Starting phenix.real_space_refine on Sat Aug 3 11:46:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enf_19833/08_2024/9enf_19833.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enf_19833/08_2024/9enf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enf_19833/08_2024/9enf_19833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enf_19833/08_2024/9enf_19833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enf_19833/08_2024/9enf_19833.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9enf_19833/08_2024/9enf_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 Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.50, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 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: 4.58 Conformation dependent library (CDL) restraints added in 894.1 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: 3.58 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: 2.64 Time building geometry restraints manager: 4.85 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: 97.61 - 104.88: 848 104.88 - 112.15: 4630 112.15 - 119.42: 2951 119.42 - 126.69: 3821 126.69 - 133.96: 525 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: 1.640 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 29.740 Find NCS groups from input model: 0.230 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:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.010 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.672 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: 0.9480 time to fit residues: 39.4666 Evaluate side-chains 27 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 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 fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 0.575 Fit side-chains REVERT: A 228 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.6230 (tmm) REVERT: B 316 MET cc_start: 0.5742 (tpt) cc_final: 0.5394 (tpt) outliers start: 12 outliers final: 3 residues processed: 37 average time/residue: 0.9889 time to fit residues: 39.8581 Evaluate side-chains 31 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 56 optimal weight: 50.0000 chunk 21 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8791 Z= 0.190 Angle : 0.632 8.537 12775 Z= 0.324 Chirality : 0.037 0.218 1557 Planarity : 0.004 0.050 955 Dihedral : 25.023 169.829 3465 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.36 % Allowed : 15.02 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.91 (0.35), residues: 510 helix: 0.86 (0.44), residues: 141 sheet: -1.07 (0.58), residues: 73 loop : -2.55 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP A 74 HIS 0.002 0.001 HIS A 162 PHE 0.017 0.001 PHE A 320 TYR 0.028 0.002 TYR A 276 ARG 0.004 0.000 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 40 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 29 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.6149 (tmm) REVERT: B 307 LYS cc_start: 0.6731 (mptt) cc_final: 0.5394 (mppt) REVERT: B 316 MET cc_start: 0.5198 (tpt) cc_final: 0.4785 (tpt) outliers start: 11 outliers final: 3 residues processed: 35 average time/residue: 0.9417 time to fit residues: 36.1896 Evaluate side-chains 31 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 40.0000 chunk 38 optimal weight: 6.9990 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 277 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.2414 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= 0.352 Angle : 0.756 9.267 12775 Z= 0.385 Chirality : 0.042 0.224 1557 Planarity : 0.005 0.053 955 Dihedral : 25.174 167.495 3465 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 4.08 % Allowed : 16.52 % Favored : 79.40 % 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: 0.26 (0.42), residues: 142 sheet: -1.19 (0.64), residues: 61 loop : -2.82 (0.30), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP A 74 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.002 PHE A 55 TYR 0.048 0.003 TYR A 276 ARG 0.008 0.001 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 47 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 28 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.6195 (tmm) REVERT: B 307 LYS cc_start: 0.6858 (mptt) cc_final: 0.5521 (mppt) REVERT: B 316 MET cc_start: 0.5915 (tpt) cc_final: 0.5574 (tpt) outliers start: 19 outliers final: 9 residues processed: 41 average time/residue: 0.8481 time to fit residues: 38.3858 Evaluate side-chains 36 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 26 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 171 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain B residue 365 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 17 optimal weight: 0.0070 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.2253 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= 0.141 Angle : 0.605 9.894 12775 Z= 0.309 Chirality : 0.036 0.227 1557 Planarity : 0.004 0.046 955 Dihedral : 24.766 171.299 3465 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.36 % Allowed : 18.45 % 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: -1.79 (0.35), residues: 510 helix: 0.89 (0.43), residues: 148 sheet: -0.62 (0.62), residues: 63 loop : -2.57 (0.31), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 74 HIS 0.002 0.001 HIS B 355 PHE 0.021 0.001 PHE A 320 TYR 0.017 0.001 TYR A 276 ARG 0.003 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 fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 316 MET cc_start: 0.4943 (tpt) cc_final: 0.4597 (tpt) outliers start: 11 outliers final: 4 residues processed: 38 average time/residue: 1.1020 time to fit residues: 45.5219 Evaluate side-chains 33 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 16 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 chunk 31 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 65 optimal weight: 50.0000 chunk 7 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8791 Z= 0.275 Angle : 0.685 7.946 12775 Z= 0.347 Chirality : 0.038 0.228 1557 Planarity : 0.005 0.050 955 Dihedral : 24.828 167.635 3465 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % 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: -2.12 (0.35), residues: 510 helix: 0.64 (0.44), residues: 142 sheet: -1.49 (0.60), residues: 68 loop : -2.56 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.005 TRP A 74 HIS 0.005 0.001 HIS A 162 PHE 0.024 