Starting phenix.real_space_refine on Thu Jul 2 09:41:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oz3_13119/07_2026/7oz3_13119.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oz3_13119/07_2026/7oz3_13119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oz3_13119/07_2026/7oz3_13119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oz3_13119/07_2026/7oz3_13119.map" model { file = "/net/cci-nas-00/data/ceres_data/7oz3_13119/07_2026/7oz3_13119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oz3_13119/07_2026/7oz3_13119.cif" } resolution = 4.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 92 5.49 5 S 8 5.16 5 C 4932 2.51 5 N 1411 2.21 5 O 1766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8209 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1584 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "B" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "C" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1580 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "D" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1558 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain: "F" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 900 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "G" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 904 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'2BA': 1} Classifications: {'RNA_mixed': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'2BA': 1} Classifications: {'RNA_mixed': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ARG C 210 " occ=0.75 ... (9 atoms not shown) pdb=" NH2 ARG C 210 " occ=0.75 Time building chain proxies: 1.88, per 1000 atoms: 0.23 Number of scatterers: 8209 At special positions: 0 Unit cell: (77.404, 93.094, 161.084, 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 8 16.00 P 92 15.00 O 1766 8.00 N 1411 7.00 C 4932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 277.4 milliseconds 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 9 sheets defined 58.5% alpha, 9.7% beta 44 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 11 through 27 Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 48 through 62 removed outlier: 3.528A pdb=" N LEU A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 128 Processing helix chain 'A' and resid 129 through 132 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 157 through 163 Processing helix chain 'A' and resid 196 through 207 Processing helix chain 'B' and resid 11 through 27 Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 48 through 62 removed outlier: 4.067A pdb=" N LEU B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 128 removed outlier: 3.603A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 157 through 163 Processing helix chain 'B' and resid 196 through 207 Processing helix chain 'C' and resid 11 through 27 removed outlier: 4.157A pdb=" N ILE C 16 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA C 17 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 46 Processing helix chain 'C' and resid 48 through 62 Processing helix chain 'C' and resid 77 through 92 removed outlier: 4.144A pdb=" N ALA C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 127 removed outlier: 3.712A pdb=" N ARG C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 157 Processing helix chain 'C' and resid 157 through 163 Processing helix chain 'C' and resid 196 through 208 Processing helix chain 'D' and resid 14 through 26 Processing helix chain 'D' and resid 37 through 45 Processing helix chain 'D' and resid 48 through 62 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 94 through 126 Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 153 through 157 Processing helix chain 'D' and resid 157 through 163 Processing helix chain 'D' and resid 196 through 207 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 3.637A pdb=" N GLY A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 141 removed outlier: 3.500A pdb=" N PHE A 193 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 194 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE A 166 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 