Starting phenix.real_space_refine on Fri Jul 3 05:55:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhz_24472/07_2026/7rhz_24472_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhz_24472/07_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_24472/07_2026/7rhz_24472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhz_24472/07_2026/7rhz_24472.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhz_24472/07_2026/7rhz_24472_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhz_24472/07_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-dev-6108/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: 2.31, 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: 0.99 Conformation dependent library (CDL) restraints added in 334.4 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: 2.08 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: 2.61 Time building geometry restraints manager: 1.43 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: 20996 2.37 - 4.74: 1338 4.74 - 7.11: 635 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: 0.130 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: 0.070 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.810 Find NCS groups from input model: 0.140 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.610 ------------------------------------------------------------------------------- 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= 1.473 Angle : 1.667 11.844 9788 Z= 1.422 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 1.66682 / 1.42 ( 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 : 0.286 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: 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: 0.8167 (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: 0.9365 (m-80) REVERT: A 289 HIS cc_start: 0.9049 (m90) cc_final: 0.8714 (m-70) 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: 0.7654 (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: 0.2737 time to fit residues: 59.3224 Evaluate side-chains 135 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 94 GLN A 124 ASN B 59 ASN 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 = 0.3448 r_free = 0.3448 target = 0.062247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.046312 restraints weight = 127595.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.048845 restraints weight = 67037.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.050647 restraints weight = 42474.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.051941 restraints weight = 30333.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.052811 restraints weight = 23596.606| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 6973 Z= 0.233 Angle : 0.750 6.895 9788 Z= 0.473 Chirality : 0.047 0.198 1080 Planarity : 0.007 0.098 959 Dihedral : 24.558 88.676 1664 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.48 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: -0.14 (0.32), residues: 607 helix: 0.29 (0.25), residues: 383 sheet: -0.26 (0.88), residues: 28 loop : -0.61 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 24 TYR 0.008 0.002 TYR A 324 PHE 0.018 0.002 PHE A 64 TRP 0.016 0.002 TRP B 52 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.23 ( 6973) covalent geometry : angle 0.74963 / 0.47 ( 9788) hydrogen bonds : bond 0.07563 / 5.08 ( 407) hydrogen bonds : angle 5.16010 / 3.83 ( 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 145 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.254 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: A 39 GLU cc_start: 0.9680 (mt-10) cc_final: 0.9478 (pm20) REVERT: A 43 LYS cc_start: 0.8793 (tttt) cc_final: 0.8488 (tmmt) REVERT: A 108 SER cc_start: 0.9240 (m) cc_final: 0.9037 (m) REVERT: A 109 ASP cc_start: 0.9156 (m-30) cc_final: 0.8731 (p0) REVERT: A 129 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6408 (mm-30) REVERT: A 130 ARG cc_start: 0.8940 (mtt180) cc_final: 0.8277 (ptt-90) REVERT: A 265 PHE cc_start: 0.9680 (m-80) cc_final: 0.9313 (m-80) REVERT: A 289 HIS cc_start: 0.9074 (m90) cc_final: 0.8805 (m-70) REVERT: A 298 ASP cc_start: 0.9504 (t0) cc_final: 0.9055 (m-30) REVERT: B 49 CYS cc_start: 0.9521 (m) cc_final: 0.9314 (m) REVERT: B 77 TYR cc_start: 0.9041 (t80) cc_final: 0.8677 (t80) REVERT: B 89 GLN cc_start: 0.9782 (mt0) cc_final: 0.9523 (mt0) REVERT: B 273 TYR cc_start: 0.8877 (m-80) cc_final: 0.8281 (m-80) REVERT: B 277 ASP cc_start: 0.9549 (m-30) cc_final: 0.9033 (p0) REVERT: B 319 ASN cc_start: 0.9563 (m-40) cc_final: 0.9266 (t0) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.2704 time to fit residues: 46.7430 Evaluate side-chains 130 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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: 10.0000 chunk 50 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS B 35 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.062194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.046497 restraints weight = 132809.