Starting phenix.real_space_refine on Sat Sep 12 00:07:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhz_24472/09_2026/7rhz_24472_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhz_24472/09_2026/7rhz_24472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rhz_24472/09_2026/7rhz_24472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhz_24472/09_2026/7rhz_24472.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhz_24472/09_2026/7rhz_24472_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhz_24472/09_2026/7rhz_24472_neut.cif" } resolution = 4.48 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= -0.003 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 88 5.49 5 S 29 5.16 5 C 3888 2.51 5 N 1253 2.21 5 O 1417 1.98 5 H 5875 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12550 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 4987 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 7, 'TRANS': 307} Chain breaks: 1 Chain: "B" Number of atoms: 4764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4764 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 1 Chain: "C" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 1395 Classifications: {'DNA': 44} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 43} Chain: "D" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 1404 Classifications: {'DNA': 44} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 43} Time building chain proxies: 2.24, per 1000 atoms: 0.18 Number of scatterers: 12550 At special positions: 0 Unit cell: (73.718, 88.102, 163.618, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 P 88 15.00 O 1417 8.00 N 1253 7.00 C 3888 6.00 H 5875 1.00 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: 1.14 Conformation dependent library (CDL) restraints added in 352.0 milliseconds 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1146 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 66.7% alpha, 3.6% beta 44 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 Processing helix chain 'A' and resid 38 through 59 Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.609A pdb=" N ILE A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 126 Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 214 through 229 Processing helix chain 'A' and resid 257 through 273 Processing helix chain 'A' and resid 287 through 303 removed outlier: 3.825A pdb=" N ALA A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.920A pdb=" N MET A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 38 through 59 Processing helix chain 'B' and resid 67 through 81 Processing helix chain 'B' and resid 84 through 103 Processing helix chain 'B' and resid 109 through 126 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 154 through 171 Processing helix chain 'B' and resid 173 through 180 removed outlier: 3.552A pdb=" N ILE B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 214 through 229 Processing helix chain 'B' and resid 257 through 273 Processing helix chain 'B' and resid 287 through 303 removed outlier: 4.113A pdb=" N ALA B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 314 Processing helix chain 'B' and resid 318 through 326 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 187 removed outlier: 4.282A pdb=" N MET B 193 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 242 through 243 300 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5236 1.03 - 1.22: 685 1.22 - 1.42: 3191 1.42 - 1.62: 3686 1.62 - 1.81: 50 Bond restraints: 12848 Sorted by residual: bond pdb=" C6 DA D 14 " pdb=" N6 DA D 14 " ideal model delta sigma weight residual 1.335 1.236 0.099 8.00e-03 1.56e+04 1.54e+02 bond pdb=" C6 DA D 18 " pdb=" N6 DA D 18 " ideal model delta sigma weight residual 1.335 1.237 0.098 8.00e-03 1.56e+04 1.51e+02 bond pdb=" C6 DA D 23 " pdb=" N6 DA D 23 " ideal model delta sigma weight residual 1.335 1.237 0.098 8.00e-03 1.56e+04 1.49e+02 bond pdb=" C6 DA D 25 " pdb=" N6 DA D 25 " ideal model delta sigma weight residual 1.335 1.238 0.097 8.00e-03 1.56e+04 1.48e+02 bond pdb=" C6 DA C 20 " pdb=" N6 DA C 20 " ideal model delta sigma weight residual 1.335 1.239 0.096 8.00e-03 1.56e+04 1.43e+02 ... (remaining 12843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 20989 2.37 - 4.74: 1344 4.74 - 7.11: 636 7.11 - 9.47: 123 9.47 - 11.84: 69 Bond angle restraints: 23161 Sorted by residual: angle pdb=" N1 DA D 18 " pdb=" C2 DA D 18 " pdb=" N3 DA D 18 " ideal model delta sigma weight residual 129.30 135.26 -5.96 5.00e-01 4.00e+00 1.42e+02 angle pdb=" N9 DG C 9 " pdb=" C8 DG C 9 " pdb=" N7 DG C 9 " ideal model delta sigma weight residual 113.10 119.00 -5.90 5.00e-01 4.00e+00 1.39e+02 angle pdb=" N9 DG D 16 " pdb=" C8 DG D 16 " pdb=" N7 DG D 16 " ideal model delta sigma weight residual 113.10 118.94 -5.84 5.00e-01 4.00e+00 1.36e+02 angle pdb=" N9 DG D 20 " pdb=" C8 DG D 20 " pdb=" N7 DG D 20 " ideal model delta sigma weight residual 113.10 118.91 -5.81 5.00e-01 4.00e+00 1.35e+02 angle pdb=" N1 DA D 25 " pdb=" C2 DA D 25 " pdb=" N3 DA D 25 " ideal model delta sigma weight residual 129.30 135.11 -5.81 5.00e-01 4.00e+00 1.35e+02 ... (remaining 23156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4677 17.96 - 35.92: 502 35.92 - 53.88: 319 53.88 - 71.84: 157 71.84 - 89.80: 11 Dihedral angle restraints: 5666 sinusoidal: 3639 harmonic: 2027 Sorted by residual: dihedral pdb=" CA TRP B 315 " pdb=" C TRP B 315 " pdb=" N THR B 316 " pdb=" CA THR B 316 " ideal model delta harmonic sigma weight residual 180.00 150.15 29.85 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA PRO B 107 " pdb=" C PRO B 107 " pdb=" N SER B 108 " pdb=" CA SER B 108 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA LEU B 172 " pdb=" C LEU B 172 " pdb=" N ARG B 173 " pdb=" CA ARG B 173 " ideal model delta harmonic sigma weight residual 180.00 152.27 27.73 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 5663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 899 0.146 - 0.292: 56 0.292 - 0.437: 29 0.437 - 0.583: 77 0.583 - 0.729: 19 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CB VAL A 293 " pdb=" CA VAL A 293 " pdb=" CG1 VAL A 293 " pdb=" CG2 VAL A 293 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB ILE A 320 " pdb=" CA ILE A 320 " pdb=" CG1 ILE A 320 " pdb=" CG2 ILE A 320 " both_signs ideal model delta sigma weight residual False 2.64 1.93 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CB VAL B 113 " pdb=" CA VAL B 113 " pdb=" CG1 VAL B 113 " pdb=" CG2 VAL B 113 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.71 2.00e-01 2.50e+01 1.28e+01 ... (remaining 1077 not shown) Planarity restraints: 1619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA C 16 " -0.243 2.00e-02 2.50e+03 9.63e-02 3.01e+02 pdb=" N9 DA C 16 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DA C 16 " 0.060 2.00e-02 2.50e+03 pdb=" N7 DA C 16 " 0.083 2.00e-02 2.50e+03 pdb=" C5 DA C 16 " 0.051 2.00e-02 2.50e+03 pdb=" C6 DA C 16 " -0.025 2.00e-02 2.50e+03 pdb=" N6 DA C 16 " -0.183 2.00e-02 2.50e+03 pdb=" N1 DA C 16 " -0.013 2.00e-02 2.50e+03 pdb=" C2 DA C 16 " 0.039 2.00e-02 2.50e+03 pdb=" N3 DA C 16 " 0.037 2.00e-02 2.50e+03 pdb=" C4 DA C 16 " 0.049 2.00e-02 2.50e+03 pdb=" H8 DA C 16 " 0.061 2.00e-02 2.50e+03 pdb=" H2 DA C 16 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 17 " -0.199 2.00e-02 2.50e+03 7.92e-02 1.88e+02 pdb=" N1 DT C 17 " 0.021 2.00e-02 2.50e+03 pdb=" C2 DT C 17 " 0.059 2.00e-02 2.50e+03 pdb=" O2 DT C 17 " 0.049 2.00e-02 2.50e+03 pdb=" N3 DT C 17 " 0.080 2.00e-02 2.50e+03 pdb=" C4 DT C 17 " -0.014 2.00e-02 2.50e+03 pdb=" O4 DT C 17 " -0.115 2.00e-02 2.50e+03 pdb=" C5 DT C 17 " 0.020 2.00e-02 2.50e+03 pdb=" C7 DT C 17 " -0.013 2.00e-02 2.50e+03 pdb=" C6 DT C 17 " 0.058 2.00e-02 2.50e+03 pdb=" H3 DT C 17 " -0.019 2.00e-02 2.50e+03 pdb=" H6 DT C 17 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 14 " -0.165 2.00e-02 2.50e+03 6.69e-02 1.57e+02 pdb=" N9 DG C 14 " 0.003 2.00e-02 2.50e+03 pdb=" C8 DG C 14 " 0.060 2.00e-02 2.50e+03 pdb=" N7 DG C 14 " 0.031 2.00e-02 2.50e+03 pdb=" C5 DG C 14 " -0.015 2.00e-02 2.50e+03 pdb=" C6 DG C 14 " -0.059 2.00e-02 2.50e+03 pdb=" O6 DG C 14 " -0.058 2.00e-02 2.50e+03 pdb=" N1 DG C 14 " -0.047 2.00e-02 2.50e+03 pdb=" C2 DG C 14 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DG C 14 " 0.107 2.00e-02 2.50e+03 pdb=" N3 DG C 14 " 0.020 2.00e-02 2.50e+03 pdb=" C4 DG C 14 " 0.007 2.00e-02 2.50e+03 pdb=" H8 DG C 14 " 0.097 2.00e-02 2.50e+03 pdb=" H1 DG C 14 " 0.015 2.00e-02 2.50e+03 ... (remaining 1616 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 293 2.08 - 2.71: 19222 2.71 - 3.34: 35324 3.34 - 3.97: 43437 3.97 - 4.60: 66634 Nonbonded interactions: 164910 Sorted by model distance: nonbonded pdb="HH21 ARG A 106 " pdb=" OP1 DG D 20 " model vdw 1.453 2.450 nonbonded pdb="HH21 ARG B 106 " pdb=" OP1 DA C 20 " model vdw 1.467 2.450 nonbonded pdb=" H ARG B 181 " pdb=" OD2 ASP B 184 " model vdw 1.492 2.450 nonbonded pdb=" O LEU B 215 " pdb=" HG1 THR B 218 " model vdw 1.494 2.450 nonbonded pdb=" H TYR A 283 " pdb=" OP1 DC D 26 " model vdw 1.498 2.450 ... (remaining 164905 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' and (resid 20 through 32 or resid 34 through 35 or resid 37 through 7 \ 1 or resid 73 through 114 or resid 116 through 118 or resid 120 through 191 or r \ esid 193 through 327)) selection = (chain 'B' and (resid 20 through 32 or resid 34 through 35 or resid 37 through 7 \ 1 or resid 73 through 114 or resid 116 through 118 or resid 120 through 191 or r \ esid 193 through 198 or resid 208 through 327)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 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: 0.080 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.920 Find NCS groups from input model: 0.130 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 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 : 0.020 0.134 6973 Z= 1.474 Angle : 1.670 11.844 9788 Z= 1.425 Chirality : 0.186 0.729 1080 Planarity : 0.012 0.102 959 Dihedral : 21.166 89.798 2838 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.59 % Allowed : 1.76 % Favored : 97.65 % Cbeta Deviations : 5.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.29), residues: 607 helix: -1.03 (0.23), residues: 378 sheet: 0.59 (1.02), residues: 28 loop : -1.03 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG B 61 TYR 0.049 0.006 TYR A 283 PHE 0.007 0.001 PHE A 163 TRP 0.016 0.004 TRP B 52 HIS 0.008 0.002 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.01963 / 1.47 ( 6973) covalent geometry : angle 1.66978 / 1.43 ( 9788) hydrogen bonds : bond 0.12436 / 7.91 ( 407) hydrogen bonds : angle 5.70280 / 4.23 ( 1102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8914 (tttt) cc_final: 0.8674 (tmmt) REVERT: A 109 ASP cc_start: 0.8909 (m-30) cc_final: 0.8335 (p0) REVERT: A 129 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6431 (mm-30) REVERT: A 130 ARG cc_start: 0.8722 (mtt180) cc_final: 0.8157 (ptm-80) REVERT: A 172 LEU cc_start: 0.8169 (mt) cc_final: 0.7057 (mt) REVERT: A 265 PHE cc_start: 0.9737 (m-80) cc_final: 0.9366 (m-80) REVERT: A 298 ASP cc_start: 0.9312 (t0) cc_final: 0.9019 (m-30) REVERT: A 315 TRP cc_start: 0.8043 (OUTLIER) cc_final: 0.7653 (t60) REVERT: B 273 TYR cc_start: 0.8783 (m-80) cc_final: 0.8196 (m-80) REVERT: B 277 ASP cc_start: 0.9384 (m-30) cc_final: 0.9018 (p0) REVERT: B 319 ASN cc_start: 0.9517 (m-40) cc_final: 0.9234 (t0) outliers start: 3 outliers final: 1 residues processed: 182 average time/residue: 0.2734 time to fit residues: 59.2083 Evaluate side-chains 133 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN B 59 ASN B 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.062137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.046321 restraints weight = 127950.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.048790 restraints weight = 66139.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.050581 restraints weight = 41980.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.051875 restraints weight = 30016.