169 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 35 Processing sheet with id=AA4, first strand: chain 'B' and resid 140 through 141 removed outlier: 6.586A pdb=" N VAL B 194 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE B 166 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 169 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.610A pdb=" N ILE C 74 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 138 through 141 removed outlier: 3.656A pdb=" N HIS C 190 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C 194 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE C 166 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 151 through 152 removed outlier: 4.587A pdb=" N LYS C 151 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 138 through 141 removed outlier: 6.462A pdb=" N VAL D 194 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE D 166 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS D 171 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 151 through 152 removed outlier: 4.588A pdb=" N LYS D 151 " --> pdb=" O ILE D 185 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1578 1.33 - 1.45: 2406 1.45 - 1.57: 4362 1.57 - 1.69: 185 1.69 - 1.81: 16 Bond restraints: 8547 Sorted by residual: bond pdb=" C1' 2BA A 301 " pdb=" C2' 2BA A 301 " ideal model delta sigma weight residual 1.541 1.347 0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" C1' 2BA B 301 " pdb=" C2' 2BA B 301 " ideal model delta sigma weight residual 1.541 1.347 0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb="C1'1 2BA A 301 " pdb="C2'1 2BA A 301 " ideal model delta sigma weight residual 1.532 1.349 0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb="C1'1 2BA B 301 " pdb="C2'1 2BA B 301 " ideal model delta sigma weight residual 1.532 1.349 0.183 2.00e-02 2.50e+03 8.38e+01 bond pdb="C1'1 2BA B 301 " pdb="O4'1 2BA B 301 " ideal model delta sigma weight residual 1.408 1.573 -0.165 2.00e-02 2.50e+03 6.84e+01 ... (remaining 8542 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 11274 2.69 - 5.38: 641 5.38 - 8.08: 38 8.08 - 10.77: 1 10.77 - 13.46: 1 Bond angle restraints: 11955 Sorted by residual: angle pdb=" N SER C 143 " pdb=" CA SER C 143 " pdb=" C SER C 143 " ideal model delta sigma weight residual 111.69 103.91 7.78 1.23e+00 6.61e-01 4.00e+01 angle pdb=" N GLU D 147 " pdb=" CA GLU D 147 " pdb=" C GLU D 147 " ideal model delta sigma weight residual 112.54 105.73 6.81 1.22e+00 6.72e-01 3.11e+01 angle pdb=" N GLU C 147 " pdb=" CA GLU C 147 " pdb=" C GLU C 147 " ideal model delta sigma weight residual 112.54 105.75 6.79 1.22e+00 6.72e-01 3.09e+01 angle pdb=" N ILE B 41 " pdb=" CA ILE B 41 " pdb=" C ILE B 41 " ideal model delta sigma weight residual 111.44 104.21 7.23 1.34e+00 5.57e-01 2.91e+01 angle pdb=" O3' DA F 22 " pdb=" C3' DA F 22 " pdb=" C2' DA F 22 " ideal model delta sigma weight residual 109.40 122.86 -13.46 2.50e+00 1.60e-01 2.90e+01 ... (remaining 11950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.97: 3890 19.97 - 39.94: 707 39.94 - 59.91: 384 59.91 - 79.88: 8 79.88 - 99.85: 4 Dihedral angle restraints: 4993 sinusoidal: 2661 harmonic: 2332 Sorted by residual: dihedral pdb=" C PHE A 207 " pdb=" N PHE A 207 " pdb=" CA PHE A 207 " pdb=" CB PHE A 207 " ideal model delta harmonic sigma weight residual -122.60 -133.85 11.25 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" C PHE B 207 " pdb=" N PHE B 207 " pdb=" CA PHE B 207 " pdb=" CB PHE B 207 " ideal model delta harmonic sigma weight residual -122.60 -133.83 11.23 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" CA ASN A 157 " pdb=" C ASN A 157 " pdb=" N VAL A 158 " pdb=" CA VAL A 158 " ideal model delta harmonic sigma weight residual 180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 4990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1079 0.082 - 0.165: 218 0.165 - 0.247: 60 0.247 - 0.329: 8 0.329 - 0.411: 6 Chirality restraints: 1371 Sorted by residual: chirality pdb=" C2' 2BA A 301 " pdb=" C1' 2BA A 301 " pdb=" C3' 2BA A 301 " pdb=" O2' 2BA A 301 " both_signs ideal model delta sigma weight residual False -2.80 -2.39 