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.048976 restraints weight = 70132.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.050772 restraints weight = 44761.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.052000 restraints weight = 32103.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.052916 restraints weight = 25206.758| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6973 Z= 0.210 Angle : 0.697 7.243 9788 Z= 0.449 Chirality : 0.044 0.190 1080 Planarity : 0.006 0.071 959 Dihedral : 24.623 88.610 1664 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: 0.27 (0.32), residues: 607 helix: 0.71 (0.25), residues: 383 sheet: -0.19 (0.88), residues: 28 loop : -0.67 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 50 TYR 0.008 0.001 TYR B 77 PHE 0.007 0.001 PHE B 163 TRP 0.014 0.001 TRP B 52 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.21 ( 6973) covalent geometry : angle 0.69747 / 0.45 ( 9788) hydrogen bonds : bond 0.06962 / 4.64 ( 407) hydrogen bonds : angle 4.99134 / 3.71 ( 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 145 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.222 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 39 GLU cc_start: 0.9683 (mt-10) cc_final: 0.9457 (pm20) REVERT: A 43 LYS cc_start: 0.8832 (tttt) cc_final: 0.8520 (tmmt) REVERT: A 109 ASP cc_start: 0.9134 (m-30) cc_final: 0.8744 (p0) REVERT: A 129 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6441 (mm-30) REVERT: A 130 ARG cc_start: 0.8960 (mtt180) cc_final: 0.8349 (ptt-90) REVERT: A 265 PHE cc_start: 0.9709 (m-80) cc_final: 0.9365 (m-80) REVERT: A 289 HIS cc_start: 0.9085 (m90) cc_final: 0.8800 (m-70) REVERT: A 298 ASP cc_start: 0.9501 (t0) cc_final: 0.9024 (t0) REVERT: B 42 TRP cc_start: 0.9552 (t60) cc_final: 0.9321 (t-100) REVERT: B 77 TYR cc_start: 0.9125 (t80) cc_final: 0.8794 (t80) REVERT: B 97 MET cc_start: 0.8489 (mtt) cc_final: 0.8094 (mmt) REVERT: B 273 TYR cc_start: 0.8902 (m-80) cc_final: 0.8329 (m-80) REVERT: B 277 ASP cc_start: 0.9562 (m-30) cc_final: 0.9027 (p0) REVERT: B 319 ASN cc_start: 0.9544 (m-40) cc_final: 0.9254 (t0) outliers start: 1 outliers final: 1 residues processed: 145 average time/residue: 0.2348 time to fit residues: 41.1684 Evaluate side-chains 123 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.060356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.044941 restraints weight = 136544.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.047311 restraints weight = 70787.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.049015 restraints weight = 44992.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.050245 restraints weight = 32234.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051062 restraints weight = 25157.958| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 6973 Z= 0.263 Angle : 0.716 7.302 9788 Z= 0.457 Chirality : 0.043 0.176 1080 Planarity : 0.006 0.080 959 Dihedral : 24.749 89.448 1664 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -0.23 (0.32), residues: 607 helix: 0.35 (0.25), residues: 383 sheet: -0.42 (0.85), residues: 28 loop : -0.92 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 187 TYR 0.011 0.002 TYR A 283 PHE 0.032 0.002 PHE A 64 TRP 0.016 0.001 TRP B 52 HIS 0.004 0.001 HIS B 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.26 ( 6973) covalent geometry : angle 0.71639 / 0.46 ( 9788) hydrogen bonds : bond 0.07720 / 5.13 ( 407) hydrogen bonds : angle 5.14049 / 3.80 ( 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 135 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.325 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: A 39 GLU cc_start: 0.9674 (mt-10) cc_final: 0.9453 (pm20) REVERT: A 43 LYS cc_start: 0.8835 (tttt) cc_final: 0.8494 (tmmt) REVERT: A 91 HIS