Starting phenix.real_space_refine on Fri Aug 22 14:29:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tc3_41151/08_2025/8tc3_41151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tc3_41151/08_2025/8tc3_41151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tc3_41151/08_2025/8tc3_41151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tc3_41151/08_2025/8tc3_41151.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tc3_41151/08_2025/8tc3_41151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tc3_41151/08_2025/8tc3_41151.map" } resolution = 2.57 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= 0.039 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 Fe 4 7.16 5 S 46 5.16 5 C 2570 2.51 5 N 700 2.21 5 O 809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4129 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2052 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "B" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2052 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 684 SG CYS A 97 19.145 34.501 42.446 1.00 16.69 S ATOM 939 SG CYS A 132 24.431 37.443 41.514 1.00 12.41 S ATOM 2736 SG CYS B 97 19.867 37.778 36.754 1.00 19.30 S ATOM 2991 SG CYS B 132 23.288 32.561 37.759 1.00 17.13 S Time building chain proxies: 1.15, per 1000 atoms: 0.28 Number of scatterers: 4129 At special positions: 0 Unit cell: (65.65, 65.65, 80.6, 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) Fe 4 26.01 S 46 16.00 O 809 8.00 N 700 7.00 C 2570 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: 0.32 Conformation dependent library (CDL) restraints added in 124.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS A 97 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS A 132 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 132 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 97 " Number of angles added : 12 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 976 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 53.7% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 97 through 113 removed outlier: 3.592A pdb=" N GLY A 101 " --> pdb=" O CYS A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 154 through 172 Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 214 through 223 removed outlier: 4.067A pdb=" N GLN A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 234 through 249 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'B' and resid 14 through 29 Processing helix chain 'B' and resid 45 through 50 Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 71 through 76 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 97 through 112 removed outlier: 3.820A pdb=" N GLY B 101 " --> pdb=" O CYS B 97 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 154 through 173 removed outlier: 3.794A pdb=" N ASN B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 214 through 223 removed outlier: 4.024A pdb=" N GLN B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 234 through 249 Processing helix chain 'B' and resid 260 through 271 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 78 removed outlier: 6.521A pdb=" N MET A 34 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASP A 125 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 36 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN A 4 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N TYR A 148 " --> pdb=" O GLN A 4 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA A 6 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL A 150 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR A 8 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE A 147 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE A 183 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 149 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN A 185 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N CYS A 151 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 12.812A pdb=" N MET A 207 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N GLY A 180 " --> pdb=" O MET A 207 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N HIS A 209 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 182 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL A 211 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N CYS A 184 " --> pdb=" O VAL A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 78 removed outlier: 6.623A pdb=" N GLN B 4 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N TYR B 148 " --> pdb=" O GLN B 4 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA B 6 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 150 " --> pdb=" O ALA B 6 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR B 8 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 147 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE B 183 