Starting phenix.real_space_refine on Fri May 9 23:05:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tc3_41151/05_2025/8tc3_41151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tc3_41151/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tc3_41151/05_2025/8tc3_41151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tc3_41151/05_2025/8tc3_41151.map" model { file = "/net/cci-nas-00/data/ceres_data/8tc3_41151/05_2025/8tc3_41151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tc3_41151/05_2025/8tc3_41151.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.37, per 1000 atoms: 1.30 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: 0.97 Conformation dependent library (CDL) restraints added in 486.0 milliseconds 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: 0.45 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: 1.10 Time building geometry restraints manager: 1.15 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: 5.930 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.270 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (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 HIS 0.002 0.001 HIS B 50 PHE 0.010 0.001 PHE A 271 TYR 0.009 0.001 TYR B 80 ARG 0.004 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.14266 ( 199) hydrogen bonds : angle 4.99748 ( 573) metal coordination : bond 0.00885 ( 4) metal coordination : angle 4.37961 ( 12) covalent geometry : bond 0.00253 ( 4162) covalent geometry : angle 0.47489 ( 5608) *********************** 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 : 0.441 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 82 average time/residue: 1.4805 time to fit residues: 124.9779 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 : 0.500 ------------------------------------------------------------------------------- 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 45 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.138864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118297 restraints weight = 3773.572| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.64 r_work: 0.3199 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.0640 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 6.817 5620 Z= 0.241 Chirality : 0.042 0.152 644 Planarity : 0.003 0.025 730 Dihedral : 4.376 24.309 584 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 4.13 % Allowed : 21.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.37), residues: 534 helix: 1.96 (0.34), residues: 252 sheet: -0.91 (0.55), residues: 84 loop : -0.62 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.011 0.001 PHE B 271 TYR 0.008 0.001 TYR B 80 ARG 0.005 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 199) hydrogen bonds : angle 4.21301 ( 573) metal coordination : bond 0.00974 ( 4) metal coordination : angle 3.90720 ( 12) covalent geometry : bond 0.00271 ( 4162) covalent geometry : angle 0.44477 ( 5608) *********************** 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 104 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.456 Fit side-chains REVERT: A 206 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7558 (pt0) REVERT: B 60 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.5977 (mtp) REVERT: B 73 GLU cc_start: 0.7873 (mp0) cc_final: 0.7237 (tm-30) REVERT: B 261 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7453 (mmm) outliers start: 18 outliers final: 4 residues processed: 96 average time/residue: 1.4819 time to fit residues: 146.3902 Evaluate side-chains 83 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 261 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 0.7980 chunk 47 optimal weight: 0.0570 chunk 46 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.137607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117860 restraints weight = 3826.395| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.58 r_work: 0.3193 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0825 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= 0.126 Angle : 0.473 6.933 5620 Z= 0.236 Chirality : 0.042 0.144 644 Planarity : 0.003 0.021 730 Dihedral : 4.352 24.341 584 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.90 % Allowed : 22.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.37), residues: 534 helix: 2.05 (0.34), residues: 250 sheet: -0.99 (0.54), residues: 84 loop : -0.63 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.011 0.002 PHE B 271 TYR 0.007 0.001 TYR B 80 ARG 0.003 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 199) hydrogen bonds : angle 4.10324 ( 573) metal coordination : bond 0.01014 ( 4) metal coordination : angle 3.88039 ( 12) covalent geometry : bond 0.00282 ( 4162) covalent geometry : angle 0.43772 ( 5608) *********************** 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 97 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.447 Fit side-chains REVERT: A 156 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6691 (mmm) REVERT: A 206 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7563 (pt0) REVERT: A 215 ASN cc_start: 0.7225 (OUTLIER) cc_final: 0.6746 (m-40) REVERT: B 60 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6026 (mtp) REVERT: B 73 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7276 (tm-30) outliers start: 17 outliers final: 3 residues processed: 89 average time/residue: 1.3949 time to fit residues: 127.9503 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 : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 156 MET 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 73 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.134402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.114274 restraints weight = 3897.454| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.58 r_work: 0.3152 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4166 Z= 0.230 Angle : 0.570 8.374 5620 Z= 0.280 Chirality : 0.045 0.148 644 Planarity : 0.003 0.026 730 Dihedral : 4.852 29.478 584 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.13 % Allowed : 22.