Starting phenix.real_space_refine on Sun Apr 5 18:09:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhz_24472/04_2026/7rhz_24472_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhz_24472/04_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_24472/04_2026/7rhz_24472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhz_24472/04_2026/7rhz_24472.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhz_24472/04_2026/7rhz_24472_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhz_24472/04_2026/7rhz_24472_neut.cif" } resolution = 4.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 88 5.49 5 S 29 5.16 5 C 3888 2.51 5 N 1253 2.21 5 O 1417 1.98 5 H 5875 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/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: 2.52, per 1000 atoms: 0.20 Number of scatterers: 12550 At special positions: 0 Unit cell: (73.718, 88.102, 163.618, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 P 88 15.00 O 1417 8.00 N 1253 7.00 C 3888 6.00 H 5875 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 342.3 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: 2.13 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: 2.89 Time building geometry restraints manager: 1.64 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=" ND1 HIS A 40 " pdb=" CE1 HIS A 40 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.72e+01 bond pdb=" ND1 HIS A 289 " pdb=" CE1 HIS A 289 " ideal model delta sigma weight residual 1.321 1.234 0.087 1.00e-02 1.00e+04 7.51e+01 bond pdb=" ND1 HIS A 91 " pdb=" CE1 HIS A 91 " ideal model delta sigma weight residual 1.321 1.235 0.086 1.00e-02 1.00e+04 7.46e+01 bond pdb=" CZ ARG A 292 " pdb=" NH2 ARG A 292 " ideal model delta sigma weight residual 1.330 1.231 0.099 1.30e-02 5.92e+03 5.83e+01 bond pdb=" CZ ARG B 100 " pdb=" NH2 ARG B 100 " ideal model delta sigma weight residual 1.330 1.231 0.099 1.30e-02 5.92e+03 5.82e+01 ... (remaining 12843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 21070 2.37 - 4.74: 1302 4.74 - 7.11: 598 7.11 - 9.47: 122 9.47 - 11.84: 69 Bond angle restraints: 23161 Sorted by residual: angle pdb=" CA HIS A 40 " pdb=" CB HIS A 40 " pdb=" CG HIS A 40 " ideal model delta sigma weight residual 113.80 120.58 -6.78 1.00e+00 1.00e+00 4.59e+01 angle pdb=" CA HIS A 91 " pdb=" CB HIS A 91 " pdb=" CG HIS A 91 " ideal model delta sigma weight residual 113.80 120.42 -6.62 1.00e+00 1.00e+00 4.38e+01 angle pdb=" H61 DA D 14 " pdb=" N6 DA D 14 " pdb=" H62 DA D 14 " ideal model delta sigma weight residual 120.00 110.12 9.88 1.50e+00 4.44e-01 4.34e+01 angle pdb=" H61 DA D 25 " pdb=" N6 DA D 25 " pdb=" H62 DA D 25 " ideal model delta sigma weight residual 120.00 110.17 9.83 1.50e+00 4.44e-01 4.30e+01 angle pdb=" H41 DC D 21 " pdb=" N4 DC D 21 " pdb=" H42 DC D 21 " ideal model delta sigma weight residual 120.00 110.19 9.81 1.50e+00 4.44e-01 4.28e+01 ... (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: 936 0.146 - 0.292: 19 0.292 - 0.437: 30 0.437 - 0.583: 79 0.583 - 0.729: 16 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CB VAL A 293 " pdb=" CA VAL A 293 " pdb=" CG1 VAL A 293 " pdb=" CG2 VAL A 293 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB ILE A 320 " pdb=" CA ILE A 320 " pdb=" CG1 ILE A 320 " pdb=" CG2 ILE A 320 " both_signs ideal model delta sigma weight residual False 2.64 1.93 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CB VAL B 113 " pdb=" CA VAL B 113 " pdb=" CG1 VAL B 113 " pdb=" CG2 VAL B 113 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.71 2.00e-01 2.50e+01 1.28e+01 ... (remaining 1077 not shown) Planarity restraints: 1619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA C 16 " -0.243 2.00e-02 2.50e+03 9.63e-02 3.01e+02 pdb=" N9 DA C 16 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DA C 16 " 0.060 2.00e-02 2.50e+03 pdb=" N7 DA C 16 " 0.083 2.00e-02 2.50e+03 pdb=" C5 DA C 16 " 0.051 2.00e-02 2.50e+03 pdb=" C6 DA C 16 " -0.025 2.00e-02 2.50e+03 pdb=" N6 DA C 16 " -0.183 2.00e-02 2.50e+03 pdb=" N1 DA C 16 " -0.013 2.00e-02 2.50e+03 pdb=" C2 DA C 16 " 0.039 2.00e-02 2.50e+03 pdb=" N3 DA C 16 " 0.037 2.00e-02 2.50e+03 pdb=" C4 DA C 16 " 0.049 2.00e-02 2.50e+03 pdb=" H8 DA C 16 " 0.061 2.00e-02 