0.002 PHE A 320 TYR 0.038 0.002 TYR A 276 ARG 0.006 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 45 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 31 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 316 MET cc_start: 0.5665 (tpt) cc_final: 0.5367 (tpt) outliers start: 14 outliers final: 6 residues processed: 41 average time/residue: 0.8891 time to fit residues: 40.1455 Evaluate side-chains 34 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR 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 38 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8791 Z= 0.134 Angle : 0.590 8.511 12775 Z= 0.299 Chirality : 0.034 0.220 1557 Planarity : 0.004 0.045 955 Dihedral : 24.615 170.760 3465 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.72 % Allowed : 22.75 % Favored : 75.54 % 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: -1.62 (0.36), residues: 510 helix: 0.84 (0.43), residues: 148 sheet: -0.69 (0.59), residues: 72 loop : -2.35 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 74 HIS 0.005 0.001 HIS A 355 PHE 0.031 0.001 PHE A 320 TYR 0.018 0.001 TYR B 314 ARG 0.002 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 40 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: B 316 MET cc_start: 0.4868 (tpt) cc_final: 0.4544 (tpt) outliers start: 8 outliers final: 3 residues processed: 37 average time/residue: 1.0762 time to fit residues: 43.3334 Evaluate side-chains 30 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 64 optimal weight: 30.0000 chunk 58 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8791 Z= 0.184 Angle : 0.613 8.073 12775 Z= 0.309 Chirality : 0.035 0.217 1557 Planarity : 0.004 0.046 955 Dihedral : 24.616 169.014 3465 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.29 % Allowed : 24.46 % 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: -1.67 (0.35), residues: 510 helix: 0.94 (0.44), residues: 142 sheet: -0.59 (0.63), residues: 61 loop : -2.38 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 352 HIS 0.003 0.001 HIS A 162 PHE 0.030 0.001 PHE A 320 TYR 0.024 0.002 TYR A 276 ARG 0.004 0.000 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 36 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: B 316 MET cc_start: 0.5283 (tpt) cc_final: 0.4971 (tpt) outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 1.0235 time to fit residues: 39.2741 Evaluate side-chains 30 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 40.0000 chunk 59 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8791 Z= 0.408 Angle : 0.809 10.462 12775 Z= 0.406 Chirality : 0.043 0.249 1557 Planarity : 0.005 0.050 955 Dihedral : 25.081 166.883 3465 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % 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: -2.32 (0.34), residues: 510 helix: 0.18 (0.42), residues: 141 sheet: -1.42 (0.61), residues: 68 loop : -2.56 (0.31), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 74 HIS 0.005 0.001 HIS A 220 PHE 0.031 0.003 PHE A 320 TYR 0.038 0.003 TYR A 276 ARG 0.008 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 42 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 30 time to evaluate : 0.662 Fit side-chains REVERT: B 90 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6854 (tt0) REVERT: B 293 MET cc_start: 0.3728 (OUTLIER) cc_final: 0.3139 (tmm) REVERT: B 307 LYS cc_start: 0.6980 (mptt) cc_final: 0.5922 (mppt) REVERT: B 316 MET cc_start: 0.6041 (tpt) cc_final: 0.5801 (tpt) outliers start: 12 outliers final: 7 residues processed: 40 average time/residue: 1.0039 time to fit residues: 43.8009 Evaluate side-chains 35 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 26 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 359 THR Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 293 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 20.0000 chunk 64 optimal weight: 40.0000 chunk 55 optimal weight: 30.0000 chunk 5 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8791 Z= 0.183 Angle : 0.622 7.448 12775 Z= 0.319 Chirality : 0.036 0.221 1557 Planarity : 0.004 0.047 955 Dihedral : 24.728 169.344 3465 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.15 % Allowed : 24.68 % Favored : 73.18 % 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: -2.10 (0.35), residues: 510 helix: 0.36 (0.44), residues: 148 sheet: -0.89 (0.66), residues: 60 loop : -2.57 (0.31), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 352 HIS 0.003 0.001 HIS A 162 PHE 0.032 0.001 PHE A 320 TYR 0.021 0.002 TYR A 276 ARG 0.003 0.000 ARG A 193 ********************** 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 39 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 29 time to evaluate : 0.637 Fit side-chains REVERT: A 282 MET cc_start: 0.5708 (tpp) cc_final: 0.5411 (tpt) REVERT: B 293 MET cc_start: 0.3898 (OUTLIER) cc_final: 0.3325 (tmm) REVERT: B 307 LYS cc_start: 0.6647 (mptt) cc_final: 0.5600 (mppt) REVERT: B 316 MET cc_start: 0.5709 (tpt) cc_final: 0.5414 (tpt) outliers start: 10 outliers final: 7 residues processed: 37 average time/residue: 0.9292 time to fit residues: 37.6595 Evaluate side-chains 34 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN 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 285 ILE Chi-restraints excluded: chain B residue 293 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 40 optimal weight: 0.0670 chunk 63 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.106937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.083737 restraints weight = 37411.179| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 3.08 r_work: 0.3857 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 8791 Z= 0.265 Angle : 0.965 59.200 12775 Z= 0.558 Chirality : 0.036 0.220 1557 Planarity : 0.004 0.046 955 Dihedral : 24.730 169.352 3465 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.15 % Allowed : 24.68 % Favored : 73.18 % Cbeta Deviations : 0.20 % 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: -2.05 (0.35), residues: 510 helix: 0.37 (0.44), residues: 148 sheet: -0.89 (0.66), residues: 60 loop : -2.51 (0.31), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 352 HIS 0.002 0.001 HIS A 162 PHE 0.029 0.001 PHE A 320 TYR 0.020 0.002 TYR A 276 ARG 0.003 0.000 ARG A 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1981.90 seconds wall clock time: 35 minutes 46.94 seconds (2146.94 seconds total)