cc_start: 0.9791 (m90) cc_final: 0.9573 (m90) REVERT: A 109 ASP cc_start: 0.8987 (m-30) cc_final: 0.8659 (p0) REVERT: A 129 GLU cc_start: 0.6324 (mm-30) cc_final: 0.6120 (mm-30) REVERT: A 130 ARG cc_start: 0.8949 (mtt180) cc_final: 0.8465 (pmt-80) REVERT: A 176 GLU cc_start: 0.9603 (tp30) cc_final: 0.9102 (tp30) REVERT: A 289 HIS cc_start: 0.9089 (m90) cc_final: 0.8796 (m-70) REVERT: B 42 TRP cc_start: 0.9606 (t60) cc_final: 0.9292 (t-100) REVERT: B 77 TYR cc_start: 0.9152 (t80) cc_final: 0.8849 (t80) REVERT: B 97 MET cc_start: 0.8427 (mtt) cc_final: 0.8049 (mmt) REVERT: B 273 TYR cc_start: 0.9107 (m-80) cc_final: 0.8579 (m-80) REVERT: B 277 ASP cc_start: 0.9582 (m-30) cc_final: 0.9035 (p0) REVERT: B 319 ASN cc_start: 0.9554 (m-40) cc_final: 0.9239 (t0) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2459 time to fit residues: 40.3941 Evaluate side-chains 119 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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: 10.0000 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.060839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.045452 restraints weight = 141144.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.047846 restraints weight = 73601.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.049570 restraints weight = 46776.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.050784 restraints weight = 33666.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.051575 restraints weight = 26499.311| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6973 Z= 0.235 Angle : 0.708 8.733 9788 Z= 0.452 Chirality : 0.042 0.160 1080 Planarity : 0.006 0.072 959 Dihedral : 24.815 89.405 1664 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.29 (0.32), residues: 607 helix: 0.35 (0.25), residues: 382 sheet: -0.59 (0.80), residues: 28 loop : -1.03 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 139 TYR 0.011 0.002 TYR A 283 PHE 0.022 0.003 PHE A 31 TRP 0.016 0.002 TRP B 52 HIS 0.009 0.002 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.24 ( 6973) covalent geometry : angle 0.70763 / 0.45 ( 9788) hydrogen bonds : bond 0.07449 / 4.96 ( 407) hydrogen bonds : angle 5.18159 / 3.82 ( 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 133 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.289 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: 0.9680 (mt-10) cc_final: 0.9453 (pm20) REVERT: A 43 LYS cc_start: 0.8964 (tttt) cc_final: 0.8623 (tmmt) REVERT: A 108 SER cc_start: 0.9093 (m) cc_final: 0.8834 (m) REVERT: A 109 ASP cc_start: 0.9047 (m-30) cc_final: 0.8745 (p0) REVERT: A 129 GLU cc_start: 0.6293 (mm-30) cc_final: 0.6065 (mm-30) REVERT: A 130 ARG cc_start: 0.8984 (mtt180) cc_final: 0.8494 (pmt-80) REVERT: A 265 PHE cc_start: 0.9680 (m-80) cc_final: 0.9364 (m-80) REVERT: A 289 HIS cc_start: 0.9080 (m90) cc_final: 0.8822 (m-70) REVERT: B 42 TRP cc_start: 0.9612 (t60) cc_final: 0.9312 (t-100) REVERT: B 273 TYR cc_start: 0.9095 (m-80) cc_final: 0.8578 (m-80) REVERT: B 277 ASP cc_start: 0.9579 (m-30) cc_final: 0.9051 (p0) REVERT: B 319 ASN cc_start: 0.9553 (m-40) cc_final: 0.9241 (t0) REVERT: B 327 ASN cc_start: 0.9288 (t0) cc_final: 0.9059 (t0) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2379 time to fit residues: 38.7039 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 : 0.305 ------------------------------------------------------------------------------- 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: 6.9990 chunk 14 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN A 245 ASN B 59 ASN B 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.061223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.046209 restraints weight = 138303.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.048502 restraints weight = 72459.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.050187 restraints weight = 46731.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.051322 restraints weight = 33786.