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE B 149 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN B 185 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N CYS B 151 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 12.922A pdb=" N MET B 207 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 10.653A pdb=" N GLY B 180 " --> pdb=" O MET B 207 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N HIS B 209 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 182 " --> pdb=" O HIS B 209 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL B 211 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N CYS B 184 " --> pdb=" O VAL B 211 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 573 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: 0.68 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.44: 1649 1.44 - 1.65: 2431 1.65 - 1.86: 70 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 4162 Sorted by residual: bond pdb=" C ILE B 273 " pdb=" O ILE B 273 " ideal model delta sigma weight residual 1.231 1.241 -0.009 1.02e-02 9.61e+03 8.34e-01 bond pdb=" C TYR A 8 " pdb=" N GLY A 9 " ideal model delta sigma weight residual 1.319 1.328 -0.009 1.34e-02 5.57e+03 4.78e-01 bond pdb=" C MET A 137 " pdb=" O MET A 137 " ideal model delta sigma weight residual 1.244 1.237 0.007 1.00e-02 1.00e+04 4.25e-01 bond pdb=" CA GLY A 96 " pdb=" C GLY A 96 " ideal model delta sigma weight residual 1.523 1.514 0.009 1.36e-02 5.41e+03 4.18e-01 bond pdb=" CB MET B 155 " pdb=" CG MET B 155 " ideal model delta sigma weight residual 1.520 1.501 0.019 3.00e-02 1.11e+03 3.90e-01 ... (remaining 4157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 5515 1.48 - 2.96: 84 2.96 - 4.44: 6 4.44 - 5.92: 2 5.92 - 7.40: 1 Bond angle restraints: 5608 Sorted by residual: angle pdb=" NE ARG B 100 " pdb=" CZ ARG B 100 " pdb=" NH2 ARG B 100 " ideal model delta sigma weight residual 119.20 121.48 -2.28 9.00e-01 1.23e+00 6.44e+00 angle pdb=" NE ARG B 100 " pdb=" CZ ARG B 100 " pdb=" NH1 ARG B 100 " ideal model delta sigma weight residual 121.50 119.16 2.34 1.00e+00 1.00e+00 5.46e+00 angle pdb=" C CYS A 38 " pdb=" N ASP A 39 " pdb=" CA ASP A 39 " ideal model delta sigma weight residual 121.27 128.67 -7.40 3.40e+00 8.65e-02 4.74e+00 angle pdb=" C ALA A 136 " pdb=" N MET A 137 " pdb=" CA MET A 137 " ideal model delta sigma weight residual 120.26 122.64 -2.38 1.34e+00 5.57e-01 3.15e+00 angle pdb=" CA GLY B 9 " pdb=" C GLY B 9 " pdb=" N LYS B 10 " ideal model delta sigma weight residual 115.34 116.70 -1.36 8.10e-01 1.52e+00 2.81e+00 ... (remaining 5603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 2196 17.90 - 35.79: 251 35.79 - 53.69: 78 53.69 - 71.59: 16 71.59 - 89.48: 11 Dihedral angle restraints: 2552 sinusoidal: 1020 harmonic: 1532 Sorted by residual: dihedral pdb=" CA ASP A 39 " pdb=" CB ASP A 39 " pdb=" CG ASP A 39 " pdb=" OD1 ASP A 39 " ideal model delta sinusoidal sigma weight residual -30.00 -89.08 59.08 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP A 262 " pdb=" CB ASP A 262 " pdb=" CG ASP A 262 " pdb=" OD1 ASP A 262 " ideal model delta sinusoidal sigma weight residual -30.00 -87.79 57.79 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP B 262 " pdb=" CB ASP B 262 " pdb=" CG ASP B 262 " pdb=" OD1 ASP B 262 " ideal model delta sinusoidal sigma weight residual -30.00 -87.22 57.22 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 2549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 384 0.028 - 0.056: 161 0.056 - 0.084: 57 0.084 - 0.112: 31 0.112 - 0.140: 11 Chirality restraints: 644 Sorted by residual: chirality pdb=" CA ILE B 255 " pdb=" N ILE B 255 " pdb=" C ILE B 255 " pdb=" CB ILE B 255 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE A 255 " pdb=" N ILE A 255 " pdb=" C ILE A 255 " pdb=" CB ILE A 255 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL B 150 " pdb=" N VAL B 150 " pdb=" C VAL B 150 " pdb=" CB VAL B 150 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 641 not shown) Planarity restraints: 730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 130 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.08e+00 pdb=" C VAL A 130 " -0.018 2.00e-02 2.50e+03 pdb=" O VAL A 130 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL A 131 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 211 " -0.015 5.00e-02 4.00e+02 2.33e-02 8.70e-01 pdb=" N PRO B 212 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO B 212 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 212 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 211 " 0.014 5.00e-02 4.00e+02 2.06e-02 6.76e-01 pdb=" N PRO A 212 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " 0.011 5.00e-02 4.00e+02 ... (remaining 727 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 972 2.79 - 3.32: 3856 3.32 - 3.85: 7462 3.85 - 4.37: 9078 4.37 - 4.90: 14890 Nonbonded interactions: 36258 Sorted by model distance: nonbonded pdb=" O GLY A 133 " pdb=" NH2 ARG A 140 " model vdw 2.266 3.120 nonbonded pdb=" O GLY A 94 " pdb=" OH TYR B 171 " model vdw 2.289 3.040 nonbonded pdb=" NE2 GLN B 145 " pdb=" OG SER B 176 " model vdw 2.301 3.120 nonbonded pdb=" OG1 THR B 45 " pdb=" OE1 GLN B 54 " model vdw 2.301 3.040 nonbonded pdb=" NZ LYS B 10 " pdb=" O GLY B 11 " model vdw 2.337 3.120 ... (remaining 36253 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 274) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.350 Find NCS groups from input model: 0.070 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:7.