Starting phenix.real_space_refine on Wed Sep 17 10:20:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9enf_19833/09_2025/9enf_19833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9enf_19833/09_2025/9enf_19833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9enf_19833/09_2025/9enf_19833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9enf_19833/09_2025/9enf_19833.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9enf_19833/09_2025/9enf_19833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9enf_19833/09_2025/9enf_19833.map" } resolution = 2.97 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 180 5.49 5 S 28 5.16 5 C 4522 2.51 5 N 1450 2.21 5 O 2055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8235 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2083 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain breaks: 4 Chain: "B" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2270 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 4 Chain: "C" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1941 Classifications: {'RNA': 91} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 38} Link IDs: {'rna2p': 20, 'rna3p': 70} Chain: "D" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1941 Classifications: {'RNA': 91} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 38} Link IDs: {'rna2p': 20, 'rna3p': 70} Time building chain proxies: 2.23, per 1000 atoms: 0.27 Number of scatterers: 8235 At special positions: 0 Unit cell: (103.2, 147.92, 83.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 180 15.00 O 2055 8.00 N 1450 7.00 C 4522 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 179.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1014 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 34.7% alpha, 19.2% beta 50 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 88 through 96 Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 205 through 214 removed outlier: 3.691A pdb=" N MET A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.601A pdb=" N ASN A 232 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 338 through 369 removed outlier: 3.714A pdb=" N GLU A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 100 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 159 through 166 removed outlier: 3.860A pdb=" N ARG B 166 " --> pdb=" O HIS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 213 through 217 removed outlier: 3.703A pdb=" N TYR B 216 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 217 " --> pdb=" O GLN B 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 213 through 217' Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 277 through 291 Processing helix chain 'B' and resid 297 through 304 removed outlier: 3.696A pdb=" N GLU B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 369 removed outlier: 3.661A pdb=" N PHE B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 174 removed outlier: 6.741A pdb=" N GLY A 61 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG A 133 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ARG A 63 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP A 131 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 65 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER A 129 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 67 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL A 127 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE A 69 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 125 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 123 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASP A 326 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLN A 126 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR A 194 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 269 " --> pdb=" O TYR A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 219 Processing sheet with id=AA3, first strand: chain 'B' and resid 173 through 178 removed outlier: 5.623A pdb=" N ILE B 174 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA B 70 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA B 176 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 68 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 178 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR B 71 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE B 124 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP B 326 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLN B 126 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR B 194 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B 239 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS B 220 " --> pdb=" O ARG B 239 " (cutoff:3.500A) 162 hydrogen bonds defined for protein. 