Starting phenix.real_space_refine on Wed Jan 15 05:53:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9enf_19833/01_2025/9enf_19833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9enf_19833/01_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_19833/01_2025/9enf_19833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9enf_19833/01_2025/9enf_19833.map" model { file = "/net/cci-nas-00/data/ceres_data/9enf_19833/01_2025/9enf_19833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9enf_19833/01_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 5.74, per 1000 atoms: 0.70 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: 2.38 Conformation dependent library (CDL) restraints added in 568.3 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: 3.43 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: 2.55 Time building geometry restraints manager: 2.72 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: 1.520 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.530 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.520 ------------------------------------------------------------------------------- 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 : 0.618 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: 1.1010 time to fit residues: 45.4502 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 : 0.688 ------------------------------------------------------------------------------- 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: 3.9990 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: 5.3990 ------------------------------------------------------------------------------- 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 = 0.4459 r_free = 0.4459 target = 0.104862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.081386 restraints weight = 37035.368| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.98 r_work: 0.3795 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8791 Z= 0.380 Angle : 0.779 8.168 12775 Z= 0.398 Chirality : 0.042 0.221 1557 Planarity : 0.006 0.052 955 Dihedral : 25.299 167.768 3465 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.58 % Allowed : 11.16 % Favored : 86.27 % 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: -2.45 (0.34), residues: 510 helix: 0.02 (0.41), residues: 148 sheet: -1.26 (0.54), residues: 83 loop : -2.79 (0.32), residues: 279 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 0.018 0.002 PHE A 55 TYR 0.046 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 43 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.597 Fit side-chains REVERT: A 228 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6547 (tmm) REVERT: B 316 MET cc_start: 0.5850 (tpt) cc_final: 0.5500 (tpt) outliers start: 12 outliers final: 3 residues processed: 37 average time/residue: 0.9952 time to fit residues: 40.2084 Evaluate side-chains 31 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 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: 1.9990 chunk 63 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.104476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.080889 restraints weight = 37821.771| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 3.09 r_work: 0.3780 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8791 Z= 0.364 Angle : 0.771 9.223 12775 Z= 0.394 Chirality : 0.042 0.224 1557 Planarity : 0.006 0.056 955 Dihedral : 25.182 169.090 3465 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 3.22 % Allowed : 17.60 % Favored : 79.18 % 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: -2.74 (0.33), residues: 510 helix: -0.10 (0.41), residues: 142 sheet: -1.17 (0.64), residues: 61 loop : -2.99 (0.29), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP A 74 HIS 0.005 0.002 HIS A 220 PHE 0.018 0.002 PHE A 55 TYR 0.053 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 43 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.6558 (tmm) REVERT: B 293 MET cc_start: 0.3471 (tmm) cc_final: 0.2974 (tmm) REVERT: B 307 LYS cc_start: 0.6966 (mptt) cc_final: 0.5674 (mppt) REVERT: B 316 MET cc_start: 0.6037 (tpt) cc_final: 0.5814 (tpt) outliers start: 15 outliers final: 7 residues processed: 39 average time/residue: 0.9542 time to fit residues: 40.9099 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 : 0.601 ------------------------------------------------------------------------------- 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 167 VAL Chi-restraints excluded: chain B residue 171 ASP 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: 2.9990 chunk 63 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 64 optimal weight: 40.0000 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.4529 r_free = 0.4529 target = 0.108411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.085258 restraints weight = 37306.771| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 3.06 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.2229 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= 0.156 Angle : 0.604 9.253 12775 Z= 0.311 Chirality : 0.036 0.220 1557 Planarity : 0.004 0.049 955 Dihedral : 24.758 170.255 3465 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % 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: -2.02 (0.35), residues: 510 helix: 0.75 (0.43), residues: 148 sheet: -0.66 (0.61), residues: 63 loop : -2.77 (0.31), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 352 HIS 0.002 0.001 HIS B 355 