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 0.020 4166 Z= 0.122 Angle : 0.516 7.399 5620 Z= 0.267 Chirality : 0.040 0.140 644 Planarity : 0.003 0.023 730 Dihedral : 18.012 89.482 1576 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.46 % Allowed : 25.00 % Favored : 74.54 % 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 aren not related in a simple way. whole: 0.50 (0.36), residues: 534 helix: 1.69 (0.34), residues: 248 sheet: -0.80 (0.54), residues: 84 loop : -0.83 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 100 TYR 0.009 0.001 TYR B 80 PHE 0.010 0.001 PHE A 271 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4162) covalent geometry : angle 0.47489 ( 5608) hydrogen bonds : bond 0.14266 ( 199) hydrogen bonds : angle 4.99748 ( 573) metal coordination : bond 0.00885 ( 4) metal coordination : angle 4.37961 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.168 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 82 average time/residue: 0.7321 time to fit residues: 61.6756 Evaluate side-chains 81 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 177 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.0670 chunk 25 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119012 restraints weight = 3858.011| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.67 r_work: 0.3207 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4166 Z= 0.114 Angle : 0.467 6.556 5620 Z= 0.235 Chirality : 0.041 0.146 644 Planarity : 0.003 0.023 730 Dihedral : 4.311 23.402 584 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 4.59 % Allowed : 20.41 % Favored : 75.00 % 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 aren not related in a simple way. whole: 0.84 (0.37), residues: 534 helix: 2.01 (0.34), residues: 252 sheet: -0.93 (0.55), residues: 84 loop : -0.62 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 100 TYR 0.007 0.001 TYR B 80 PHE 0.010 0.001 PHE A 271 HIS 0.001 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 4162) covalent geometry : angle 0.43321 ( 5608) hydrogen bonds : bond 0.03560 ( 199) hydrogen bonds : angle 4.16989 ( 573) metal coordination : bond 0.00868 ( 4) metal coordination : angle 3.78481 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.165 Fit side-chains REVERT: A 206 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8266 (pm20) REVERT: B 60 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.5940 (mtp) REVERT: B 73 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: B 261 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7431 (mmm) outliers start: 20 outliers final: 4 residues processed: 96 average time/residue: 0.7489 time to fit residues: 73.8476 Evaluate side-chains 86 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 261 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 25 optimal weight: 0.0040 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.0270 chunk 34 optimal weight: 0.9980 overall best weight: 0.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122574 restraints weight = 3787.558| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.59 r_work: 0.3255 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4166 Z= 0.085 Angle : 0.421 5.369 5620 Z= 0.215 Chirality : 0.040 0.138 644 Planarity : 0.002 0.021 730 Dihedral : 3.970 20.631 584 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.75 % Allowed : 22.71 % Favored : 74.54 % 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 aren not related in a simple way. whole: 1.05 (0.37), residues: 534 helix: 2.26 (0.34), residues: 252 sheet: -0.83 (0.55), residues: 82 loop : -0.65 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 100 TYR 0.003 0.001 TYR A 124 PHE 0.010 0.001 PHE B 271 HIS 0.001 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 4162) covalent geometry : angle 0.39445 ( 5608) hydrogen bonds : bond 0.02954 ( 199) hydrogen bonds : angle 3.97176 ( 573) metal coordination : bond 0.00719 ( 4) metal coordination : angle 3.19949 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.173 Fit side-chains REVERT: A 141 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8170 (mm-30) REVERT: B 60 