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C2' 2BA B 301 " pdb=" C1' 2BA B 301 " pdb=" C3' 2BA B 301 " pdb=" O2' 2BA B 301 " both_signs ideal model delta sigma weight residual False -2.80 -2.40 -0.41 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA PHE A 207 " pdb=" N PHE A 207 " pdb=" C PHE A 207 " pdb=" CB PHE A 207 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 1368 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 64 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ILE B 64 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE B 64 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 65 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 70 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.91e+00 pdb=" C GLY A 70 " -0.052 2.00e-02 2.50e+03 pdb=" O GLY A 70 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 71 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT F 19 " 0.001 2.00e-02 2.50e+03 1.84e-02 8.49e+00 pdb=" N1 DT F 19 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DT F 19 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT F 19 " -0.030 2.00e-02 2.50e+03 pdb=" N3 DT F 19 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DT F 19 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT F 19 " 0.015 2.00e-02 2.50e+03 pdb=" C5 DT F 19 " 0.006 2.00e-02 2.50e+03 pdb=" C7 DT F 19 " -0.037 2.00e-02 2.50e+03 pdb=" C6 DT F 19 " 0.016 2.00e-02 2.50e+03 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 2675 2.85 - 3.36: 7752 3.36 - 3.87: 14924 3.87 - 4.39: 16813 4.39 - 4.90: 25946 Nonbonded interactions: 68110 Sorted by model distance: nonbonded pdb=" NZ LYS A 98 " pdb=" OD1 ASP B 120 " model vdw 2.334 3.120 nonbonded pdb=" OD1 ASP B 28 " pdb=" N TYR B 29 " model vdw 2.334 3.120 nonbonded pdb=" O ALA D 107 " pdb=" OE1 GLU D 111 " model vdw 2.381 3.040 nonbonded pdb=" O LEU A 85 " pdb=" OE1 GLU A 89 " model vdw 2.407 3.040 nonbonded pdb=" O LEU C 123 " pdb=" OG1 THR C 126 " model vdw 2.432 3.040 ... (remaining 68105 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 13 through 209) selection = (chain 'B' and resid 13 through 209) selection = (chain 'C' and resid 13 through 209) selection = (chain 'D' and resid 13 through 209) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.980 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 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 : 0.011 0.194 8547 Z= 0.719 Angle : 1.270 13.460 11955 Z= 0.915 Chirality : 0.076 0.411 1371 Planarity : 0.005 0.038 1203 Dihedral : 23.029 99.849 3489 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.29 % Allowed : 3.80 % Favored : 95.91 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.30), residues: 796 helix: 1.86 (0.24), residues: 431 sheet: -1.60 (0.54), residues: 72 loop : -1.23 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 127 TYR 0.025 0.002 TYR A 206 PHE 0.019 0.002 PHE A 122 TRP 0.025 0.005 TRP B 159 HIS 0.004 0.001 HIS C 148 Details of bonding type rmsd/Z covalent geometry : bond 0.01111 / 0.72 ( 8547) covalent geometry : angle 1.27012 / 0.91 (11955) hydrogen bonds : bond 0.14259 / 10.11 ( 486) hydrogen bonds : angle 5.61186 / 4.06 ( 1310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8328 (tp30) cc_final: 0.7812 (tp30) REVERT: A 189 ASP cc_start: 0.8403 (m-30) cc_final: 0.7807 (m-30) REVERT: A 207 PHE cc_start: 0.8466 (m-80) cc_final: 0.7295 (m-10) REVERT: B 110 GLN cc_start: 0.8990 (mt0) cc_final: 0.8499 (mp10) REVERT: B 121 ASP cc_start: 0.9039 (t70) cc_final: 0.8564 (t70) REVERT: B 133 TYR cc_start: 0.8333 (p90) cc_final: 0.7765 (p90) REVERT: B 189 ASP cc_start: 0.7421 (m-30) cc_final: 0.7169 (m-30) REVERT: B 191 ILE cc_start: 0.9263 (mt) cc_final: 0.8887 (mt) REVERT: C 190 HIS cc_start: 0.8223 (m-70) cc_final: 0.7519 (m170) REVERT: D 26 ASN cc_start: 0.9393 (t0) cc_final: 0.8860 (t0) REVERT: D 28 ASP cc_start: 0.8251 (m-30) cc_final: 0.7361 (m-30) REVERT: D 142 VAL cc_start: 0.8832 (m) cc_final: 0.8517 (p) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.0922 time to fit residues: 22.6559 Evaluate side-chains 87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 GLN B 161 GLN B 171 HIS C 26 ASN C 57 ASN C 69 HIS C 92 HIS C 208 ASN D 92 HIS D 171 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.065418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.052863 restraints weight = 35945.