PHE 0.017 0.001 PHE A 320 TYR 0.020 0.002 TYR A 276 ARG 0.004 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 43 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.6106 (tmm) REVERT: B 307 LYS cc_start: 0.6893 (mptt) cc_final: 0.5602 (mppt) REVERT: B 316 MET cc_start: 0.5350 (tpt) cc_final: 0.4935 (tpt) outliers start: 14 outliers final: 5 residues processed: 38 average time/residue: 1.0296 time to fit residues: 42.6685 Evaluate side-chains 33 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 365 MET 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: 7.9990 chunk 51 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 = 0.4485 r_free = 0.4485 target = 0.105980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.082485 restraints weight = 37072.156| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.04 r_work: 0.3830 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.2370 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= 0.253 Angle : 0.671 7.766 12775 Z= 0.341 Chirality : 0.038 0.226 1557 Planarity : 0.005 0.051 955 Dihedral : 24.814 167.826 3465 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.22 % Allowed : 20.60 % 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: -2.23 (0.34), residues: 510 helix: 0.47 (0.43), residues: 148 sheet: -1.28 (0.62), residues: 62 loop : -2.71 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP A 74 HIS 0.003 0.001 HIS A 220 PHE 0.025 0.002 PHE A 320 TYR 0.035 0.002 TYR A 276 ARG 0.006 0.000 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: 15 poor density : 28 time to evaluate : 0.631 Fit side-chains REVERT: A 228 MET cc_start: 0.6600 (OUTLIER) cc_final: 0.6384 (tmm) REVERT: B 307 LYS cc_start: 0.6923 (mptt) cc_final: 0.5621 (mppt) REVERT: B 316 MET cc_start: 0.5859 (tpt) cc_final: 0.5578 (tpt) outliers start: 15 outliers final: 5 residues processed: 37 average time/residue: 0.9499 time to fit residues: 38.6425 Evaluate side-chains 33 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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: 3.9990 chunk 49 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4467 r_free = 0.4467 target = 0.105255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.081607 restraints weight = 37682.290| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 3.03 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.2674 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= 0.301 Angle : 0.715 7.833 12775 Z= 0.363 Chirality : 0.039 0.228 1557 Planarity : 0.005 0.053 955 Dihedral : 24.951 167.790 3465 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.58 % Allowed : 23.18 % Favored : 74.25 % 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: -2.46 (0.34), residues: 510 helix: 0.21 (0.42), residues: 148 sheet: -1.18 (0.68), residues: 57 loop : -2.86 (0.30), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.005 TRP A 74 HIS 0.004 0.001 HIS A 220 PHE 0.019 0.002 PHE A 320 TYR 0.038 0.002 TYR A 276 ARG 0.007 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 41 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.655 Fit side-chains REVERT: A 228 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6241 (tmm) REVERT: B 307 LYS cc_start: 0.7046 (mptt) cc_final: 0.5794 (mppt) REVERT: B 316 MET cc_start: 0.5998 (tpt) cc_final: 0.5705 (tpt) outliers start: 12 outliers final: 6 residues processed: 38 average time/residue: 1.0213 time to fit residues: 42.3464 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 : 0.629 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 15 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 = 0.4495 r_free = 0.4495 target = 0.106516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.083106 restraints weight = 37656.097| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 3.03 r_work: 0.3842 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.2654 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= 0.218 Angle : 0.648 7.652 12775 Z= 0.331 Chirality : 0.037 0.224 1557 Planarity : 0.005 0.051 955 Dihedral : 24.851 168.506 3465 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.86 % Allowed : 22.53 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.15 (0.35), residues: 510 helix: 0.48 (0.43), residues: 148 sheet: -0.84 (0.67), residues: 56 loop : -2.70 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.005 TRP A 74 HIS 0.002 0.001 HIS A 220 PHE 0.024 0.002 PHE A 320 TYR 0.025 0.002 TYR A 276 ARG 0.005 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 49 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 31 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.6423 (tmm) REVERT: B 307 LYS cc_start: 0.7042 (mptt) cc_final: 0.6083 (mppt) REVERT: B 316 MET cc_start: 0.5796 (tpt) cc_final: 0.5497 (tpt) outliers start: 18 outliers final: 10 residues processed: 44 average time/residue: 0.9391 time to fit residues: 45.1287 Evaluate side-chains 39 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 234 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: 0.8980 chunk 36 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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 ** 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 = 0.4439 r_free = 0.4439 target = 0.103753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.079948 restraints weight = 38217.067| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.05 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8791 