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.052735 restraints weight = 23359.629| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 6973 Z= 0.235 Angle : 0.769 7.030 9788 Z= 0.480 Chirality : 0.047 0.203 1080 Planarity : 0.007 0.117 959 Dihedral : 24.548 88.714 1664 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.20 % Allowed : 1.76 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.32), residues: 607 helix: 0.29 (0.25), residues: 383 sheet: -0.30 (0.88), residues: 28 loop : -0.60 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 24 TYR 0.008 0.002 TYR B 74 PHE 0.026 0.002 PHE A 64 TRP 0.016 0.002 TRP B 52 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.24 ( 6973) covalent geometry : angle 0.76917 / 0.48 ( 9788) hydrogen bonds : bond 0.07544 / 5.07 ( 407) hydrogen bonds : angle 5.17293 / 3.84 ( 1102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.9682 (mt-10) cc_final: 0.9481 (pm20) REVERT: A 43 LYS cc_start: 0.8787 (tttt) cc_final: 0.8484 (tmmt) REVERT: A 108 SER cc_start: 0.9240 (m) cc_final: 0.9035 (m) REVERT: A 109 ASP cc_start: 0.9158 (m-30) cc_final: 0.8732 (p0) REVERT: A 129 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6429 (mm-30) REVERT: A 130 ARG cc_start: 0.8934 (mtt180) cc_final: 0.8275 (ptt-90) REVERT: A 265 PHE cc_start: 0.9678 (m-80) cc_final: 0.9313 (m-80) REVERT: A 298 ASP cc_start: 0.9502 (t0) cc_final: 0.9024 (t0) REVERT: B 49 CYS cc_start: 0.9524 (m) cc_final: 0.9317 (m) REVERT: B 77 TYR cc_start: 0.9043 (t80) cc_final: 0.8680 (t80) REVERT: B 273 TYR cc_start: 0.8876 (m-80) cc_final: 0.8281 (m-80) REVERT: B 277 ASP cc_start: 0.9549 (m-30) cc_final: 0.9032 (p0) REVERT: B 319 ASN cc_start: 0.9561 (m-40) cc_final: 0.9265 (t0) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.2400 time to fit residues: 41.2882 Evaluate side-chains 127 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 65 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 4 optimal weight: 0.0270 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS A 124 ASN B 35 GLN B 89 GLN B 169 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.064292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.048418 restraints weight = 128872.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.050969 restraints weight = 67156.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.052780 restraints weight = 42685.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.054073 restraints weight = 30588.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.054938 restraints weight = 23889.852| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6973 Z= 0.174 Angle : 0.694 9.669 9788 Z= 0.442 Chirality : 0.044 0.190 1080 Planarity : 0.006 0.076 959 Dihedral : 24.585 88.697 1664 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.20 % Allowed : 0.78 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.33), residues: 607 helix: 0.87 (0.26), residues: 382 sheet: -0.10 (0.87), residues: 28 loop : -0.52 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 50 TYR 0.008 0.001 TYR A 168 PHE 0.014 0.001 PHE B 163 TRP 0.012 0.001 TRP B 52 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.17 ( 6973) covalent geometry : angle 0.69414 / 0.44 ( 9788) hydrogen bonds : bond 0.06337 / 4.24 ( 407) hydrogen bonds : angle 4.86863 / 3.63 ( 1102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8814 (tttt) cc_final: 0.8502 (tmmt) REVERT: A 108 SER cc_start: 0.9210 (m) cc_final: 0.8996 (m) REVERT: A 109 ASP cc_start: 0.9127 (m-30) cc_final: 0.8781 (p0) REVERT: A 129 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6427 (mm-30) REVERT: A 130 ARG cc_start: 0.8949 (mtt180) cc_final: 0.8347 (ptt-90) REVERT: A 173 ARG cc_start: 0.9743 (mtt-85) cc_final: 0.9486 (mmm160) REVERT: A 262 GLU cc_start: 0.9758 (mt-10) cc_final: 0.9517 (mm-30) REVERT: A 265 PHE cc_start: 0.9690 (m-80) cc_final: 0.9042 (m-80) REVERT: B 42 TRP cc_start: 0.9545 (t60) cc_final: 0.9303 (t-100) REVERT: B 77 TYR cc_start: 0.9097 (t80) cc_final: 0.8763 (t80) REVERT: B 273 TYR cc_start: 0.8882 (m-80) cc_final: 0.8304 (m-80) REVERT: B 277 ASP cc_start: 0.9551 (m-30) cc_final: 0.9021 (p0) REVERT: B 289 HIS cc_start: 0.9129 (m90) cc_final: 0.8917 (m90) REVERT: B 319 ASN cc_start: 0.9540 (m-40) cc_final: 0.9254 (t0) outliers start: 1 outliers final: 1 residues processed: 142 average time/residue: 0.2342 time to fit residues: 40.5776 Evaluate side-chains 125 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.059477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.044953 restraints weight = 141346.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.047059 restraints weight = 75523.