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.054483 restraints weight = 19800.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.055640 restraints weight = 13007.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.056439 restraints weight = 9524.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.057034 restraints weight = 7568.679| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8547 Z= 0.153 Angle : 0.744 6.836 11955 Z= 0.416 Chirality : 0.054 0.267 1371 Planarity : 0.004 0.043 1203 Dihedral : 25.571 93.235 1969 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.29 % Allowed : 5.70 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.30), residues: 796 helix: 2.07 (0.24), residues: 437 sheet: -1.03 (0.58), residues: 68 loop : -1.21 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 38 TYR 0.019 0.002 TYR D 200 PHE 0.022 0.002 PHE A 192 TRP 0.017 0.003 TRP C 159 HIS 0.025 0.002 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 8547) covalent geometry : angle 0.74374 / 0.42 (11955) hydrogen bonds : bond 0.04563 / 3.17 ( 486) hydrogen bonds : angle 4.51084 / 3.17 ( 1310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.9186 (tpt) cc_final: 0.8821 (tpp) REVERT: A 207 PHE cc_start: 0.8642 (m-80) cc_final: 0.7831 (m-10) REVERT: B 110 GLN cc_start: 0.8980 (mt0) cc_final: 0.8484 (mp10) REVERT: B 121 ASP cc_start: 0.9124 (t70) cc_final: 0.8580 (t70) REVERT: B 133 TYR cc_start: 0.8132 (p90) cc_final: 0.7888 (p90) REVERT: C 57 ASN cc_start: 0.8928 (m110) cc_final: 0.8624 (m110) REVERT: C 190 HIS cc_start: 0.7911 (m-70) cc_final: 0.7389 (m170) REVERT: C 192 PHE cc_start: 0.8996 (m-80) cc_final: 0.8726 (m-80) REVERT: D 26 ASN cc_start: 0.9437 (t0) cc_final: 0.9178 (t0) REVERT: D 28 ASP cc_start: 0.8351 (m-30) cc_final: 0.7990 (m-30) REVERT: D 142 VAL cc_start: 0.8923 (m) cc_final: 0.8613 (p) REVERT: D 157 ASN cc_start: 0.8593 (t0) cc_final: 0.7763 (t0) outliers start: 2 outliers final: 1 residues processed: 128 average time/residue: 0.0768 time to fit residues: 14.0201 Evaluate side-chains 76 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 45 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 chunk 37 optimal weight: 4.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 HIS C 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.064775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.052136 restraints weight = 35583.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.053756 restraints weight = 19943.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.054861 restraints weight = 13152.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.055671 restraints weight = 9698.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.056269 restraints weight = 7703.900| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8547 Z= 0.143 Angle : 0.643 6.904 11955 Z= 0.370 Chirality : 0.047 0.179 1371 Planarity : 0.004 0.050 1203 Dihedral : 25.196 83.690 1969 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.15 % Allowed : 4.24 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.30), residues: 796 helix: 2.17 (0.24), residues: 432 sheet: -1.24 (0.56), residues: 70 loop : -1.04 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 202 TYR 0.025 0.002 TYR C 206 PHE 0.017 0.002 PHE A 207 TRP 0.012 0.002 TRP C 159 HIS 0.010 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 8547) covalent geometry : angle 0.64293 / 0.37 (11955) hydrogen bonds : bond 0.04067 / 2.80 ( 486) hydrogen bonds : angle 4.33775 / 3.09 ( 1310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8531 (t80) cc_final: 0.8330 (t80) REVERT: A 207 PHE cc_start: 0.8592 (m-80) cc_final: 0.8141 (m-10) REVERT: B 79 GLU cc_start: 0.8456 (mp0) cc_final: 0.7826 (pm20) REVERT: B 121 ASP cc_start: 0.9151 (t70) cc_final: 0.8452 (t0) REVERT: B 133 TYR cc_start: 0.8357 (p90) cc_final: 0.7894 (p90) REVERT: B 189 ASP cc_start: 0.7329 (m-30) cc_final: 0.7081 (m-30) REVERT: C 57 ASN cc_start: 0.8857 (m110) cc_final: 