441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 128 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1699 1.33 - 1.45: 2964 1.45 - 1.57: 3724 1.57 - 1.69: 360 1.69 - 1.81: 44 Bond restraints: 8791 Sorted by residual: bond pdb=" C3' C D 23 " pdb=" O3' C D 23 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.28e+00 bond pdb=" C3' A D 61 " pdb=" O3' A D 61 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.27e+00 bond pdb=" C3' C C 23 " pdb=" O3' C C 23 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.26e+00 bond pdb=" CG LYS A 358 " pdb=" CD LYS A 358 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.25e+00 bond pdb=" C3' A C 61 " pdb=" O3' A C 61 " ideal model delta sigma weight residual 1.427 1.443 -0.016 1.50e-02 4.44e+03 1.18e+00 ... (remaining 8786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 12515 1.79 - 3.58: 207 3.58 - 5.37: 44 5.37 - 7.16: 8 7.16 - 8.95: 1 Bond angle restraints: 12775 Sorted by residual: angle pdb=" C3' C C 23 " pdb=" O3' C C 23 " pdb=" P G C 24 " ideal model delta sigma weight residual 120.20 125.19 -4.99 1.50e+00 4.44e-01 1.11e+01 angle pdb=" C3' C D 23 " pdb=" O3' C D 23 " pdb=" P G D 24 " ideal model delta sigma weight residual 120.20 125.15 -4.95 1.50e+00 4.44e-01 1.09e+01 angle pdb=" C3' A D 61 " pdb=" O3' A D 61 " pdb=" P A D 62 " ideal model delta sigma weight residual 120.20 125.05 -4.85 1.50e+00 4.44e-01 1.04e+01 angle pdb=" C3' A C 61 " pdb=" O3' A C 61 " pdb=" P A C 62 " ideal model delta sigma weight residual 120.20 125.02 -4.82 1.50e+00 4.44e-01 1.03e+01 angle pdb=" CB LYS B 295 " pdb=" CG LYS B 295 " pdb=" CD LYS B 295 " ideal model delta sigma weight residual 111.30 118.46 -7.16 2.30e+00 1.89e-01 9.69e+00 ... (remaining 12770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 4921 35.45 - 70.90: 536 70.90 - 106.35: 67 106.35 - 141.81: 0 141.81 - 177.26: 8 Dihedral angle restraints: 5532 sinusoidal: 3974 harmonic: 1558 Sorted by residual: dihedral pdb=" O4' C C 23 " pdb=" C1' C C 23 " pdb=" N1 C C 23 " pdb=" C2 C C 23 " ideal model delta sinusoidal sigma weight residual 232.00 75.14 156.86 1 1.70e+01 3.46e-03 6.38e+01 dihedral pdb=" O4' C D 23 " pdb=" C1' C D 23 " pdb=" N1 C D 23 " pdb=" C2 C D 23 " ideal model delta sinusoidal sigma weight residual 232.00 75.40 156.60 1 1.70e+01 3.46e-03 6.37e+01 dihedral pdb=" O4' G C 48 " pdb=" C1' G C 48 " pdb=" N9 G C 48 " pdb=" C4 G C 48 " ideal model delta sinusoidal sigma weight residual -106.00 -171.32 65.32 1 1.70e+01 3.46e-03 1.94e+01 ... (remaining 5529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1305 0.043 - 0.087: 188 0.087 - 0.130: 55 0.130 - 0.173: 2 0.173 - 0.217: 7 Chirality restraints: 1557 Sorted by residual: chirality pdb=" C3' A C 61 " pdb=" C4' A C 61 " pdb=" O3' A C 61 " pdb=" C2' A C 61 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C3' A D 61 " pdb=" C4' A D 61 " pdb=" O3' A D 61 " pdb=" C2' A D 61 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C3' C D 23 " pdb=" C4' C D 23 " pdb=" O3' C D 23 " pdb=" C2' C D 23 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 1554 not shown) Planarity restraints: 955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 74 " -0.017 2.00e-02 2.50e+03 2.37e-02 1.40e+01 pdb=" CG TRP A 74 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A 74 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP A 74 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 74 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 74 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 74 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 74 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 74 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP A 74 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 260 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.88e+00 pdb=" N PRO A 261 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 320 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO B 321 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 321 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 321 " 0.023 5.00e-02 4.00e+02 ... (remaining 952 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 421 2.67 - 3.23: 7502 3.23 - 3.79: 14786 3.79 - 4.34: 18493 4.34 - 4.90: 26964 Nonbonded interactions: 68166 Sorted by model distance: nonbonded pdb=" O6 G C 30 " pdb=" O4 U C 57 " model vdw 2.114 2.432 nonbonded pdb=" OH TYR B 197 " pdb=" O VAL B 318 " model vdw 2.163 3.040 nonbonded pdb=" O SER A 185 " pdb=" OG SER A 189 " model vdw 2.172 3.040 nonbonded pdb=" O2' G C 64 " pdb=" OP1 U C 66 " model vdw 2.180 3.040 nonbonded pdb=" O2' G D 64 " pdb=" OP1 U D 66 " model vdw 2.182 3.040 ... (remaining 68161 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 58 through 228 or resid 234 through 369)) selection = (chain 'B' and (resid 58 through 289 or resid 319 through 328 or resid 337 throu \ gh 369)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.170 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8791 Z= 0.139 Angle : 0.608 8.953 12775 Z= 0.315 Chirality : 0.035 0.217 1557 Planarity : 0.004 0.042 955 Dihedral : 24.216 177.257 4518 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.36), residues: 510 helix: 0.39 (0.43), residues: 154 sheet: -0.61 (0.53), residues: 93 loop : -2.31 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 280 TYR 0.020 0.002 TYR A 276 PHE 0.009 0.001 PHE B 184 TRP 0.059 0.004 TRP A 74 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8791) covalent geometry : angle 0.60777 (12775) hydrogen bonds : bond 0.13766 ( 290) hydrogen bonds : angle 5.23570 ( 661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: B 316 MET cc_start: 0.4995 (tpt) cc_final: 0.4640 (tpt) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.4685 time to fit residues: 19.2988 Evaluate side-chains 27 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN B 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.106263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.082818 restraints weight = 37394.124| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.02 r_work: 0.3833 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8791 Z= 0.220 Angle : 0.701 7.374 12775 Z= 0.359 Chirality : 0.039 0.216 1557 Planarity : 0.005 0.049 955 Dihedral : 25.176 168.805 3465 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.72 % Allowed : 10.30 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.35), residues: 510 helix: 0.42 (0.42), residues: 147 sheet: -1.00 (0.55), residues: 84 loop : -2.68 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 173 TYR 0.035 0.002 TYR A 276 PHE 0.013 0.002 PHE A 55 TRP 0.048 0.004 TRP A 74 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 8791) covalent geometry : angle 0.70089 (12775) hydrogen bonds : bond 0.07584 ( 290) hydrogen bonds : angle 4.75308 ( 661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: B 316 MET cc_start: 0.5499 (tpt) cc_final: 0.5269 (tpt) outliers start: 8 outliers final: 3 residues processed: 32 average time/residue: 0.4649 time to fit residues: 16.0904 Evaluate side-chains 29 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 16 optimal weight: 0.0970 chunk 55 optimal weight: 30.0000 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 overall best weight: 4.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.105192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.081735 restraints weight = 37269.867| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 3.03 r_work: 0.3804 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8791 Z= 0.233 Angle : 0.726 8.446 12775 Z= 0.371 Chirality : 0.040 0.219 1557 Planarity : 0.005 0.054 955 Dihedral : 25.174 168.749 3465 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.22 % Allowed : 14.16 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.34), residues: 510 helix: 0.29 (0.42), residues: 147 sheet: -1.09 (0.61), residues: 66 loop : -2.84 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 173 TYR 0.046 0.003 TYR A 276 PHE 0.015 0.002 PHE A 320 TRP 0.026 0.004 TRP A 74 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 8791) covalent geometry : angle 0.72647 (12775) hydrogen bonds : bond 0.07880 ( 290) hydrogen bonds : angle 4.85567 ( 661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.234 Fit side-chains REVERT: A 228 MET cc_start: 0.6604 (OUTLIER) cc_final: 0.6375 (tmm) REVERT: B 307 LYS cc_start: 0.6941 (mptt) cc_final: 0.5626 (mppt) REVERT: B 316 MET cc_start: 0.5816 (tpt) cc_final: 0.5470 (tpt) outliers start: 15 outliers final: 5 residues processed: 38 average time/residue: 0.4458 time to fit residues: 18.5285 Evaluate side-chains 32 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 355 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 45 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 277 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.107888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.084795 restraints weight = 37918.964| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 3.11 r_work: 0.3881 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8791 Z= 0.132 Angle : 0.609 9.319 12775 Z= 0.313 Chirality : 0.036 0.217 1557 Planarity : 0.004 0.048 955 Dihedral : 24.930 169.701 3465 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.00 % Allowed : 16.74 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.35), residues: 510 helix: 0.76 (0.43), residues: 148 sheet: -1.06 (0.58), residues: 70 loop : -2.66 (0.31), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.027 0.002 TYR A 276 PHE 0.021 0.001 PHE A 320 TRP 0.031 0.003 TRP A 74 HIS 0.002 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8791) covalent geometry : angle 0.60860 (12775) hydrogen bonds : bond 0.05725 ( 290) hydrogen bonds : angle 4.26295 ( 661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.6264 (tmm) REVERT: B 307 LYS cc_start: 0.6774 (mptt) cc_final: 0.5486 (mppt) REVERT: B 316 MET cc_start: 0.5332 (tpt) cc_final: 0.4923 (tpt) outliers start: 14 outliers final: 5 residues processed: 39 