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.048593 restraints weight = 49396.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.049660 restraints weight = 36229.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.050393 restraints weight = 28955.665| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 6973 Z= 0.404 Angle : 0.856 6.677 9788 Z= 0.530 Chirality : 0.045 0.177 1080 Planarity : 0.007 0.053 959 Dihedral : 24.845 88.821 1664 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.30), residues: 607 helix: -0.47 (0.24), residues: 382 sheet: -0.65 (0.84), residues: 28 loop : -1.13 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 154 TYR 0.015 0.002 TYR A 283 PHE 0.028 0.004 PHE A 64 TRP 0.043 0.003 TRP A 42 HIS 0.009 0.003 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.40 ( 6973) covalent geometry : angle 0.85554 / 0.53 ( 9788) hydrogen bonds : bond 0.10338 / 6.84 ( 407) hydrogen bonds : angle 5.58569 / 4.13 ( 1102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8872 (mtt180) cc_final: 0.8656 (ttp80) REVERT: A 43 LYS cc_start: 0.9054 (tttt) cc_final: 0.8617 (tmmt) REVERT: A 106 ARG cc_start: 0.9294 (ttt180) cc_final: 0.8976 (tmt170) REVERT: A 109 ASP cc_start: 0.9117 (m-30) cc_final: 0.8753 (p0) REVERT: A 129 GLU cc_start: 0.6129 (mm-30) cc_final: 0.5917 (mm-30) REVERT: A 130 ARG cc_start: 0.8870 (mtt180) cc_final: 0.8385 (pmt-80) REVERT: A 289 HIS cc_start: 0.9189 (m-70) cc_final: 0.8800 (m-70) REVERT: B 42 TRP cc_start: 0.9623 (t60) cc_final: 0.9339 (t-100) REVERT: B 273 TYR cc_start: 0.9124 (m-80) cc_final: 0.8605 (m-80) REVERT: B 277 ASP cc_start: 0.9437 (m-30) cc_final: 0.8859 (p0) REVERT: B 319 ASN cc_start: 0.9588 (m-40) cc_final: 0.9269 (t0) REVERT: B 327 ASN cc_start: 0.9144 (t0) cc_final: 0.8887 (t0) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2216 time to fit residues: 35.7999 Evaluate side-chains 114 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 30 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN A 245 ASN B 91 HIS B 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.061192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.045692 restraints weight = 137415.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.048069 restraints weight = 73029.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.049819 restraints weight = 46952.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.050951 restraints weight = 33808.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.051851 restraints weight = 26869.439| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6973 Z= 0.214 Angle : 0.705 9.152 9788 Z= 0.450 Chirality : 0.043 0.159 1080 Planarity : 0.006 0.073 959 Dihedral : 24.885 89.273 1664 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.32), residues: 607 helix: 0.08 (0.25), residues: 380 sheet: -0.71 (0.78), residues: 28 loop : -1.09 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 159 TYR 0.012 0.002 TYR A 283 PHE 0.020 0.002 PHE A 31 TRP 0.055 0.003 TRP B 224 HIS 0.010 0.002 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.21 ( 6973) covalent geometry : angle 0.70513 / 0.45 ( 9788) hydrogen bonds : bond 0.07553 / 4.97 ( 407) hydrogen bonds : angle 5.18808 / 3.85 ( 1102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8934 (tttt) cc_final: 0.8592 (tmmt) REVERT: A 108 SER cc_start: 0.8960 (m) cc_final: 0.8692 (m) REVERT: A 109 ASP cc_start: 0.9189 (m-30) cc_final: 0.8863 (p0) REVERT: A 129 GLU cc_start: 0.6335 (mm-30) cc_final: 0.6092 (mm-30) REVERT: A 130 ARG cc_start: 0.8963 (mtt180) cc_final: 0.8473 (pmt-80) REVERT: A 265 PHE cc_start: 0.9666 (m-80) cc_final: 0.9341 (m-80) REVERT: A 289 HIS cc_start: 0.9153 (m-70) cc_final: 0.8693 (m-70) REVERT: B 42 TRP cc_start: 0.9619 (t60) cc_final: 0.9287 (t-100) REVERT: B 273 TYR cc_start: 0.8964 (m-80) cc_final: 0.8425 (m-80) REVERT: B 276 LYS cc_start: 0.7029 (mmtt) cc_final: 0.6753 (mmtt) REVERT: B 277 ASP cc_start: 0.9403 (m-30) cc_final: 0.8757 (p0) REVERT: B 319 ASN cc_start: 0.9556 (m-40) cc_final: 0.9241 (t0) REVERT: B 327 ASN cc_start: 0.9304 (t0) cc_final: 0.9065 (t0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2292 time to fit residues: 36.4619 Evaluate side-chains 116 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.061001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.045510 restraints weight = 136119.