Starting phenix.real_space_refine on Wed Mar 12 15:41:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9enf_19833/03_2025/9enf_19833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9enf_19833/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9enf_19833/03_2025/9enf_19833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9enf_19833/03_2025/9enf_19833.map" model { file = "/net/cci-nas-00/data/ceres_data/9enf_19833/03_2025/9enf_19833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9enf_19833/03_2025/9enf_19833.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.86, per 1000 atoms: 0.71 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: 2.28 Conformation dependent library (CDL) restraints added in 491.4 milliseconds 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: 3.49 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: 3.13 Time building geometry restraints manager: 2.51 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: 1.320 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: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 25.610 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:15.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.450 ------------------------------------------------------------------------------- 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= 0.185 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 : 15.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.059 0.004 TRP A 74 HIS 0.003 0.001 HIS A 64 PHE 0.009 0.001 PHE B 184 TYR 0.020 0.002 TYR A 276 ARG 0.002 0.000 ARG B 280 *********************** 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 : 0.586 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: 0.9904 time to fit residues: 41.1057 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 : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 A 367 GLN B 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.105400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.082002 restraints weight = 37234.114| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 3.05 r_work: 0.3809 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8791 Z= 0.355 Angle : 0.751 7.574 12775 Z= 0.384 Chirality : 0.041 0.217 1557 Planarity : 0.005 0.051 955 Dihedral : 25.251 168.112 3465 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.15 % Allowed : 11.37 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.34), residues: 510 helix: 0.13 (0.41), residues: 148 sheet: -1.31 (0.53), residues: 86 loop : -2.70 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.005 TRP A 74 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.002 PHE A 55 TYR 0.041 0.003 TYR A 276 ARG 0.006 0.001 ARG A 173 *********************** 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 40 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.581 Fit side-chains REVERT: A 228 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.6512 (tmm) REVERT: B 316 MET cc_start: 0.5877 (tpt) cc_final: 0.5530 (tpt) outliers start: 10 outliers final: 4 residues processed: 34 average time/residue: 0.9731 time to fit residues: 36.1044 Evaluate side-chains 32 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 347 HIS 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 57 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 chunk 50 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.104465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.080806 restraints weight = 37851.564| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 3.01 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8791 Z= 0.367 Angle : 0.772 8.981 12775 Z= 0.395 Chirality : 0.042 0.223 1557 Planarity : 0.006 0.056 955 Dihedral : 25.212 168.984 3465 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 3.65 % Allowed : 16.31 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.33), residues: 510 helix: -0.35 (0.40), residues: 148 sheet: -1.39 (0.59), residues: 68 loop : -2.89 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.005 TRP A 74 HIS 0.005 0.001 HIS A 220 PHE 0.019 0.002 PHE A 55 TYR 0.055 0.003 TYR A 276 ARG 0.010 0.001 ARG A 173 *********************** 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 45 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 28 time to evaluate : 0.861 Fit side-chains REVERT: A 228 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.6277 (tmm) REVERT: B 293 MET cc_start: 0.3440 (tmm) cc_final: 0.2995 (tmm) REVERT: B 307 LYS cc_start: 0.7026 (mptt) cc_final: 0.5755 (mppt) REVERT: B 316 MET cc_start: 0.6019 (tpt) cc_final: 0.5786 (tpt) outliers start: 17 outliers final: 8 residues processed: 41 average time/residue: 1.0167 time to fit residues: 46.3635 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 : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU 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 355 HIS Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 31 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.108534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.085296 restraints weight = 37326.082| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.12 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8791 Z= 0.153 Angle : 0.611 9.889 12775 Z= 0.314 Chirality : 0.036 0.225 1557 Planarity : 0.004 0.049 955 Dihedral : 24.819 170.243 3465 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.00 % Allowed : 18.67 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.35), residues: 510 helix: 0.70 (0.43), residues: 148 sheet: -0.73 (0.61), residues: 63 loop : -2.78 (0.31), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP A 74 HIS 0.002 0.001 HIS B 112 PHE 0.012 0.001 PHE B 184 TYR 0.021 0.002 TYR A 276 ARG 0.003 0.000 ARG A 173 *********************** 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 45 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.6118 (tmm) REVERT: B 293 MET cc_start: 0.3973 (tmm) cc_final: 0.3418 (tmm) REVERT: B 307 LYS cc_start: 0.6857 (mptt) cc_final: 0.5595 (mppt) REVERT: B 316 MET cc_start: 0.5351 (tpt) cc_final: 0.4916 (tpt) outliers start: 14 outliers final: 3 residues processed: 40 average time/residue: 1.0191 time to fit residues: 44.2867 Evaluate side-chains 34 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 chunk 46 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 3 optimal weight: 0.4980 chunk 49 optimal weight: 9.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.105480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.081867 restraints weight = 37217.512| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 3.03 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8791 Z= 0.294 Angle : 0.702 8.300 12775 Z= 0.358 Chirality : 0.039 0.227 1557 Planarity : 0.005 0.052 955 Dihedral : 24.879 167.668 3465 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.00 % Allowed : 20.82 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.34), residues: 510 helix: 0.33 (0.43), residues: 148 sheet: -1.31 (0.62), residues: 62 loop : -2.81 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.005 TRP A 74 HIS 0.004 0.001 HIS A 220 PHE 0.013 0.002 PHE A 55 TYR 0.039 0.002 TYR A 276 ARG 0.006 0.001 ARG A 173 *********************** 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 43 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.6164 (tmm) REVERT: B 307 LYS cc_start: 0.6999 (mptt) cc_final: 0.5709 (mppt) REVERT: B 316 MET cc_start: 0.5962 (tpt) cc_final: 0.5654 (tpt) outliers start: 14 outliers final: 5 residues processed: 38 average time/residue: 0.9448 time to fit residues: 39.5073 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 : 0.636 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 63 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.104826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.081213 restraints weight = 37747.071| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 3.02 r_work: 0.3786 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8791 Z= 0.328 Angle : 0.737 7.900 12775 Z= 0.376 Chirality : 0.040 0.229 1557 Planarity : 0.005 0.054 955 Dihedral : 25.035 168.017 3465 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.83 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.33), residues: 510 helix: -0.06 (0.42), residues: 148 sheet: -0.53 (0.78), residues: 47 loop : -3.02 (0.28), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.006 TRP A 74 HIS 0.004 0.001 HIS A 220 PHE 0.016 0.002 PHE A 55 TYR 0.040 0.003 TYR A 276 ARG 0.008 0.001 ARG A 173 *********************** 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 49 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 30 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 209 MET cc_start: 0.5248 (mmp) cc_final: 0.5017 (mmt) REVERT: A 228 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6486 (tmm) REVERT: B 316 MET cc_start: 0.5925 (tpt) cc_final: 0.5648 (tpt) outliers start: 19 outliers final: 8 residues processed: 43 average time/residue: 0.9379 time to fit residues: 43.9350 Evaluate side-chains 35 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR 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 167 VAL Chi-restraints excluded: chain B residue 347 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 55 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.105865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.082494 restraints weight = 37806.620| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.04 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8791 Z= 0.223 Angle : 0.651 7.336 12775 Z= 0.334 Chirality : 0.037 0.224 1557 Planarity : 0.005 0.052 955 Dihedral : 24.856 168.503 3465 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.58 % Allowed : 24.03 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.35), residues: 510 helix: 0.41 (0.43), residues: 148 sheet: -0.75 (0.68), residues: 56 loop : -2.75 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 352 HIS 0.003 0.001 HIS A 360 PHE 0.014 0.001 PHE B 184 TYR 0.025 0.002 TYR A 276 ARG 0.004 0.000 ARG A 173 *********************** 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 41 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.600 Fit side-chains REVERT: A 228 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.6205 (tmm) REVERT: B 307 LYS cc_start: 0.7054 (mptt) cc_final: 0.6120 (mppt) REVERT: B 316 MET cc_start: 0.5996 (tpt) cc_final: 0.5676 (tpt) outliers start: 12 outliers final: 6 residues processed: 37 average time/residue: 1.0119 time to fit residues: 40.8626 Evaluate side-chains 33 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 228 MET Chi-restraints excluded: chain A residue 347 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 overall best weight: 5.1992 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.103691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.080010 restraints weight = 38204.646| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 3.03 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8791 Z= 0.370 Angle : 0.773 8.844 12775 Z= 0.391 Chirality : 0.041 0.232 1557 Planarity : 0.006 0.055 955 Dihedral : 25.023 167.471 3465 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 3.86 % Allowed : 23.