2.50e+03 pdb=" H2 DA C 16 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 17 " -0.199 2.00e-02 2.50e+03 7.92e-02 1.88e+02 pdb=" N1 DT C 17 " 0.021 2.00e-02 2.50e+03 pdb=" C2 DT C 17 " 0.059 2.00e-02 2.50e+03 pdb=" O2 DT C 17 " 0.049 2.00e-02 2.50e+03 pdb=" N3 DT C 17 " 0.080 2.00e-02 2.50e+03 pdb=" C4 DT C 17 " -0.014 2.00e-02 2.50e+03 pdb=" O4 DT C 17 " -0.115 2.00e-02 2.50e+03 pdb=" C5 DT C 17 " 0.020 2.00e-02 2.50e+03 pdb=" C7 DT C 17 " -0.013 2.00e-02 2.50e+03 pdb=" C6 DT C 17 " 0.058 2.00e-02 2.50e+03 pdb=" H3 DT C 17 " -0.019 2.00e-02 2.50e+03 pdb=" H6 DT C 17 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 14 " -0.165 2.00e-02 2.50e+03 6.69e-02 1.57e+02 pdb=" N9 DG C 14 " 0.003 2.00e-02 2.50e+03 pdb=" C8 DG C 14 " 0.060 2.00e-02 2.50e+03 pdb=" N7 DG C 14 " 0.031 2.00e-02 2.50e+03 pdb=" C5 DG C 14 " -0.015 2.00e-02 2.50e+03 pdb=" C6 DG C 14 " -0.059 2.00e-02 2.50e+03 pdb=" O6 DG C 14 " -0.058 2.00e-02 2.50e+03 pdb=" N1 DG C 14 " -0.047 2.00e-02 2.50e+03 pdb=" C2 DG C 14 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DG C 14 " 0.107 2.00e-02 2.50e+03 pdb=" N3 DG C 14 " 0.020 2.00e-02 2.50e+03 pdb=" C4 DG C 14 " 0.007 2.00e-02 2.50e+03 pdb=" H8 DG C 14 " 0.097 2.00e-02 2.50e+03 pdb=" H1 DG C 14 " 0.015 2.00e-02 2.50e+03 ... (remaining 1616 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 293 2.08 - 2.71: 19222 2.71 - 3.34: 35324 3.34 - 3.97: 43437 3.97 - 4.60: 66634 Nonbonded interactions: 164910 Sorted by model distance: nonbonded pdb="HH21 ARG A 106 " pdb=" OP1 DG D 20 " model vdw 1.453 2.450 nonbonded pdb="HH21 ARG B 106 " pdb=" OP1 DA C 20 " model vdw 1.467 2.450 nonbonded pdb=" H ARG B 181 " pdb=" OD2 ASP B 184 " model vdw 1.492 2.450 nonbonded pdb=" O LEU B 215 " pdb=" HG1 THR B 218 " model vdw 1.494 2.450 nonbonded pdb=" H TYR A 283 " pdb=" OP1 DC D 26 " model vdw 1.498 2.450 ... (remaining 164905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 32 or resid 34 through 35 or resid 37 through 7 \ 1 or resid 73 through 114 or resid 116 through 118 or resid 120 through 191 or r \ esid 193 through 327)) selection = (chain 'B' and (resid 20 through 32 or resid 34 through 35 or resid 37 through 7 \ 1 or resid 73 through 114 or resid 116 through 118 or resid 120 through 191 or r \ esid 193 through 198 or resid 208 through 327)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.970 Find NCS groups from input model: 0.120 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 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= 1.063 Angle : 1.621 11.844 9788 Z= 1.046 Chirality : 0.180 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 covalent geometry : bond 0.01962 ( 6973) covalent geometry : angle 1.62057 ( 9788) hydrogen bonds : bond 0.12436 ( 407) hydrogen bonds : angle 5.70280 ( 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 : 0.268 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: 0.3241 time to fit residues: 68.7902 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 : 0.286 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 94 GLN A 124 ASN B 89 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.062879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.047046 restraints weight = 124943.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.049583 restraints weight = 64490.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.051435 restraints weight = 40672.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.052703 restraints weight = 28766.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.053652 restraints weight = 22413.169| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6973 Z= 0.198 Angle : 0.672 8.207 9788 Z= 0.407 Chirality : 0.041 0.139 1080 Planarity : 0.005 0.040 959 Dihedral : 24.527 86.345 1664 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.33), residues: 607 helix: 0.75 (0.26), residues: 383 sheet: 0.07 (0.81), residues: 33 loop : -0.69 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 139 TYR 0.009 0.002 TYR B 324 PHE 0.010 0.001 PHE A 64 TRP 0.013 0.002 TRP B 55 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 6973) covalent geometry : angle 0.67210 ( 9788) hydrogen bonds : bond 0.05955 ( 407) hydrogen bonds : angle 