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.047851 restraints weight = 71957.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.049551 restraints weight = 46725.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.050737 restraints weight = 33950.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.051509 restraints weight = 26844.515| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6973 Z= 0.215 Angle : 0.720 8.688 9788 Z= 0.455 Chirality : 0.043 0.159 1080 Planarity : 0.006 0.083 959 Dihedral : 24.877 88.768 1664 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.32), residues: 607 helix: 0.16 (0.25), residues: 380 sheet: -0.75 (0.76), residues: 28 loop : -1.06 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 130 TYR 0.017 0.002 TYR B 74 PHE 0.019 0.003 PHE B 142 TRP 0.028 0.002 TRP B 224 HIS 0.010 0.002 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.22 ( 6973) covalent geometry : angle 0.72011 / 0.46 ( 9788) hydrogen bonds : bond 0.07149 / 4.74 ( 407) hydrogen bonds : angle 5.23279 / 3.87 ( 1102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8905 (tttt) cc_final: 0.8432 (tmmt) REVERT: A 109 ASP cc_start: 0.9166 (m-30) cc_final: 0.8871 (p0) REVERT: A 129 GLU cc_start: 0.6368 (mm-30) cc_final: 0.5861 (mm-30) REVERT: A 130 ARG cc_start: 0.8972 (mtt180) cc_final: 0.8402 (ptt90) REVERT: A 265 PHE cc_start: 0.9687 (m-80) cc_final: 0.9364 (m-80) REVERT: A 289 HIS cc_start: 0.9156 (m-70) cc_final: 0.8699 (m-70) REVERT: B 42 TRP cc_start: 0.9618 (t60) cc_final: 0.9302 (t-100) REVERT: B 74 TYR cc_start: 0.9324 (t80) cc_final: 0.9002 (t80) REVERT: B 77 TYR cc_start: 0.9547 (t80) cc_final: 0.9239 (t80) REVERT: B 273 TYR cc_start: 0.9073 (m-80) cc_final: 0.8582 (m-80) REVERT: B 277 ASP cc_start: 0.9298 (m-30) cc_final: 0.8627 (p0) REVERT: B 319 ASN cc_start: 0.9553 (m-40) cc_final: 0.9241 (t0) REVERT: B 327 ASN cc_start: 0.8807 (t0) cc_final: 0.8572 (t0) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2441 time to fit residues: 38.1607 Evaluate side-chains 115 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 ASN B 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.062848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.047554 restraints weight = 135986.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.049949 restraints weight = 70627.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.051702 restraints weight = 45320.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.052914 restraints weight = 32588.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.053726 restraints weight = 25580.862| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6973 Z= 0.168 Angle : 0.645 7.367 9788 Z= 0.418 Chirality : 0.041 0.168 1080 Planarity : 0.005 0.055 959 Dihedral : 24.832 86.826 1664 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.32), residues: 607 helix: 0.59 (0.26), residues: 380 sheet: -0.88 (0.74), residues: 29 loop : -1.01 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 130 TYR 0.010 0.001 TYR A 283 PHE 0.011 0.002 PHE B 142 TRP 0.029 0.002 TRP B 224 HIS 0.006 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.17 ( 6973) covalent geometry : angle 0.64506 / 0.42 ( 9788) hydrogen bonds : bond 0.05861 / 3.90 ( 407) hydrogen bonds : angle 4.84180 / 3.59 ( 1102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8732 (m-80) cc_final: 0.8394 (m-80) REVERT: A 108 SER cc_start: 0.8910 (m) cc_final: 0.8197 (p) REVERT: A 129 GLU cc_start: 0.6347 (mm-30) cc_final: 0.5843 (mm-30) REVERT: A 130 ARG cc_start: 0.8965 (mtt180) cc_final: 0.8361 (ptt90) REVERT: A 265 PHE cc_start: 0.9705 (m-80) cc_final: 0.9398 (m-80) REVERT: A 289 HIS cc_start: 0.9119 (m-70) cc_final: 0.8722 (m-70) REVERT: B 74 TYR cc_start: 0.9309 (t80) cc_final: 0.9028 (t80) REVERT: B 77 TYR cc_start: 0.9532 (t80) cc_final: 0.9159 (t80) REVERT: B 273 TYR cc_start: 0.8984 (m-80) cc_final: 0.8483 (m-80) REVERT: B 277 ASP cc_start: 0.9425 (m-30) cc_final: 0.8776 (p0) REVERT: B 283 TYR cc_start: 0.8596 (m-10) cc_final: 0.8203 (m-10) REVERT: B 319 ASN cc_start: 0.9555 (m-40) cc_final: 0.9169 (t0) REVERT: B 327 ASN cc_start: 0.8804 (t0) cc_final: 0.8586 (t0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2122 time to fit residues: 33.0101 Evaluate side-chains 111 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.062903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.047503 restraints weight = 134110.