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.34), residues: 510 helix: -0.03 (0.42), residues: 148 sheet: -1.48 (0.64), residues: 64 loop : -2.93 (0.30), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP A 352 HIS 0.004 0.001 HIS A 220 PHE 0.024 0.002 PHE A 320 TYR 0.043 0.003 TYR A 276 ARG 0.008 0.001 ARG A 173 *********************** 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 47 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 29 time to evaluate : 0.627 Fit side-chains REVERT: A 209 MET cc_start: 0.4788 (mmp) cc_final: 0.4515 (mmt) REVERT: B 206 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7455 (pp) REVERT: B 307 LYS cc_start: 0.7139 (mptt) cc_final: 0.6231 (mppt) REVERT: B 316 MET cc_start: 0.6235 (tpt) cc_final: 0.6016 (tpt) outliers start: 18 outliers final: 11 residues processed: 41 average time/residue: 0.8495 time to fit residues: 38.4263 Evaluate side-chains 38 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 88 THR 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 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 234 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 41 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.105637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.082280 restraints weight = 38654.877| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 3.07 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.3090 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= 0.242 Angle : 0.678 8.297 12775 Z= 0.345 Chirality : 0.037 0.225 1557 Planarity : 0.005 0.053 955 Dihedral : 24.844 168.352 3465 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.79 % Allowed : 24.89 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.35), residues: 510 helix: 0.36 (0.43), residues: 147 sheet: -0.97 (0.67), residues: 58 loop : -2.68 (0.31), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 352 HIS 0.003 0.001 HIS A 360 PHE 0.028 0.002 PHE A 320 TYR 0.033 0.002 TYR A 276 ARG 0.005 0.001 ARG A 173 *********************** 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 41 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.571 Fit side-chains REVERT: B 206 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7571 (pp) REVERT: B 307 LYS cc_start: 0.7028 (mptt) cc_final: 0.6081 (mppt) REVERT: B 316 MET cc_start: 0.5960 (tpt) cc_final: 0.5662 (tpt) outliers start: 13 outliers final: 7 residues processed: 37 average time/residue: 0.8873 time to fit residues: 36.2640 Evaluate side-chains 34 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 362 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 206 ILE 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 5 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 40.0000 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 0.0030 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.109801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.087072 restraints weight = 37770.091| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 3.09 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8791 Z= 0.142 Angle : 0.590 8.548 12775 Z= 0.300 Chirality : 0.034 0.220 1557 Planarity : 0.004 0.049 955 Dihedral : 24.559 169.785 3465 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.29 % Allowed : 26.61 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.36), residues: 510 helix: 0.72 (0.44), residues: 147 sheet: -1.02 (0.55), residues: 79 loop : -2.37 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 352 HIS 0.003 0.001 HIS B 360 PHE 0.030 0.001 PHE A 320 TYR 0.013 0.002 TYR A 276 ARG 0.002 0.000 ARG B 106 ********************** 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 36 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.594 Fit side-chains REVERT: A 209 MET cc_start: 0.4081 (mmp) cc_final: 0.3782 (mmt) REVERT: B 293 MET cc_start: 0.3743 (tmm) cc_final: 0.2370 (tmt) REVERT: B 307 LYS cc_start: 0.6894 (mptt) cc_final: 0.5899 (mppt) REVERT: B 316 MET cc_start: 0.5632 (tpt) cc_final: 0.5417 (tpp) outliers start: 6 outliers final: 3 residues processed: 35 average time/residue: 1.0908 time to fit residues: 41.4303 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 : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 chunk 11 optimal weight: 0.0030 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- 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 = 0.4534 r_free = 0.4534 target = 0.108545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.085517 restraints weight = 38462.430| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 3.12 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8791 Z= 0.157 Angle : 0.593 12.404 12775 Z= 0.301 Chirality : 0.034 0.222 1557 Planarity : 0.004 0.050 955 Dihedral : 24.543 169.281 3465 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.29 % Allowed : 26.82 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.36), residues: 510 helix: 0.74 (0.44), residues: 147 sheet: -0.60 (0.58), residues: 72 loop : -2.45 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 352 HIS 0.002 0.001 HIS B 277 PHE 0.030 0.001 PHE A 320 TYR 0.024 0.002 TYR A 276 ARG 0.004 0.000 ARG A 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5330.27 seconds wall clock time: 93 minutes 14.50 seconds (5594.50 seconds total)