4.71760 ( 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 148 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8798 (tttt) cc_final: 0.8479 (tmmt) REVERT: A 108 SER cc_start: 0.9198 (m) cc_final: 0.8989 (m) REVERT: A 109 ASP cc_start: 0.9081 (m-30) cc_final: 0.8801 (p0) REVERT: A 130 ARG cc_start: 0.9004 (mtt180) cc_final: 0.8647 (pmt-80) REVERT: A 265 PHE cc_start: 0.9685 (m-80) cc_final: 0.9327 (m-80) REVERT: A 289 HIS cc_start: 0.9037 (m90) cc_final: 0.8782 (m-70) REVERT: A 298 ASP cc_start: 0.9532 (t0) cc_final: 0.9050 (t0) REVERT: B 52 TRP cc_start: 0.9612 (t-100) cc_final: 0.9373 (t-100) REVERT: B 77 TYR cc_start: 0.9052 (t80) cc_final: 0.8673 (t80) REVERT: B 273 TYR cc_start: 0.8957 (m-80) cc_final: 0.8387 (m-80) REVERT: B 277 ASP cc_start: 0.9561 (m-30) cc_final: 0.9034 (p0) REVERT: B 319 ASN cc_start: 0.9542 (m-40) cc_final: 0.9252 (t0) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.3060 time to fit residues: 53.1825 Evaluate side-chains 129 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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: 5.9990 chunk 50 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 245 ASN ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.057539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.042931 restraints weight = 146150.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.045121 restraints weight = 77208.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.046664 restraints weight = 49910.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.047768 restraints weight = 36180.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.048514 restraints weight = 28570.129| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 6973 Z= 0.342 Angle : 0.761 6.262 9788 Z= 0.463 Chirality : 0.047 0.158 1080 Planarity : 0.006 0.045 959 Dihedral : 24.831 83.173 1664 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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: -0.84 (0.32), residues: 607 helix: -0.15 (0.25), residues: 386 sheet: -0.73 (0.78), residues: 29 loop : -1.10 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 241 TYR 0.016 0.002 TYR A 283 PHE 0.019 0.003 PHE A 137 TRP 0.021 0.003 TRP B 52 HIS 0.006 0.002 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00691 ( 6973) covalent geometry : angle 0.76146 ( 9788) hydrogen bonds : bond 0.09035 ( 407) hydrogen bonds : angle 5.30277 ( 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 131 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.280 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 43 LYS cc_start: 0.9181 (tttt) cc_final: 0.8803 (tmmt) REVERT: A 91 HIS cc_start: 0.9788 (m90) cc_final: 0.9429 (m90) REVERT: A 109 ASP cc_start: 0.9172 (m-30) cc_final: 0.8967 (p0) REVERT: A 129 GLU cc_start: 0.6615 (mp0) cc_final: 0.6278 (mp0) REVERT: A 130 ARG cc_start: 0.8863 (mtt180) cc_final: 0.8352 (ptt90) REVERT: A 172 LEU cc_start: 0.8585 (mt) cc_final: 0.8213 (mt) REVERT: A 176 GLU cc_start: 0.9798 (tp30) cc_final: 0.9365 (tp30) REVERT: B 273 TYR cc_start: 0.9106 (m-80) cc_final: 0.8650 (m-80) REVERT: B 277 ASP cc_start: 0.9383 (m-30) cc_final: 0.8691 (p0) REVERT: B 319 ASN cc_start: 0.9578 (m-40) cc_final: 0.9277 (t0) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.3178 time to fit residues: 48.9861 Evaluate side-chains 110 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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: 9.9990 chunk 66 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 44 optimal weight: 0.0570 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.062662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.047244 restraints weight = 135268.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.049720 restraints weight = 69587.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.051485 restraints weight = 44315.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.052687 restraints weight = 31905.