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.5946 (mtp) REVERT: B 73 GLU cc_start: 0.7813 (mp0) cc_final: 0.7241 (tm-30) REVERT: B 238 ASP cc_start: 0.7936 (m-30) cc_final: 0.7612 (m-30) outliers start: 12 outliers final: 1 residues processed: 93 average time/residue: 0.7025 time to fit residues: 67.1321 Evaluate side-chains 80 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN B 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119516 restraints weight = 3822.012| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.58 r_work: 0.3220 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4166 Z= 0.116 Angle : 0.457 6.521 5620 Z= 0.228 Chirality : 0.041 0.142 644 Planarity : 0.003 0.027 730 Dihedral : 4.036 15.343 582 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.21 % Allowed : 23.17 % Favored : 73.62 % 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 aren not related in a simple way. whole: 1.09 (0.37), residues: 534 helix: 2.23 (0.34), residues: 252 sheet: -0.94 (0.55), residues: 78 loop : -0.47 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 100 TYR 0.007 0.001 TYR B 80 PHE 0.011 0.001 PHE A 271 HIS 0.001 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 4162) covalent geometry : angle 0.42745 ( 5608) hydrogen bonds : bond 0.03201 ( 199) hydrogen bonds : angle 3.96856 ( 573) metal coordination : bond 0.00970 ( 4) metal coordination : angle 3.54358 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.166 Fit side-chains REVERT: A 141 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8228 (mm-30) REVERT: A 206 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7421 (pt0) REVERT: A 215 ASN cc_start: 0.7248 (OUTLIER) cc_final: 0.6755 (m-40) REVERT: B 60 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6009 (mtp) REVERT: B 73 GLU cc_start: 0.7774 (mp0) cc_final: 0.7276 (tm-30) outliers start: 14 outliers final: 2 residues processed: 89 average time/residue: 0.7185 time to fit residues: 65.7874 Evaluate side-chains 86 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118848 restraints weight = 3873.723| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.58 r_work: 0.3214 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4166 Z= 0.120 Angle : 0.463 6.716 5620 Z= 0.229 Chirality : 0.041 0.142 644 Planarity : 0.003 0.032 730 Dihedral : 4.076 15.714 582 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.21 % Allowed : 23.62 % Favored : 73.17 % 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 aren not related in a simple way. whole: 1.09 (0.37), residues: 534 helix: 2.23 (0.34), residues: 252 sheet: -0.94 (0.55), residues: 78 loop : -0.47 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 100 TYR 0.007 0.001 TYR A 171 PHE 0.011 0.001 PHE B 271 HIS 0.001 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4162) covalent geometry : angle 0.43147 ( 5608) hydrogen bonds : bond 0.03177 ( 199) hydrogen bonds : angle 3.94998 ( 573) metal coordination : bond 0.01066 ( 4) metal coordination : angle 3.66401 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.171 Fit side-chains REVERT: A 141 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8222 (mm-30) REVERT: A 206 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8377 (pm20) REVERT: A 215 ASN cc_start: 0.7240 (OUTLIER) cc_final: 0.6748 (m-40) REVERT: A 274 MET cc_start: 0.7508 (ppp) cc_final: 0.7246 (ppp) REVERT: B 60 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.5981 (mtp) REVERT: B 73 GLU cc_start: 0.7800 (mp0) cc_final: 0.7283 (tm-30) REVERT: B 238 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7774 (m-30) outliers start: 14 outliers final: 4 residues processed: 89 average time/residue: 0.7192 time to fit residues: 65.7819 Evaluate side-chains 87 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 266 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116417 restraints weight = 3937.298| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.61 r_work: 0.3171 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4166 Z= 0.156 Angle : 0.502 7.760 5620 Z= 0.246 Chirality : 0.042 0.144 644 Planarity : 0.003 0.032 730 Dihedral : 4.286 16.638 582 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.21 % Allowed : 22.94 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.37), residues: 534 helix: 2.07 (0.34), residues: 250 sheet: -0.95 (0.55), residues: 78 loop : -0.52 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 100 TYR 0.009 0.001 TYR A 171 PHE 0.013 0.002 PHE B 271 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4162) covalent geometry : angle 0.46318 ( 5608) hydrogen bonds : bond 0.03473 ( 199) hydrogen bonds : angle 4.01196 ( 573) metal coordination : bond 0.01289 ( 4) metal coordination : angle 4.20591 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.179 Fit side-chains REVERT: A 206 