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.050021 restraints weight = 69553.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.051787 restraints weight = 44311.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.053032 restraints weight = 31734.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053879 restraints weight = 24798.001| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 6973 Z= 0.171 Angle : 0.657 7.168 9788 Z= 0.420 Chirality : 0.041 0.170 1080 Planarity : 0.005 0.053 959 Dihedral : 24.821 86.070 1664 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.32), residues: 607 helix: 0.71 (0.26), residues: 381 sheet: -0.89 (0.74), residues: 29 loop : -0.98 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 139 TYR 0.010 0.001 TYR A 283 PHE 0.018 0.002 PHE B 142 TRP 0.027 0.002 TRP B 224 HIS 0.004 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 ( 6973) covalent geometry : angle 0.65684 / 0.42 ( 9788) hydrogen bonds : bond 0.05871 / 3.94 ( 407) hydrogen bonds : angle 4.81163 / 3.57 ( 1102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.6380 (mm-30) cc_final: 0.6163 (mm-30) REVERT: A 130 ARG cc_start: 0.8949 (mtt180) cc_final: 0.8488 (pmt-80) REVERT: A 265 PHE cc_start: 0.9688 (m-80) cc_final: 0.9370 (m-80) REVERT: A 289 HIS cc_start: 0.9112 (m-70) cc_final: 0.8883 (m-70) REVERT: B 74 TYR cc_start: 0.9299 (t80) cc_final: 0.9066 (t80) REVERT: B 77 TYR cc_start: 0.9562 (t80) cc_final: 0.9195 (t80) REVERT: B 142 PHE cc_start: 0.9539 (p90) cc_final: 0.9071 (p90) REVERT: B 273 TYR cc_start: 0.9017 (m-80) cc_final: 0.8516 (m-80) REVERT: B 277 ASP cc_start: 0.9561 (m-30) cc_final: 0.8950 (p0) REVERT: B 319 ASN cc_start: 0.9593 (m-40) cc_final: 0.9232 (t0) REVERT: B 327 ASN cc_start: 0.8783 (t0) cc_final: 0.8558 (t0) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2010 time to fit residues: 30.9235 Evaluate side-chains 106 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 61 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 HIS B 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.062805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.047387 restraints weight = 136175.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.049894 restraints weight = 71127.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.051574 restraints weight = 45190.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.052877 restraints weight = 32845.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.053676 restraints weight = 25476.357| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6973 Z= 0.173 Angle : 0.648 8.485 9788 Z= 0.417 Chirality : 0.041 0.166 1080 Planarity : 0.005 0.052 959 Dihedral : 24.833 85.351 1664 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.32), residues: 607 helix: 0.71 (0.26), residues: 381 sheet: -0.97 (0.74), residues: 29 loop : -0.94 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 173 TYR 0.010 0.001 TYR A 283 PHE 0.020 0.002 PHE B 163 TRP 0.026 0.002 TRP B 224 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.17 ( 6973) covalent geometry : angle 0.64816 / 0.42 ( 9788) hydrogen bonds : bond 0.05866 / 3.91 ( 407) hydrogen bonds : angle 4.82583 / 3.58 ( 1102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8489 (m-80) cc_final: 0.8271 (m-80) REVERT: A 108 SER cc_start: 0.8685 (m) cc_final: 0.8238 (p) REVERT: A 129 GLU cc_start: 0.6383 (mm-30) cc_final: 0.6158 (mm-30) REVERT: A 130 ARG cc_start: 0.8987 (mtt180) cc_final: 0.8502 (pmt-80) REVERT: A 265 PHE cc_start: 0.9710 (m-80) cc_final: 0.9399 (m-80) REVERT: A 289 HIS cc_start: 0.9045 (m-70) cc_final: 0.8805 (m-70) REVERT: B 74 TYR cc_start: 0.9330 (t80) cc_final: 0.8875 (t80) REVERT: B 77 TYR cc_start: 0.9556 (t80) cc_final: 0.9193 (t80) REVERT: B 176 GLU cc_start: 0.9295 (tp30) cc_final: 0.8961 (tp30) REVERT: B 273 TYR cc_start: 0.9009 (m-80) cc_final: 0.8520 (m-80) REVERT: B 277 ASP cc_start: 0.9559 (m-30) cc_final: 0.8948 (p0) REVERT: B 283 TYR cc_start: 0.8517 (m-10) cc_final: 0.8108 (m-10) REVERT: B 289 HIS cc_start: 0.9168 (m90) cc_final: 0.8953 (m90) REVERT: B 319 ASN cc_start: 0.9581 (m-40) cc_final: 0.9236 (t0) REVERT: B 327 ASN cc_start: 0.8815 (t0) cc_final: 0.8605 (t0) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2023 time to fit residues: 31.4234 Evaluate side-chains 110 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 0.4980 chunk 62 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.064256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.048549 restraints weight = 132874.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.051147 restraints weight = 68294.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.053021 restraints weight = 43204.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.054288 restraints weight = 30727.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.055110 restraints weight = 23872.564| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6973 Z= 0.154 Angle : 0.636 6.131 9788 Z= 0.407 Chirality : 0.041 0.157 1080 Planarity : 0.004 0.050 959 Dihedral : 24.811 84.400 1664 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.33), residues: 607 helix: 0.86 (0.26), residues: 381 sheet: -0.91 (0.75), residues: 29 loop : -0.87 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 173 TYR 0.012 0.002 TYR B 237 PHE 0.016 0.002 PHE B 163 TRP 0.026 0.002 TRP B 224 HIS 0.003 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.15 ( 6973) covalent geometry : angle 0.63561 / 0.41 ( 9788) hydrogen bonds : bond 0.05314 / 3.53 ( 407) hydrogen bonds : angle 4.64503 / 3.43 ( 1102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8385 (m-80) cc_final: 0.8113 (m-80) REVERT: A 108 SER cc_start: 0.8588 (m) cc_final: 0.8036 (p) REVERT: A 129 GLU cc_start: 0.6376 (mm-30) cc_final: 0.6171 (mm-30) REVERT: A 130 ARG cc_start: 0.8990 (mtt180) cc_final: 0.8506 (pmt-80) REVERT: A 265 PHE cc_start: 0.9698 (m-80) cc_final: 0.9106 (m-80) REVERT: B 77 TYR cc_start: 0.9568 (t80) cc_final: 0.9275 (t80) REVERT: B 176 GLU cc_start: 0.9291 (tp30) cc_final: 0.8968 (tp30) REVERT: B 273 TYR cc_start: 0.9010 (m-80) cc_final: 0.8518 (m-80) REVERT: B 277 ASP cc_start: 0.9559 (m-30) cc_final: 0.8955 (p0) REVERT: B 283 TYR cc_start: 0.8573 (m-10) cc_final: 0.8177 (m-10) REVERT: B 289 HIS cc_start: 0.9137 (m90) cc_final: 0.8916 (m90) REVERT: B 319 ASN cc_start: 0.9578 (m-40) cc_final: 0.9225 (t0) REVERT: B 327 ASN cc_start: 0.8810 (t0) cc_final: 0.8601 (t0) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2051 time to fit residues: 32.2000 Evaluate side-chains 108 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.063938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.048354 restraints weight = 134133.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.050962 restraints weight = 69037.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.052795 restraints weight = 43593.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.054077 restraints weight = 31031.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.054905 restraints weight = 24082.606| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6973 Z= 0.173 Angle : 0.652 14.787 9788 Z= 0.411 Chirality : 0.040 0.141 1080 Planarity : 0.005 0.050 959 Dihedral : 24.814 83.961 1664 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.32), residues: 607 helix: 0.81 (0.26), residues: 381 sheet: -0.87 (0.77), residues: 28 loop : -0.94 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.022 0.002 TYR A 283 PHE 0.011 0.002 PHE A 64 TRP 0.066 0.003 TRP A 224 HIS 0.003 0.001 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.17 ( 6973) covalent geometry : angle 0.65232 / 0.41 ( 9788) hydrogen bonds : bond 0.05422 / 3.63 ( 407) hydrogen bonds : angle 4.68845 / 3.47 ( 1102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2302.63 seconds wall clock time: 39 minutes 50.78 seconds (2390.78 seconds total)