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.053523 restraints weight = 25160.270| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5150 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= 0.166 Angle : 0.623 6.315 9788 Z= 0.381 Chirality : 0.038 0.131 1080 Planarity : 0.004 0.043 959 Dihedral : 24.531 86.376 1664 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.33), residues: 607 helix: 0.83 (0.26), residues: 383 sheet: -0.35 (0.84), residues: 29 loop : -0.93 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 81 TYR 0.011 0.001 TYR A 283 PHE 0.011 0.002 PHE A 64 TRP 0.026 0.002 TRP B 224 HIS 0.005 0.001 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6973) covalent geometry : angle 0.62272 ( 9788) hydrogen bonds : bond 0.05090 ( 407) hydrogen bonds : angle 4.67098 ( 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 128 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8278 (m-80) cc_final: 0.7982 (m-80) REVERT: A 130 ARG cc_start: 0.8890 (mtt180) cc_final: 0.8248 (ptt90) REVERT: A 172 LEU cc_start: 0.8429 (mt) cc_final: 0.8088 (mt) REVERT: A 176 GLU cc_start: 0.9780 (tp30) cc_final: 0.9302 (tp30) REVERT: A 265 PHE cc_start: 0.9720 (m-80) cc_final: 0.9419 (m-80) REVERT: A 289 HIS cc_start: 0.9027 (m90) cc_final: 0.8800 (m-70) REVERT: B 77 TYR cc_start: 0.9207 (t80) cc_final: 0.8888 (t80) REVERT: B 273 TYR cc_start: 0.9022 (m-80) cc_final: 0.8553 (m-80) REVERT: B 277 ASP cc_start: 0.9404 (m-30) cc_final: 0.8815 (p0) REVERT: B 319 ASN cc_start: 0.9558 (m-40) cc_final: 0.9190 (t0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2948 time to fit residues: 44.9066 Evaluate side-chains 103 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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: 3.9990 chunk 43 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN B 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.057819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.043446 restraints weight = 149415.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.045597 restraints weight = 78058.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.047028 restraints weight = 50397.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.048124 restraints weight = 37145.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.048904 restraints weight = 29247.705| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 6973 Z= 0.303 Angle : 0.702 5.641 9788 Z= 0.431 Chirality : 0.045 0.146 1080 Planarity : 0.006 0.079 959 Dihedral : 24.916 89.746 1664 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -0.71 (0.31), residues: 607 helix: -0.02 (0.24), residues: 385 sheet: -0.97 (0.87), residues: 28 loop : -1.08 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 154 TYR 0.018 0.003 TYR A 283 PHE 0.013 0.003 PHE A 163 TRP 0.028 0.003 TRP B 224 HIS 0.005 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00609 ( 6973) covalent geometry : angle 0.70220 ( 9788) hydrogen bonds : bond 0.08317 ( 407) hydrogen bonds : angle 5.16389 ( 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 123 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8252 (m-80) cc_final: 0.7941 (m-80) REVERT: A 91 HIS cc_start: 0.9776 (m90) cc_final: 0.9478 (m90) REVERT: A 94 GLN cc_start: 0.9614 (tm-30) cc_final: 0.9258 (tm-30) REVERT: A 108 SER cc_start: 0.8356 (m) cc_final: 0.8016 (p) REVERT: A 130 ARG cc_start: 0.8772 (mtt180) cc_final: 0.8385 (ptt90) REVERT: A 172 LEU cc_start: 0.8835 (mt) cc_final: 0.8346 (mt) REVERT: A 176 GLU cc_start: 0.9808 (tp30) cc_final: 0.9358 (tp30) REVERT: B 97 MET cc_start: 0.8686 (mtt) cc_final: 0.8208 (mmp) REVERT: B 273 TYR cc_start: 0.8997 (m-80) cc_final: 0.8591 (m-80) REVERT: B 277 ASP cc_start: 0.9452 (m-30) cc_final: 0.8852 (p0) REVERT: B 289 HIS cc_start: 0.9267 (m-70) cc_final: 0.9016 (m90) REVERT: B 299 MET cc_start: 0.4528 (mmm) cc_final: 0.4244 (mmm) REVERT: B 319 ASN cc_start: 0.9582 (m-40) cc_final: 0.9230 (t0) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2811 time to fit residues: 41.5263 Evaluate side-chains 105 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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: 5.9990 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.067340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.053509 restraints weight = 184416.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.055981 restraints weight = 101639.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057661 restraints weight = 66498.