average time/residue: 0.4738 time to fit residues: 20.0078 Evaluate side-chains 34 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.104772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.081179 restraints weight = 37823.468| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 3.10 r_work: 0.3794 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8791 Z= 0.243 Angle : 0.741 9.481 12775 Z= 0.378 Chirality : 0.041 0.226 1557 Planarity : 0.005 0.052 955 Dihedral : 25.090 167.247 3465 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.08 % Allowed : 19.53 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.33), residues: 510 helix: 0.30 (0.42), residues: 141 sheet: -1.31 (0.64), residues: 61 loop : -2.81 (0.29), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 173 TYR 0.045 0.003 TYR A 276 PHE 0.021 0.002 PHE A 320 TRP 0.060 0.005 TRP A 74 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 8791) covalent geometry : angle 0.74146 (12775) hydrogen bonds : bond 0.08099 ( 290) hydrogen bonds : angle 4.85679 ( 661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 29 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6447 (tmm) REVERT: B 307 LYS cc_start: 0.6926 (mptt) cc_final: 0.5642 (mppt) REVERT: B 316 MET cc_start: 0.5965 (tpt) cc_final: 0.5659 (tpt) outliers start: 19 outliers final: 8 residues processed: 43 average time/residue: 0.3903 time to fit residues: 18.4620 Evaluate side-chains 36 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 365 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 277 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.106311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.083045 restraints weight = 37157.726| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 3.08 r_work: 0.3841 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8791 Z= 0.167 Angle : 0.664 9.216 12775 Z= 0.338 Chirality : 0.038 0.220 1557 Planarity : 0.005 0.051 955 Dihedral : 24.913 168.703 3465 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.22 % Allowed : 21.89 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.34), residues: 510 helix: 0.37 (0.42), residues: 148 sheet: -1.18 (0.66), residues: 57 loop : -2.78 (0.30), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.029 0.002 TYR A 276 PHE 0.020 0.001 PHE A 320 TRP 0.063 0.005 TRP A 74 HIS 0.003 0.001 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8791) covalent geometry : angle 0.66437 (12775) hydrogen bonds : bond 0.06563 ( 290) hydrogen bonds : angle 4.53773 ( 661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 209 MET cc_start: 0.5142 (mmp) cc_final: 0.4848 (mmt) REVERT: A 228 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.6483 (tmm) REVERT: B 307 LYS cc_start: 0.6897 (mptt) cc_final: 0.5584 (mppt) REVERT: B 316 MET cc_start: 0.5800 (tpt) cc_final: 0.5494 (tpt) outliers start: 15 outliers final: 7 residues processed: 37 average time/residue: 0.4718 time to fit residues: 18.8695 Evaluate side-chains 35 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 361 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.104826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.081232 restraints weight = 38113.971| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.09 r_work: 0.3783 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8791 Z= 0.233 Angle : 0.732 8.037 12775 Z= 0.371 Chirality : 0.040 0.229 1557 Planarity : 0.005 0.053 955 Dihedral : 24.994 167.580 3465 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 4.08 % Allowed : 22.10 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.33), residues: 510 helix: 0.03 (0.42), residues: 148 sheet: -1.33 (0.66), residues: 59 loop : -2.90 (0.29), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 173 TYR 0.039 0.002 TYR A 276 PHE 0.020 0.002 PHE A 320 TRP 0.070 0.006 TRP A 74 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 8791) covalent geometry : angle 0.73220 (12775) hydrogen bonds : bond 0.07887 ( 290) hydrogen bonds : angle 4.88577 ( 661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 28 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.5237 (mmp) cc_final: 0.4996 (mmt) REVERT: A 228 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6528 (tmm) REVERT: B 316 MET cc_start: 0.6031 (tpt) cc_final: 0.5739 (tpt) outliers start: 19 outliers final: 9 residues processed: 42 average time/residue: 0.4648 time to fit residues: 21.1939 Evaluate side-chains 36 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 361 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 65 optimal weight: 40.0000 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 64 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.106196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.082751 restraints weight = 37807.638| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 3.04 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8791 Z= 0.173 Angle : 0.666 7.575 