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.37), residues: 534 helix: 1.67 (0.34), residues: 250 sheet: -1.07 (0.53), residues: 86 loop : -0.65 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.015 0.002 PHE B 271 TYR 0.011 0.002 TYR B 171 ARG 0.006 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 199) hydrogen bonds : angle 4.23212 ( 573) metal coordination : bond 0.01702 ( 4) metal coordination : angle 4.65213 ( 12) covalent geometry : bond 0.00532 ( 4162) covalent geometry : angle 0.52888 ( 5608) *********************** 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 95 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.445 Fit side-chains REVERT: A 155 MET cc_start: 0.8152 (tmm) cc_final: 0.7829 (tmt) REVERT: A 206 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: A 215 ASN cc_start: 0.7309 (OUTLIER) cc_final: 0.6816 (m-40) REVERT: A 235 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7522 (mttm) REVERT: A 264 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7527 (tt) REVERT: B 60 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6105 (mtp) REVERT: B 73 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7398 (tm-30) outliers start: 18 outliers final: 5 residues processed: 88 average time/residue: 1.4477 time to fit residues: 131.1277 Evaluate side-chains 87 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 154 GLU 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 264 LEU 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 266 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.136485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.115512 restraints weight = 3952.667| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.68 r_work: 0.3157 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.0978 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= 0.162 Angle : 0.511 7.957 5620 Z= 0.251 Chirality : 0.043 0.145 644 Planarity : 0.003 0.023 730 Dihedral : 4.656 28.504 584 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.13 % Allowed : 21.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.37), residues: 534 helix: 1.81 (0.34), residues: 250 sheet: -0.93 (0.55), residues: 78 loop : -0.67 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.014 0.002 PHE B 271 TYR 0.008 0.001 TYR B 80 ARG 0.005 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 199) hydrogen bonds : angle 4.11903 ( 573) metal coordination : bond 0.01264 ( 4) metal coordination : angle 4.29721 ( 12) covalent geometry : bond 0.00368 ( 4162) covalent geometry : angle 0.47084 ( 5608) *********************** 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 97 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.433 Fit side-chains REVERT: A 155 MET cc_start: 0.8066 (tmm) cc_final: 0.7732 (tmt) REVERT: A 206 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8099 (pt0) REVERT: A 215 ASN cc_start: 0.7212 (OUTLIER) cc_final: 0.6733 (m-40) REVERT: A 264 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7454 (tt) REVERT: B 60 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.5971 (mtp) REVERT: B 73 GLU cc_start: 0.7853 (mp0) cc_final: 0.7307 (tm-30) outliers start: 18 outliers final: 5 residues processed: 90 average time/residue: 1.4054 time to fit residues: 130.3718 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 : 0.450 ------------------------------------------------------------------------------- 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 154 GLU 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 264 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 67 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.135745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115834 restraints weight = 3845.501| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.59 r_work: 0.3163 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.0999 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= 0.161 Angle : 0.513 8.182 5620 Z= 0.250 Chirality : 0.043 0.145 644 Planarity : 0.003 0.031 730 Dihedral : 4.650 28.346 584 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.44 % Allowed : 22.