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.052156 restraints weight = 26790.375| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 6973 Z= 0.230 Angle : 0.691 6.302 9788 Z= 0.441 Chirality : 0.042 0.157 1080 Planarity : 0.006 0.091 959 Dihedral : 24.870 88.327 1664 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -0.45 (0.32), residues: 607 helix: 0.29 (0.25), residues: 382 sheet: -0.79 (0.76), residues: 28 loop : -1.22 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 130 TYR 0.012 0.002 TYR A 283 PHE 0.022 0.002 PHE A 64 TRP 0.011 0.002 TRP B 52 HIS 0.010 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.23 ( 6973) covalent geometry : angle 0.69141 / 0.44 ( 9788) hydrogen bonds : bond 0.07142 / 4.73 ( 407) hydrogen bonds : angle 5.11486 / 3.76 ( 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 132 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.285 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: A 39 GLU cc_start: 0.9676 (mt-10) cc_final: 0.9456 (pm20) REVERT: A 43 LYS cc_start: 0.8967 (tttt) cc_final: 0.8492 (tmmt) REVERT: A 94 GLN cc_start: 0.9612 (tm-30) cc_final: 0.9399 (tm-30) REVERT: A 108 SER cc_start: 0.8927 (m) cc_final: 0.8595 (m) REVERT: A 109 ASP cc_start: 0.9160 (m-30) cc_final: 0.8877 (p0) REVERT: A 129 GLU cc_start: 0.6331 (mm-30) cc_final: 0.5834 (mm-30) REVERT: A 130 ARG cc_start: 0.8948 (mtt180) cc_final: 0.8317 (ptt90) REVERT: A 265 PHE cc_start: 0.9695 (m-80) cc_final: 0.9119 (m-80) REVERT: A 289 HIS cc_start: 0.9077 (m90) cc_final: 0.8818 (m-70) REVERT: B 42 TRP cc_start: 0.9628 (t60) cc_final: 0.9300 (t-100) REVERT: B 55 TRP cc_start: 0.8278 (t60) cc_final: 0.7761 (t60) REVERT: B 273 TYR cc_start: 0.9055 (m-80) cc_final: 0.8566 (m-80) REVERT: B 277 ASP cc_start: 0.9324 (m-30) cc_final: 0.8746 (p0) REVERT: B 283 TYR cc_start: 0.8639 (m-10) cc_final: 0.8299 (m-10) REVERT: B 310 MET cc_start: 0.9350 (mmm) cc_final: 0.8791 (tpt) REVERT: B 319 ASN cc_start: 0.9552 (m-40) cc_final: 0.9238 (t0) REVERT: B 327 ASN cc_start: 0.8790 (t0) cc_final: 0.8557 (t0) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2273 time to fit residues: 36.9446 Evaluate side-chains 118 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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: 10.0000 chunk 53 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN B 91 HIS B 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.061391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.046423 restraints weight = 137885.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.048813 restraints weight = 72233.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.050498 restraints weight = 46113.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.051633 restraints weight = 33283.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.052467 restraints weight = 26338.769| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6973 Z= 0.214 Angle : 0.684 9.190 9788 Z= 0.440 Chirality : 0.041 0.160 1080 Planarity : 0.006 0.064 959 Dihedral : 24.897 87.534 1664 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 15.54 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: -0.48 (0.32), residues: 607 helix: 0.27 (0.25), residues: 381 sheet: -0.80 (0.75), residues: 28 loop : -1.25 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 159 TYR 0.012 0.002 TYR A 283 PHE 0.020 0.002 PHE B 142 TRP 0.064 0.003 TRP B 224 HIS 0.004 0.001 HIS B 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.21 ( 6973) covalent geometry : angle 0.68449 / 0.44 ( 9788) hydrogen bonds : bond 0.06995 / 4.64 ( 407) hydrogen bonds : angle 5.13499 / 3.76 ( 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 132 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.301 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: A 44 MET cc_start: 0.9003 (mmm) cc_final: 0.8781 (mmm) REVERT: A 108 SER cc_start: 0.8921 (m) cc_final: 0.8585 (m) REVERT: A 109 ASP cc_start: 0.9135 (m-30) cc_final: 0.8879 (p0) REVERT: A 129 GLU cc_start: 0.6346 (mm-30) cc_final: 0.5839 (mm-30) REVERT: A 130 ARG cc_start: 0.8988 (mtt180) cc_final: 0.8336 (ptt90) REVERT: A 265 PHE cc_start: 0.9529 (m-80) cc_final: 0.9147 (m-80) REVERT: A 289 HIS cc_start: 0.9079 (m90) cc_final: 0.8829 (m-70) REVERT: B 42 TRP cc_start: 0.9577 (t60) cc_final: 0.9270 (t-100) REVERT: B 77 TYR cc_start: 0.9547 (t80) cc_final: 0.9225 (t80) REVERT: B 273 TYR cc_start: 0.8967 (m-80) cc_final: 0.8464 (m-80) REVERT: B 277 ASP cc_start: 0.9333 (m-30) cc_final: 0.8746 (p0) REVERT: B 319 ASN cc_start: 0.9550 (m-40) cc_final: 0.9245 (t0) REVERT: B 327 ASN cc_start: 0.8789 (t0) cc_final: 0.8571 (t0) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2095 time to fit residues: 34.3489 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 : 0.309 ------------------------------------------------------------------------------- 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: 7.9990 chunk 67 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 0.0870 chunk 49 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 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 = 0.3420 r_free = 0.3420 target = 0.061710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.046709 restraints weight = 135713.