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.058792 restraints weight = 48699.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.059534 restraints weight = 38636.810| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.6154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6973 Z= 0.163 Angle : 0.605 4.948 9788 Z= 0.368 Chirality : 0.038 0.133 1080 Planarity : 0.004 0.052 959 Dihedral : 24.671 85.961 1664 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.32), residues: 607 helix: 0.82 (0.25), residues: 385 sheet: -0.82 (0.86), residues: 29 loop : -0.92 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 139 TYR 0.012 0.002 TYR A 168 PHE 0.008 0.001 PHE B 31 TRP 0.017 0.002 TRP A 224 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 6973) covalent geometry : angle 0.60512 ( 9788) hydrogen bonds : bond 0.05003 ( 407) hydrogen bonds : angle 4.69473 ( 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 129 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.341 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: A 44 MET cc_start: 0.9113 (mmt) cc_final: 0.8792 (mmm) REVERT: A 108 SER cc_start: 0.7905 (m) cc_final: 0.7551 (p) REVERT: A 130 ARG cc_start: 0.8880 (mtt180) cc_final: 0.8459 (ptt90) REVERT: A 172 LEU cc_start: 0.8851 (mt) cc_final: 0.8326 (mt) REVERT: A 176 GLU cc_start: 0.9781 (tp30) cc_final: 0.9316 (tp30) REVERT: A 265 PHE cc_start: 0.9742 (m-80) cc_final: 0.9093 (m-80) REVERT: B 52 TRP cc_start: 0.9467 (t-100) cc_final: 0.9179 (t-100) REVERT: B 256 LEU cc_start: 0.9578 (tp) cc_final: 0.9197 (mm) REVERT: B 273 TYR cc_start: 0.9051 (m-80) cc_final: 0.8670 (m-80) REVERT: B 277 ASP cc_start: 0.9595 (m-30) cc_final: 0.9062 (p0) REVERT: B 289 HIS cc_start: 0.9250 (m-70) cc_final: 0.9019 (m-70) REVERT: B 319 ASN cc_start: 0.9548 (m-40) cc_final: 0.9127 (t0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2869 time to fit residues: 44.4118 Evaluate side-chains 109 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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: 9.9990 chunk 53 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.060445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.045458 restraints weight = 149212.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.047813 restraints weight = 77741.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.049478 restraints weight = 49486.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.050624 restraints weight = 35653.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.051458 restraints weight = 28151.298| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.6633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6973 Z= 0.219 Angle : 0.623 4.386 9788 Z= 0.380 Chirality : 0.041 0.145 1080 Planarity : 0.005 0.050 959 Dihedral : 24.781 87.345 1664 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.33), residues: 607 helix: 0.71 (0.25), residues: 386 sheet: -1.22 (0.77), residues: 29 loop : -0.99 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 101 TYR 0.017 0.002 TYR A 168 PHE 0.018 0.002 PHE B 163 TRP 0.016 0.002 TRP B 42 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 6973) covalent geometry : angle 0.62348 ( 9788) hydrogen bonds : bond 0.06293 ( 407) hydrogen bonds : angle 4.72659 ( 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 122 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.302 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: A 90 GLN cc_start: 0.9583 (tm-30) cc_final: 0.9267 (tm-30) REVERT: A 94 GLN cc_start: 0.9662 (tm-30) cc_final: 0.9360 (tm-30) REVERT: A 108 SER cc_start: 0.8028 (m) cc_final: 0.7633 (p) REVERT: A 130 ARG cc_start: 0.8554 (mtt180) cc_final: 0.8319 (ppt170) REVERT: A 176 GLU cc_start: 0.9822 (tp30) cc_final: 0.9352 (tp30) REVERT: A 265 PHE cc_start: 0.9501 (m-80) cc_final: 0.9007 (m-80) REVERT: B 64 PHE cc_start: 0.9080 (t80) cc_final: 0.8797 (t80) REVERT: B 77 TYR cc_start: 0.9623 (t80) cc_final: 0.9218 (t80) REVERT: B 256 LEU cc_start: 0.9299 (tp) cc_final: 0.8860 (mm) REVERT: B 273 TYR cc_start: 0.8972 (m-80) cc_final: 0.8573 (m-80) REVERT: B 277 ASP cc_start: 0.9538 (m-30) cc_final: 0.9071 (p0) REVERT: B 319 ASN cc_start: 0.9563 (m-40) cc_final: 0.9105 (t0) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2823 time to fit residues: 41.3178 Evaluate side-chains 107 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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: 8.9990 chunk 67 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.061208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.045874 restraints weight = 142870.