Z= 0.398 Angle : 0.806 9.143 12775 Z= 0.406 Chirality : 0.043 0.234 1557 Planarity : 0.006 0.055 955 Dihedral : 25.088 167.571 3465 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 4.51 % Allowed : 23.18 % 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: -2.80 (0.33), residues: 510 helix: -0.19 (0.41), residues: 148 sheet: -1.31 (0.68), residues: 59 loop : -3.02 (0.29), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.007 TRP A 74 HIS 0.005 0.001 HIS A 220 PHE 0.027 0.002 PHE A 320 TYR 0.022 0.002 TYR B 195 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 49 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 28 time to evaluate : 0.622 Fit side-chains REVERT: A 228 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.6395 (tmm) REVERT: B 307 LYS cc_start: 0.7112 (mptt) cc_final: 0.6168 (mppt) outliers start: 21 outliers final: 11 residues processed: 43 average time/residue: 0.8142 time to fit residues: 38.7261 Evaluate side-chains 40 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 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 234 VAL Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 357 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4457 r_free = 0.4457 target = 0.104706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.081329 restraints weight = 38670.306| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.08 r_work: 0.3785 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 8791 Z= 0.314 Angle : 0.741 9.682 12775 Z= 0.374 Chirality : 0.040 0.228 1557 Planarity : 0.005 0.054 955 Dihedral : 24.991 168.241 3465 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 3.22 % Allowed : 24.68 % 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: -2.66 (0.34), residues: 510 helix: 0.01 (0.42), residues: 147 sheet: -1.14 (0.68), residues: 58 loop : -3.00 (0.30), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP A 74 HIS 0.004 0.001 HIS A 220 PHE 0.031 0.002 PHE A 320 TYR 0.019 0.002 TYR B 195 ARG 0.007 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 45 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.616 Fit side-chains REVERT: A 209 MET cc_start: 0.5043 (mmp) cc_final: 0.4643 (mmt) REVERT: B 307 LYS cc_start: 0.7067 (mptt) cc_final: 0.5890 (mppt) REVERT: B 361 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.6187 (ptm) outliers start: 15 outliers final: 11 residues processed: 41 average time/residue: 0.8948 time to fit residues: 40.4371 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 : 0.660 ------------------------------------------------------------------------------- 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 167 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 361 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 0.0770 chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 40.0000 chunk 17 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- 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 = 0.4534 r_free = 0.4534 target = 0.108712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.085714 restraints weight = 37713.462| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.08 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8791 Z= 0.161 Angle : 0.622 9.392 12775 Z= 0.315 Chirality : 0.035 0.220 1557 Planarity : 0.004 0.049 955 Dihedral : 24.694 169.877 3465 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.93 % Allowed : 25.97 % 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: -1.96 (0.35), residues: 510 helix: 0.59 (0.44), residues: 147 sheet: -0.45 (0.67), residues: 59 loop : -2.62 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 352 HIS 0.004 0.001 HIS B 360 PHE 0.031 0.001 PHE A 320 TYR 0.014 0.002 TYR B 314 ARG 0.002 0.000 ARG A 173 ********************** 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 41 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.770 Fit side-chains REVERT: A 209 MET cc_start: 0.3985 (mmp) cc_final: 0.3733 (mmt) REVERT: B 293 MET cc_start: 0.3598 (tmm) cc_final: 0.2427 (tmt) REVERT: B 307 LYS cc_start: 0.6879 (mptt) cc_final: 0.5872 (mppt) outliers start: 9 outliers final: 6 residues processed: 40 average time/residue: 1.0231 time to fit residues: 44.5740 Evaluate side-chains 31 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 347 HIS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 357 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: 0.3980 chunk 27 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 56 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.4503 r_free = 0.4503 target = 0.106793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.083630 restraints weight = 38494.335| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 3.13 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8791 Z= 0.207 Angle : 0.652 9.445 12775 Z= 0.330 Chirality : 0.036 0.229 1557 Planarity : 0.005 0.051 955 Dihedral : 24.717 167.963 3465 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.50 % Allowed : 26.61 % 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: -2.10 (0.35), residues: 510 helix: 0.44 (0.44), residues: 147 sheet: -0.94 (0.61), residues: 68 loop : -2.62 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 352 HIS 0.002 0.001 HIS A 277 PHE 0.032 0.001 PHE A 320 TYR 0.018 0.002 TYR B 216 ARG 0.004 0.000 ARG B 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5216.23 seconds wall clock time: 93 minutes 3.27 seconds (5583.27 seconds total)