.208 Angle : 0.571 7.648 6448 Z= 0.302 Chirality : 0.043 0.133 781 Planarity : 0.003 0.021 844 Dihedral : 9.861 154.607 768 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 6.07 % Allowed : 26.32 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.33), residues: 717 helix: 2.93 (0.33), residues: 257 sheet: -1.64 (0.39), residues: 175 loop : -1.77 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 178 TYR 0.012 0.002 TYR A 74 PHE 0.016 0.002 PHE B 241 TRP 0.012 0.002 TRP B 297 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 4677) covalent geometry : angle 0.57068 ( 6448) hydrogen bonds : bond 0.03547 ( 229) hydrogen bonds : angle 3.69446 ( 654) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.179 Fit side-chains REVERT: A 131 TRP cc_start: 0.7965 (t-100) cc_final: 0.7728 (t-100) REVERT: B 49 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8131 (mtt90) outliers start: 15 outliers final: 12 residues processed: 54 average time/residue: 0.0628 time to fit residues: 4.5276 Evaluate side-chains 50 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.122077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093946 restraints weight = 10850.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.093582 restraints weight = 7452.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.094432 restraints weight = 6525.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094797 restraints weight = 5454.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.095068 restraints weight = 5149.778| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4677 Z= 0.108 Angle : 0.501 7.279 6448 Z= 0.260 Chirality : 0.041 0.133 781 Planarity : 0.002 0.025 844 Dihedral : 9.564 150.402 768 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.86 % Allowed : 27.94 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.34), residues: 717 helix: 3.02 (0.34), residues: 256 sheet: -1.55 (0.39), residues: 175 loop : -1.75 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 178 TYR 0.009 0.001 TYR B 264 PHE 0.012 0.001 PHE A 274 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 4677) covalent geometry : angle 0.50078 ( 6448) hydrogen bonds : bond 0.02827 ( 229) hydrogen bonds : angle 3.37152 ( 654) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.176 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 51 average time/residue: 0.0728 time to fit residues: 4.8311 Evaluate side-chains 47 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 55 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.123464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.094674 restraints weight = 10616.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.095496 restraints weight = 6518.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.096162 restraints weight = 5657.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.096492 restraints weight = 4927.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096586 restraints weight = 4607.438| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4677 Z= 0.089 Angle : 0.490 7.012 6448 Z= 0.252 Chirality : 0.040 0.132 781 Planarity : 0.002 0.026 844 Dihedral : 9.355 148.115 768 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.05 % Allowed : 28.34 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.34), residues: 717 helix: 3.06 (0.34), residues: 256 sheet: -1.41 (0.40), residues: 175 loop : -1.71 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 49 TYR 0.008 0.001 TYR B 264 PHE 0.013 0.001 PHE A 274 TRP 0.019 0.001 TRP A 131 HIS 0.002 0.000 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 4677) covalent geometry : angle 0.48972 ( 6448) hydrogen bonds : bond 0.02529 ( 229) hydrogen bonds : angle 3.19706 ( 654) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.168 Fit side-chains REVERT: A 131 TRP cc_start: 0.8140 (t-100) cc_final: 0.7830 (t-100) outliers start: 10 outliers final: 8 residues processed: 48 average time/residue: 0.0592 time to fit residues: 3.8553 Evaluate side-chains 47 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 62 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.119498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.089131 restraints weight = 10898.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.091186 restraints weight = 7208.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.092426 restraints weight = 5520.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.093579 restraints weight = 4648.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.093970 restraints weight = 4115.228| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4677 Z= 0.200 Angle : 0.572 7.526 6448 Z= 0.301 Chirality : 0.043 0.135 781 Planarity : 0.003 0.037 844 Dihedral : 9.827 153.983 768 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.05 % Allowed : 28.34 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.33), residues: 717 helix: 2.89 (0.33), residues: 257 sheet: -1.54 (0.40), residues: 169 loop : -1.88 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 49 TYR 0.012 0.001 TYR B 264 PHE 0.016 0.002 PHE B 241 TRP 0.017 0.002 TRP A 131 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 4677) covalent geometry : angle 0.57196 ( 6448) hydrogen bonds : bond 0.03444 ( 229) hydrogen bonds : angle 3.65971 ( 654) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.150 Fit side-chains REVERT: A 131 TRP cc_start: 0.8152 (t-100) cc_final: 0.7827 (t-100) outliers start: 10 outliers final: 9 residues processed: 47 average time/residue: 0.0657 time to fit residues: 4.0926 Evaluate side-chains 47 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 9 optimal weight: 40.0000 chunk 20 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.122146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.094873 restraints weight = 10879.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.094072 restraints weight = 7378.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.095113 restraints weight = 6213.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.095310 restraints weight = 5201.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.097134 restraints weight = 4923.638| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4677 Z= 0.100 Angle : 0.499 7.198 6448 Z= 0.259 Chirality : 0.040 0.136 781 Planarity : 0.002 0.037 844 Dihedral : 9.490 149.149 768 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.45 % Allowed : 27.94 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.33), residues: 717 helix: 3.03 (0.33), residues: 256 sheet: -1.36 (0.41), residues: 168 loop : -1.87 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 49 TYR 0.011 0.001 TYR B 264 PHE 0.014 0.001 PHE A 274 TRP 0.014 0.001 TRP A 131 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 4677) covalent geometry : angle 0.49919 ( 6448) hydrogen bonds : bond 0.02678 ( 229) hydrogen bonds : angle 3.31846 ( 654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 833.66 seconds wall clock time: 14 minutes 52.78 seconds (892.78 seconds total)