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.36), residues: 534 helix: 1.80 (0.33), residues: 250 sheet: -0.98 (0.55), residues: 78 loop : -0.65 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.014 0.002 PHE B 271 TYR 0.007 0.001 TYR B 80 ARG 0.006 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 199) hydrogen bonds : angle 4.08764 ( 573) metal coordination : bond 0.01336 ( 4) metal coordination : angle 4.38671 ( 12) covalent geometry : bond 0.00367 ( 4162) covalent geometry : angle 0.47141 ( 5608) *********************** 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 95 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.510 Fit side-chains REVERT: A 155 MET cc_start: 0.8088 (tmm) cc_final: 0.7750 (tmt) REVERT: A 206 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8114 (pt0) REVERT: A 215 ASN cc_start: 0.7258 (OUTLIER) cc_final: 0.6778 (m-40) REVERT: A 235 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7505 (mttm) REVERT: A 264 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7496 (tt) REVERT: A 274 MET cc_start: 0.7546 (ppp) cc_final: 0.7120 (ppp) REVERT: B 60 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6073 (mtp) REVERT: B 73 GLU cc_start: 0.7838 (mp0) cc_final: 0.7318 (tm-30) REVERT: B 238 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7746 (m-30) outliers start: 15 outliers final: 6 residues processed: 89 average time/residue: 1.4344 time to fit residues: 131.4494 Evaluate side-chains 90 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 154 GLU 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 264 LEU 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 46 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.136448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.116291 restraints weight = 3824.984| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.57 r_work: 0.3174 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.0998 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 : 0.511 8.370 5620 Z= 0.250 Chirality : 0.043 0.145 644 Planarity : 0.003 0.034 730 Dihedral : 4.614 27.772 584 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 : 22.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.37), residues: 534 helix: 1.83 (0.34), residues: 250 sheet: -0.99 (0.55), residues: 78 loop : -0.62 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.014 0.002 PHE B 271 TYR 0.007 0.001 TYR B 80 ARG 0.007 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 199) hydrogen bonds : angle 4.06975 ( 573) metal coordination : bond 0.01325 ( 4) metal coordination : angle 4.41049 ( 12) covalent geometry : bond 0.00356 ( 4162) covalent geometry : angle 0.46943 ( 5608) *********************** 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 95 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.486 Fit side-chains REVERT: A 155 MET cc_start: 0.8084 (tmm) cc_final: 0.7802 (tmt) REVERT: A 156 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.7137 (mmp) REVERT: A 206 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7594 (pt0) REVERT: A 215 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.6798 (m-40) REVERT: A 235 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7506 (mttm) REVERT: A 264 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7512 (tt) REVERT: B 60 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6072 (mtp) REVERT: B 73 GLU cc_start: 0.7850 (mp0) cc_final: 0.7349 (tm-30) REVERT: B 238 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7795 (m-30) outliers start: 15 outliers final: 5 residues processed: 90 average time/residue: 1.5105 time to fit residues: 139.7928 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 : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 156 MET 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 264 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.136815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116048 restraints weight = 3816.354| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.65 r_work: 0.3163 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1015 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= 0.162 Angle : 0.523 8.555 5620 Z= 0.255 Chirality : 0.043 0.145 644 Planarity : 0.003 0.049 730 Dihedral : 4.640 27.901 584 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.44 % Allowed : 22.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.37), residues: 534 helix: 1.80 (0.34), residues: 250 sheet: -0.99 (0.55), residues: 78 loop : -0.64 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.014 0.002 PHE B 271 TYR 0.007 0.001 TYR B 80 ARG 0.008 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 199) hydrogen bonds : angle 4.06371 ( 573) metal coordination : bond 0.01390 ( 4) metal coordination : angle 4.46095 ( 12) covalent geometry : bond 0.00369 ( 4162) covalent geometry : angle 0.48135 ( 5608) *********************** 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 95 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.489 Fit side-chains REVERT: A 155 MET cc_start: 0.8024 (tmm) cc_final: 0.7742 (tmt) REVERT: A 156 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7072 (mmp) REVERT: A 206 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8084 (pt0) REVERT: A 215 ASN cc_start: 0.7223 (OUTLIER) cc_final: 0.6743 (m-40) REVERT: A 235 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7458 (mttm) REVERT: A 264 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7414 (tt) REVERT: B 60 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6018 (mtp) REVERT: B 71 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6973 (mm-30) REVERT: B 73 GLU cc_start: 0.7825 (mp0) cc_final: 0.7336 (tm-30) REVERT: B 238 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7738 (m-30) outliers start: 15 outliers final: 5 residues processed: 88 average time/residue: 1.4642 time to fit residues: 132.5929 Evaluate side-chains 90 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 156 MET 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 264 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.138319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117526 restraints weight = 3823.876| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.65 r_work: 0.3181 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1019 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= 0.129 Angle : 0.495 8.168 5620 Z= 0.243 Chirality : 0.042 0.142 644 Planarity : 0.003 0.043 730 Dihedral : 4.481 25.909 584 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.52 % Allowed : 23.