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.048233 restraints weight = 75349.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.049965 restraints weight = 48572.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.051152 restraints weight = 35064.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.051965 restraints weight = 27577.801| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 6973 Z= 0.185 Angle : 0.608 4.731 9788 Z= 0.368 Chirality : 0.040 0.218 1080 Planarity : 0.004 0.047 959 Dihedral : 24.739 87.933 1664 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.33), residues: 607 helix: 0.88 (0.26), residues: 386 sheet: -1.40 (0.75), residues: 29 loop : -0.88 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.013 0.001 TYR A 168 PHE 0.019 0.002 PHE B 163 TRP 0.017 0.002 TRP B 42 HIS 0.003 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6973) covalent geometry : angle 0.60768 ( 9788) hydrogen bonds : bond 0.05275 ( 407) hydrogen bonds : angle 4.68731 ( 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 121 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.317 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: A 90 GLN cc_start: 0.9639 (tm-30) cc_final: 0.9381 (tm-30) REVERT: A 108 SER cc_start: 0.8056 (m) cc_final: 0.7624 (p) REVERT: A 130 ARG cc_start: 0.8624 (mtt180) cc_final: 0.8289 (ppt170) REVERT: A 173 ARG cc_start: 0.8924 (ttt180) cc_final: 0.8441 (ttp-170) REVERT: A 265 PHE cc_start: 0.9497 (m-80) cc_final: 0.9036 (m-80) REVERT: B 64 PHE cc_start: 0.9031 (t80) cc_final: 0.8659 (t80) REVERT: B 74 TYR cc_start: 0.9400 (t80) cc_final: 0.8903 (t80) REVERT: B 77 TYR cc_start: 0.9669 (t80) cc_final: 0.9265 (t80) REVERT: B 256 LEU cc_start: 0.9459 (tp) cc_final: 0.9014 (mm) REVERT: B 273 TYR cc_start: 0.9006 (m-80) cc_final: 0.8615 (m-80) REVERT: B 277 ASP cc_start: 0.9550 (m-30) cc_final: 0.9103 (p0) REVERT: B 319 ASN cc_start: 0.9599 (m-40) cc_final: 0.9175 (t0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2658 time to fit residues: 39.0208 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 : 0.229 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.106338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.092901 restraints weight = 186814.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.095259 restraints weight = 81918.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.096676 restraints weight = 46200.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.097547 restraints weight = 30166.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.098108 restraints weight = 21726.119| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.7064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6973 Z= 0.202 Angle : 0.616 5.554 9788 Z= 0.374 Chirality : 0.040 0.153 1080 Planarity : 0.005 0.048 959 Dihedral : 24.752 88.659 1664 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.33), residues: 607 helix: 0.88 (0.26), residues: 387 sheet: -1.37 (0.75), residues: 29 loop : -0.91 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 106 TYR 0.013 0.001 TYR A 168 PHE 0.009 0.002 PHE B 31 TRP 0.064 0.003 TRP B 224 HIS 0.003 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 6973) covalent geometry : angle 0.61565 ( 9788) hydrogen bonds : bond 0.05781 ( 407) hydrogen bonds : angle 4.69578 ( 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 118 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.311 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: A 44 MET cc_start: 0.9306 (mmt) cc_final: 0.8939 (mmm) REVERT: A 90 GLN cc_start: 0.9652 (tm-30) cc_final: 0.9403 (tm-30) REVERT: A 108 SER cc_start: 0.8444 (m) cc_final: 0.8093 (p) REVERT: A 130 ARG cc_start: 0.8568 (mtt180) cc_final: 0.8275 (ppt170) REVERT: A 265 PHE cc_start: 0.9582 (m-80) cc_final: 0.9193 (m-80) REVERT: B 64 PHE cc_start: 0.9055 (t80) cc_final: 0.8747 (t80) REVERT: B 256 LEU cc_start: 0.9575 (tp) cc_final: 0.9188 (mm) REVERT: B 273 TYR cc_start: 0.8956 (m-80) cc_final: 0.8593 (m-80) REVERT: B 277 ASP cc_start: 0.9604 (m-30) cc_final: 0.9077 (p0) REVERT: B 319 ASN cc_start: 0.9592 (m-40) cc_final: 0.9177 (t0) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2539 time to fit residues: 36.5281 Evaluate side-chains 101 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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: 7.9990 chunk 24 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 6 optimal weight: 0.0770 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.061563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.046265 restraints weight = 141666.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.048706 restraints weight = 74013.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.050424 restraints weight = 47387.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.051635 restraints weight = 33992.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.052447 restraints weight = 26573.951| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.7296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6973 Z= 0.175 Angle : 0.592 5.779 9788 Z= 0.359 Chirality : 0.038 0.152 1080 Planarity : 0.004 0.044 959 Dihedral : 24.674 89.097 1664 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.33), residues: 607 helix: 1.14 (0.26), residues: 386 sheet: -1.12 (0.78), residues: 29 loop : -1.01 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.011 0.001 TYR A 168 PHE 0.012 0.001 PHE B 64 TRP 0.061 0.003 TRP B 224 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6973) covalent geometry : angle 0.59237 ( 9788) hydrogen bonds : bond 0.05067 ( 407) hydrogen bonds : angle 4.56425 ( 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 118 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9304 (mmt) cc_final: 0.8899 (mmm) REVERT: A 90 GLN cc_start: 0.9652 (tm-30) cc_final: 0.9432 (tm-30) REVERT: A 108 SER cc_start: 0.8114 (m) cc_final: 0.7638 (p) REVERT: A 130 ARG cc_start: 0.8693 (mtt180) cc_final: 0.8303 (ppt170) REVERT: A 265 PHE cc_start: 0.9508 (m-80) cc_final: 0.9070 (m-80) REVERT: B 64 PHE cc_start: 0.9138 (t80) cc_final: 0.8864 (t80) REVERT: B 256 LEU cc_start: 0.9436 (tp) cc_final: 0.8972 (mm) REVERT: B 273 TYR cc_start: 0.9013 (m-80) cc_final: 0.8630 (m-80) REVERT: B 277 ASP cc_start: 0.9538 (m-30) cc_final: 0.9122 (p0) REVERT: B 319 ASN cc_start: 0.9581 (m-40) cc_final: 0.9065 (t0) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2589 time to fit residues: 37.2931 Evaluate side-chains 104 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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: 6.9990 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN B 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.060011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.045163 restraints weight = 144450.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.047498 restraints weight = 74317.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.049168 restraints weight = 47381.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.050313 restraints weight = 33946.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.051101 restraints weight = 26577.079| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.7471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6973 Z= 0.213 Angle : 0.612 5.839 9788 Z= 0.373 Chirality : 0.040 0.145 1080 Planarity : 0.005 0.047 959 Dihedral : 24.791 89.839 1664 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.33), residues: 607 helix: 0.88 (0.26), residues: 386 sheet: -1.05 (0.86), residues: 28 loop : -1.05 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.012 0.002 TYR A 168 PHE 0.009 0.002 PHE B 31 TRP 0.051 0.003 TRP B 224 HIS 0.004 0.001 HIS B 196 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 6973) covalent geometry : angle 0.61170 ( 9788) hydrogen bonds : bond 0.06087 ( 407) hydrogen bonds : angle 4.69963 ( 1102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2614.24 seconds wall clock time: 45 minutes 8.69 seconds (2708.69 seconds total)