12775 Z= 0.339 Chirality : 0.038 0.224 1557 Planarity : 0.005 0.052 955 Dihedral : 24.902 168.448 3465 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.43 % Allowed : 22.75 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.34), residues: 510 helix: 0.28 (0.42), residues: 148 sheet: -0.84 (0.67), residues: 56 loop : -2.83 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 173 TYR 0.029 0.002 TYR A 276 PHE 0.024 0.002 PHE A 320 TRP 0.048 0.004 TRP A 74 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8791) covalent geometry : angle 0.66642 (12775) hydrogen bonds : bond 0.06647 ( 290) hydrogen bonds : angle 4.58681 ( 661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 30 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: B 307 LYS cc_start: 0.6997 (mptt) cc_final: 0.6043 (mppt) REVERT: B 316 MET cc_start: 0.5974 (tpt) cc_final: 0.5645 (tpt) outliers start: 16 outliers final: 7 residues processed: 41 average time/residue: 0.4567 time to fit residues: 20.3430 Evaluate side-chains 34 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 29 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.105876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.082429 restraints weight = 37882.462| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 3.05 r_work: 0.3811 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8791 Z= 0.189 Angle : 0.695 8.336 12775 Z= 0.351 Chirality : 0.038 0.227 1557 Planarity : 0.005 0.052 955 Dihedral : 24.918 167.957 3465 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.22 % Allowed : 24.03 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.34), residues: 510 helix: 0.17 (0.42), residues: 148 sheet: -1.32 (0.60), residues: 66 loop : -2.77 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 173 TYR 0.031 0.002 TYR A 276 PHE 0.020 0.002 PHE A 320 TRP 0.052 0.005 TRP A 74 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8791) covalent geometry : angle 0.69525 (12775) hydrogen bonds : bond 0.06993 ( 290) hydrogen bonds : angle 4.66676 ( 661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 209 MET cc_start: 0.4909 (mmp) cc_final: 0.4559 (mmt) REVERT: B 307 LYS cc_start: 0.7039 (mptt) cc_final: 0.6098 (mppt) REVERT: B 316 MET cc_start: 0.6066 (tpt) cc_final: 0.5745 (tpt) outliers start: 15 outliers final: 8 residues processed: 42 average time/residue: 0.4215 time to fit residues: 19.2776 Evaluate side-chains 36 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.104508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.080775 restraints weight = 37811.889| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 3.02 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8791 Z= 0.247 Angle : 0.777 10.340 12775 Z= 0.391 Chirality : 0.041 0.232 1557 Planarity : 0.005 0.054 955 Dihedral : 25.036 167.657 3465 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.79 % Allowed : 24.68 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.33), residues: 510 helix: -0.18 (0.41), residues: 147 sheet: -1.07 (0.72), residues: 52 loop : -2.97 (0.29), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 173 TYR 0.036 0.003 TYR A 276 PHE 0.017 0.002 PHE A 55 TRP 0.063 0.005 TRP A 74 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 8791) covalent geometry : angle 0.77689 (12775) hydrogen bonds : bond 0.08203 ( 290) hydrogen bonds : angle 5.02445 ( 661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.4599 (mmp) cc_final: 0.4328 (mmt) REVERT: A 282 MET cc_start: 0.6187 (tpp) cc_final: 0.5970 (tpt) outliers start: 13 outliers final: 9 residues processed: 39 average time/residue: 0.4280 time to fit residues: 18.2220 Evaluate side-chains 37 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 0.0980 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 13 optimal weight: 0.2980 chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN B 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.110374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.087508 restraints weight = 37782.951| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 3.09 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8791 Z= 0.116 Angle : 0.602 9.073 12775 Z= 0.310 Chirality : 0.035 0.221 1557 Planarity : 0.005 0.053 955 Dihedral : 24.590 170.704 3465 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.29 % Allowed : 25.75 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.35), residues: 510 helix: 0.64 (0.44), residues: 147 sheet: -0.56 (0.65), residues: 61 loop : -2.59 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 106 TYR 0.013 0.002 TYR B 216 PHE 0.034 0.002 PHE A 320 TRP 0.023 0.003 TRP A 352 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 8791) covalent geometry : angle 0.60211 (12775) hydrogen bonds : bond 0.04990 ( 290) hydrogen bonds : angle 4.01156 ( 661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2860.35 seconds wall clock time: 49 minutes 30.05 seconds (2970.05 seconds total)