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.37), residues: 534 helix: 1.95 (0.34), residues: 250 sheet: -0.99 (0.56), residues: 78 loop : -0.62 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 209 PHE 0.013 0.002 PHE B 271 TYR 0.005 0.001 TYR B 80 ARG 0.009 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 199) hydrogen bonds : angle 4.04123 ( 573) metal coordination : bond 0.01264 ( 4) metal coordination : angle 4.19032 ( 12) covalent geometry : bond 0.00291 ( 4162) covalent geometry : angle 0.45618 ( 5608) *********************** 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 90 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.464 Fit side-chains REVERT: A 206 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7573 (pt0) REVERT: A 215 ASN cc_start: 0.7197 (OUTLIER) cc_final: 0.6717 (m-40) REVERT: B 60 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.5936 (mtp) REVERT: B 71 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6967 (mm-30) REVERT: B 73 GLU cc_start: 0.7823 (mp0) cc_final: 0.7284 (tm-30) REVERT: B 238 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: B 261 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7508 (mmm) outliers start: 11 outliers final: 3 residues processed: 85 average time/residue: 1.5012 time to fit residues: 131.2480 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 : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 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 261 MET Chi-restraints excluded: chain B residue 266 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 5 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.137494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.117296 restraints weight = 3841.703| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.58 r_work: 0.3179 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1054 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= 0.138 Angle : 0.510 8.368 5620 Z= 0.249 Chirality : 0.042 0.143 644 Planarity : 0.003 0.045 730 Dihedral : 4.492 25.528 583 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.06 % Allowed : 24.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.37), residues: 534 helix: 1.91 (0.34), residues: 250 sheet: -1.00 (0.56), residues: 78 loop : -0.60 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.014 0.002 PHE B 271 TYR 0.005 0.001 TYR B 80 ARG 0.009 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 199) hydrogen bonds : angle 4.07974 ( 573) metal coordination : bond 0.01291 ( 4) metal coordination : angle 4.19819 ( 12) covalent geometry : bond 0.00313 ( 4162) covalent geometry : angle 0.47202 ( 5608) ********************** 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 87 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.492 Fit side-chains REVERT: A 206 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7593 (pt0) REVERT: A 215 ASN cc_start: 0.7275 (OUTLIER) cc_final: 0.6793 (m-40) REVERT: B 60 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6019 (mtp) REVERT: B 71 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7063 (mm-30) REVERT: B 73 GLU cc_start: 0.7846 (mp0) cc_final: 0.7344 (tm-30) REVERT: B 100 ARG cc_start: 0.7184 (mtt90) cc_final: 0.6532 (mmp80) REVERT: B 238 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: B 261 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7576 (mmm) outliers start: 9 outliers final: 3 residues processed: 82 average time/residue: 1.5484 time to fit residues: 130.5557 Evaluate side-chains 83 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 261 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.137293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116855 restraints weight = 3826.077| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.58 r_work: 0.3173 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1047 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= 0.160 Angle : 0.543 8.713 5620 Z= 0.264 Chirality : 0.043 0.144 644 Planarity : 0.003 0.038 730 Dihedral : 4.617 26.469 583 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.06 % Allowed : 24.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.37), residues: 534 helix: 1.83 (0.34), residues: 250 sheet: -1.02 (0.56), residues: 78 loop : -0.59 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.014 0.002 PHE B 271 TYR 0.007 0.001 TYR B 80 ARG 0.009 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 199) hydrogen bonds : angle 4.11390 ( 573) metal coordination : bond 0.01329 ( 4) metal coordination : angle 4.40970 ( 12) covalent geometry : bond 0.00366 ( 4162) covalent geometry : angle 0.50368 ( 5608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3729.54 seconds wall clock time: 64 minutes 56.39 seconds (3896.39 seconds total)