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7437 (pt0) REVERT: A 215 ASN cc_start: 0.7271 (OUTLIER) cc_final: 0.6775 (m-40) REVERT: A 274 MET cc_start: 0.7572 (ppp) cc_final: 0.7291 (ppp) REVERT: B 60 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6083 (mtp) REVERT: B 73 GLU cc_start: 0.7811 (mp0) cc_final: 0.7284 (tm-30) REVERT: B 238 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7769 (m-30) outliers start: 14 outliers final: 4 residues processed: 88 average time/residue: 0.7069 time to fit residues: 63.9682 Evaluate side-chains 85 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 266 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.136690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116487 restraints weight = 3921.796| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.59 r_work: 0.3178 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4166 Z= 0.159 Angle : 0.511 8.016 5620 Z= 0.249 Chirality : 0.043 0.144 644 Planarity : 0.003 0.035 730 Dihedral : 4.342 16.770 582 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.44 % Allowed : 22.25 % Favored : 74.31 % 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 aren not related in a simple way. whole: 0.86 (0.37), residues: 534 helix: 2.00 (0.34), residues: 250 sheet: -0.98 (0.55), residues: 78 loop : -0.53 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 100 TYR 0.008 0.001 TYR A 171 PHE 0.013 0.002 PHE B 271 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4162) covalent geometry : angle 0.47189 ( 5608) hydrogen bonds : bond 0.03553 ( 199) hydrogen bonds : angle 4.04467 ( 573) metal coordination : bond 0.01246 ( 4) metal coordination : angle 4.24632 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.181 Fit side-chains REVERT: A 206 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: A 215 ASN cc_start: 0.7277 (OUTLIER) cc_final: 0.6783 (m-40) REVERT: A 235 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7510 (mttm) REVERT: A 274 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7241 (ppp) REVERT: B 60 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6070 (mtp) REVERT: B 73 GLU cc_start: 0.7800 (mp0) cc_final: 0.7294 (tm-30) REVERT: B 238 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7780 (m-30) outliers start: 15 outliers final: 3 residues processed: 87 average time/residue: 0.7292 time to fit residues: 65.1733 Evaluate side-chains 85 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 238 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116586 restraints weight = 3845.463| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.57 r_work: 0.3179 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4166 Z= 0.145 Angle : 0.504 8.080 5620 Z= 0.246 Chirality : 0.042 0.142 644 Planarity : 0.003 0.042 730 Dihedral : 4.302 16.651 582 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.75 % Allowed : 23.17 % Favored : 74.08 % 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 aren not related in a simple way. whole: 0.88 (0.37), residues: 534 helix: 2.04 (0.34), residues: 250 sheet: -1.00 (0.54), residues: 78 loop : -0.54 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 100 TYR 0.007 0.001 TYR B 80 PHE 0.013 0.002 PHE B 271 HIS 0.001 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4162) covalent geometry : angle 0.46580 ( 5608) hydrogen bonds : bond 0.03445 ( 199) hydrogen bonds : angle 4.03681 ( 573) metal coordination : bond 0.01280 ( 4) metal coordination : angle 4.20571 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.171 Fit side-chains REVERT: A 206 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: A 215 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.6768 (m-40) REVERT: A 235 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7504 (mttm) REVERT: A 274 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7170 (ppp) REVERT: B 60 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6025 (mtp) REVERT: B 73 GLU cc_start: 0.7806 (mp0) cc_final: 0.7294 (tm-30) REVERT: B 100 ARG cc_start: 0.7225 (mtm110) cc_final: 0.6498 (mmp80) REVERT: B 238 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7757 (m-30) outliers start: 12 outliers final: 3 residues processed: 84 average time/residue: 0.7306 time to fit residues: 63.0697 Evaluate side-chains 85 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 238 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 0.0270 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.137820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117730 restraints weight = 3975.131| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.60 r_work: 0.3197 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4166 Z= 0.123 Angle : 0.480 7.695 5620 Z= 0.237 Chirality : 0.042 0.142 644 Planarity : 0.003 0.044 730 Dihedral : 4.213 16.777 582 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.52 % Allowed : 24.08 % Favored : 73.39 % 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 aren not related in a simple way. whole: 0.93 (0.37), residues: 534 helix: 2.10 (0.34), residues: 250 sheet: -1.03 (0.54), residues: 78 loop : -0.53 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 100 TYR 0.006 0.001 TYR A 171 PHE 0.013 0.001 PHE B 271 HIS 0.001 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4162) covalent geometry : angle 0.44500 ( 5608) hydrogen bonds : bond 0.03239 ( 199) hydrogen bonds : angle 4.02461 ( 573) metal coordination : bond 0.01129 ( 4) metal coordination : angle 3.91369 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.210 Fit side-chains REVERT: A 206 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8277 (pp30) REVERT: A 215 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.6784 (m-40) REVERT: A 235 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7497 (mttm) REVERT: A 274 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7180 (ppp) REVERT: B 60 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6013 (mtp) REVERT: B 71 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7058 (mm-30) REVERT: B 73 GLU cc_start: 0.7778 (mp0) cc_final: 0.7327 (tm-30) REVERT: B 100 ARG cc_start: 0.7230 (mtm110) cc_final: 0.6488 (mmp80) REVERT: B 238 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7754 (m-30) outliers start: 11 outliers final: 3 residues processed: 86 average time/residue: 0.7452 time to fit residues: 65.9380 Evaluate side-chains 87 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 238 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.137918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117875 restraints weight = 3819.329| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.57 r_work: 0.3192 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4166 Z= 0.130 Angle : 0.490 7.821 5620 Z= 0.242 Chirality : 0.042 0.142 644 Planarity : 0.003 0.044 730 Dihedral : 4.255 19.159 582 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.52 % Allowed : 24.08 % Favored : 73.39 % 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 aren not related in a simple way. whole: 0.91 (0.37), residues: 534 helix: 2.04 (0.34), residues: 250 sheet: -1.02 (0.54), residues: 78 loop : -0.49 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 100 TYR 0.006 0.001 TYR A 171 PHE 0.013 0.001 PHE B 271 HIS 0.001 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4162) covalent geometry : angle 0.45608 ( 5608) hydrogen bonds : bond 0.03332 ( 199) hydrogen bonds : angle 4.03707 ( 573) metal coordination : bond 0.01175 ( 4) metal coordination : angle 3.92321 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.173 Fit side-chains REVERT: A 206 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8275 (pp30) REVERT: A 215 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.6768 (m-40) REVERT: A 235 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7516 (mttm) REVERT: A 274 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7177 (ppp) REVERT: B 60 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6001 (mtp) REVERT: B 71 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7059 (mm-30) REVERT: B 73 GLU cc_start: 0.7775 (mp0) cc_final: 0.7330 (tm-30) REVERT: B 100 ARG cc_start: 0.7204 (mtm110) cc_final: 0.6492 (mmp80) REVERT: B 219 ARG cc_start: 0.7481 (mtm-85) cc_final: 0.7262 (mtm-85) REVERT: B 238 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7742 (m-30) outliers start: 11 outliers final: 3 residues processed: 85 average time/residue: 0.7230 time to fit residues: 63.1524 Evaluate side-chains 87 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 238 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117606 restraints weight = 3864.947| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.57 r_work: 0.3193 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4166 Z= 0.137 Angle : 0.504 7.933 5620 Z= 0.247 Chirality : 0.042 0.141 644 Planarity : 0.003 0.039 730 Dihedral : 4.306 20.864 582 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.52 % Allowed : 24.31 % Favored : 73.17 % 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 aren not related in a simple way. whole: 0.92 (0.37), residues: 534 helix: 2.04 (0.34), residues: 250 sheet: -1.02 (0.54), residues: 78 loop : -0.46 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 100 TYR 0.006 0.001 TYR A 171 PHE 0.013 0.002 PHE B 271 HIS 0.001 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4162) covalent geometry : angle 0.46909 ( 5608) hydrogen bonds : bond 0.03346 ( 199) hydrogen bonds : angle 4.04561 ( 573) metal coordination : bond 0.01167 ( 4) metal coordination : angle 4.02171 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2032.59 seconds wall clock time: 35 minutes 33.99 seconds (2133.99 seconds total)