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.049112 restraints weight = 70198.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.050816 restraints weight = 44807.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.052013 restraints weight = 32226.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.052846 restraints weight = 25351.240| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6973 Z= 0.190 Angle : 0.667 8.379 9788 Z= 0.427 Chirality : 0.042 0.208 1080 Planarity : 0.005 0.061 959 Dihedral : 24.882 86.469 1664 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % 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: -0.44 (0.32), residues: 607 helix: 0.35 (0.26), residues: 382 sheet: -0.81 (0.75), residues: 28 loop : -1.34 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 179 TYR 0.014 0.002 TYR A 237 PHE 0.014 0.002 PHE A 64 TRP 0.039 0.002 TRP B 224 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.19 ( 6973) covalent geometry : angle 0.66692 / 0.43 ( 9788) hydrogen bonds : bond 0.06438 / 4.27 ( 407) hydrogen bonds : angle 5.00823 / 3.68 ( 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 125 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.254 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 108 SER cc_start: 0.8929 (m) cc_final: 0.8582 (m) REVERT: A 129 GLU cc_start: 0.6365 (mm-30) cc_final: 0.6112 (mm-30) REVERT: A 130 ARG cc_start: 0.9020 (mtt180) cc_final: 0.8479 (pmt-80) REVERT: A 265 PHE cc_start: 0.9542 (m-80) cc_final: 0.9162 (m-80) REVERT: A 289 HIS cc_start: 0.9140 (m90) cc_final: 0.8861 (m-70) REVERT: B 77 TYR cc_start: 0.9535 (t80) cc_final: 0.9190 (t80) REVERT: B 273 TYR cc_start: 0.8965 (m-80) cc_final: 0.8476 (m-80) REVERT: B 277 ASP cc_start: 0.9321 (m-30) cc_final: 0.8650 (p0) REVERT: B 319 ASN cc_start: 0.9588 (m-40) cc_final: 0.9248 (t0) REVERT: B 327 ASN cc_start: 0.8818 (t0) cc_final: 0.8610 (t0) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1972 time to fit residues: 30.8281 Evaluate side-chains 112 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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: 1.9990 chunk 17 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.063253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.048023 restraints weight = 136923.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.050511 restraints weight = 70642.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.052285 restraints weight = 44940.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.053516 restraints weight = 32268.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.054359 restraints weight = 25317.269| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6973 Z= 0.161 Angle : 0.629 7.372 9788 Z= 0.408 Chirality : 0.040 0.169 1080 Planarity : 0.005 0.056 959 Dihedral : 24.847 84.938 1664 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: -0.05 (0.32), residues: 607 helix: 0.66 (0.26), residues: 382 sheet: -0.93 (0.73), residues: 29 loop : -1.16 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 81 TYR 0.010 0.001 TYR A 283 PHE 0.010 0.002 PHE B 142 TRP 0.042 0.002 TRP B 224 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.16 ( 6973) covalent geometry : angle 0.62875 / 0.41 ( 9788) hydrogen bonds : bond 0.05476 / 3.66 ( 407) hydrogen bonds : angle 4.78384 / 3.52 ( 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 124 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.298 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: A 37 PHE cc_start: 0.8272 (m-80) cc_final: 0.7966 (m-80) REVERT: A 108 SER cc_start: 0.8670 (m) cc_final: 0.8201 (p) REVERT: A 129 GLU cc_start: 0.6367 (mm-30) cc_final: 0.6124 (mm-30) REVERT: A 130 ARG cc_start: 0.9047 (mtt180) cc_final: 0.8483 (pmt-80) REVERT: A 265 PHE cc_start: 0.9550 (m-80) cc_final: 0.9169 (m-80) REVERT: A 289 HIS cc_start: 0.9095 (m90) cc_final: 0.8782 (m-70) REVERT: B 55 TRP cc_start: 0.8255 (t60) cc_final: 0.7083 (t60) REVERT: B 89 GLN cc_start: 0.9774 (mt0) cc_final: 0.9524 (mt0) REVERT: B 273 TYR cc_start: 0.8968 (m-80) cc_final: 0.8486 (m-80) REVERT: B 277 ASP cc_start: 0.9552 (m-30) cc_final: 0.8955 (p0) REVERT: B 289 HIS cc_start: 0.9393 (m-70) cc_final: 0.9185 (m-70) REVERT: B 299 MET cc_start: 0.5417 (mmp) cc_final: 0.5139 (mmm) REVERT: B 319 ASN cc_start: 0.9574 (m-40) cc_final: 0.9238 (t0) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2148 time to fit residues: 33.2829 Evaluate side-chains 113 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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: 0.9990 chunk 24 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.063625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.048307 restraints weight = 134992.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.050849 restraints weight = 69010.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.052669 restraints weight = 43508.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.053900 restraints weight = 30990.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.054763 restraints weight = 24291.087| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6973 Z= 0.156 Angle : 0.628 6.682 9788 Z= 0.404 Chirality : 0.040 0.159 1080 Planarity : 0.004 0.055 959 Dihedral : 24.823 84.374 1664 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % 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: -0.05 (0.32), residues: 607 helix: 0.67 (0.26), residues: 383 sheet: -0.92 (0.73), residues: 29 loop : -1.16 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 81 TYR 0.010 0.001 TYR A 283 PHE 0.016 0.002 PHE A 64 TRP 0.040 0.002 TRP B 224 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.16 ( 6973) covalent geometry : angle 0.62780 / 0.40 ( 9788) hydrogen bonds : bond 0.05319 / 3.57 ( 407) hydrogen bonds : angle 4.74260 / 3.47 ( 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 : 0.296 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: A 37 PHE cc_start: 0.8278 (m-80) cc_final: 0.8057 (m-80) REVERT: A 44 MET cc_start: 0.9149 (mmt) cc_final: 0.8749 (mmm) REVERT: A 108 SER cc_start: 0.8699 (m) cc_final: 0.8228 (p) REVERT: A 129 GLU cc_start: 0.6372 (mm-30) cc_final: 0.6151 (mm-30) REVERT: A 130 ARG cc_start: 0.9023 (mtt180) cc_final: 0.8476 (pmt-80) REVERT: A 265 PHE cc_start: 0.9535 (m-80) cc_final: 0.9140 (m-80) REVERT: A 289 HIS cc_start: 0.9055 (m90) cc_final: 0.8711 (m-70) REVERT: B 89 GLN cc_start: 0.9767 (mt0) cc_final: 0.9555 (mt0) REVERT: B 273 TYR cc_start: 0.9004 (m-80) cc_final: 0.8510 (m-80) REVERT: B 277 ASP cc_start: 0.9566 (m-30) cc_final: 0.8967 (p0) REVERT: B 319 ASN cc_start: 0.9584 (m-40) cc_final: 0.9232 (t0) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2007 time to fit residues: 31.0661 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 : 0.206 ------------------------------------------------------------------------------- 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: 4.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 31 optimal weight: 10.9990 chunk 30 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.064291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.048795 restraints weight = 134017.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.051367 restraints weight = 68751.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.053199 restraints weight = 43333.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.054463 restraints weight = 30864.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.055336 restraints weight = 24074.499| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6973 Z= 0.150 Angle : 0.618 6.177 9788 Z= 0.400 Chirality : 0.040 0.145 1080 Planarity : 0.004 0.053 959 Dihedral : 24.809 83.714 1664 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: 0.10 (0.32), residues: 607 helix: 0.81 (0.26), residues: 383 sheet: -0.92 (0.74), residues: 29 loop : -1.16 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 101 TYR 0.026 0.002 TYR A 283 PHE 0.014 0.001 PHE B 142 TRP 0.038 0.002 TRP B 224 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.15 ( 6973) covalent geometry : angle 0.61842 / 0.40 ( 9788) hydrogen bonds : bond 0.05124 / 3.46 ( 407) hydrogen bonds : angle 4.61910 / 3.38 ( 1102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2363.86 seconds wall clock time: 40 minutes 53.07 seconds (2453.07 seconds total)