0.8558 (m110) REVERT: C 190 HIS cc_start: 0.7801 (m-70) cc_final: 0.7342 (m170) REVERT: D 26 ASN cc_start: 0.9409 (t0) cc_final: 0.9110 (t0) REVERT: D 28 ASP cc_start: 0.8363 (m-30) cc_final: 0.7893 (m-30) outliers start: 1 outliers final: 1 residues processed: 110 average time/residue: 0.0753 time to fit residues: 11.7774 Evaluate side-chains 76 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 56 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 12 optimal weight: 0.0170 chunk 86 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.064260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.051614 restraints weight = 36501.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.053199 restraints weight = 20450.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.054320 restraints weight = 13594.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.055050 restraints weight = 10030.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.055684 restraints weight = 8077.884| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8547 Z= 0.135 Angle : 0.609 6.241 11955 Z= 0.351 Chirality : 0.045 0.151 1371 Planarity : 0.003 0.035 1203 Dihedral : 25.067 74.395 1969 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.30), residues: 796 helix: 2.13 (0.24), residues: 434 sheet: -0.99 (0.59), residues: 68 loop : -1.04 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 23 TYR 0.013 0.001 TYR D 200 PHE 0.019 0.002 PHE A 122 TRP 0.012 0.002 TRP C 159 HIS 0.014 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 8547) covalent geometry : angle 0.60947 / 0.35 (11955) hydrogen bonds : bond 0.03899 / 2.68 ( 486) hydrogen bonds : angle 4.28665 / 3.04 ( 1310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.9100 (tpt) cc_final: 0.8503 (tpp) REVERT: A 207 PHE cc_start: 0.8449 (m-80) cc_final: 0.8130 (m-10) REVERT: B 79 GLU cc_start: 0.8411 (mp0) cc_final: 0.7803 (pm20) REVERT: B 121 ASP cc_start: 0.9200 (t70) cc_final: 0.8366 (t70) REVERT: B 133 TYR cc_start: 0.8210 (p90) cc_final: 0.7849 (p90) REVERT: B 189 ASP cc_start: 0.7180 (m-30) cc_final: 0.6974 (m-30) REVERT: C 57 ASN cc_start: 0.8847 (m110) cc_final: 0.8540 (m110) REVERT: C 190 HIS cc_start: 0.7726 (m-70) cc_final: 0.7423 (m170) REVERT: C 193 PHE cc_start: 0.8729 (p90) cc_final: 0.8053 (p90) REVERT: D 26 ASN cc_start: 0.9379 (t0) cc_final: 0.8666 (t0) REVERT: D 28 ASP cc_start: 0.8286 (m-30) cc_final: 0.7105 (m-30) REVERT: D 80 LYS cc_start: 0.9344 (mmtp) cc_final: 0.9066 (mttp) REVERT: D 158 VAL cc_start: 0.9039 (t) cc_final: 0.8808 (t) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0626 time to fit residues: 9.9888 Evaluate side-chains 81 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 2 optimal weight: 0.0070 chunk 53 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN C 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.063662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.051362 restraints weight = 36163.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.052811 restraints weight = 21079.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.053858 restraints weight = 14255.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.054584 restraints weight = 10709.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.055066 restraints weight = 8652.055| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8547 Z= 0.129 Angle : 0.572 6.471 11955 Z= 0.334 Chirality : 0.043 0.153 1371 Planarity : 0.003 0.036 1203 Dihedral : 24.897 68.180 1969 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.30), residues: 796 helix: 2.21 (0.24), residues: 434 sheet: -0.73 (0.61), residues: 67 loop : -0.99 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 127 TYR 0.016 0.001 TYR C 206 PHE 0.020 0.002 PHE A 122 TRP 0.011 0.002 TRP C 159 HIS 0.012 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 ( 8547) covalent geometry : angle 0.57228 / 0.33 (11955) hydrogen bonds : bond 0.03665 / 2.50 ( 486) hydrogen bonds : angle 4.23027 / 3.01 ( 1310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.9056 (tpt) cc_final: 0.8379 (mmm) REVERT: A 207 PHE cc_start: 0.8417 (m-80) cc_final: 0.8202 (m-10) REVERT: B 79 GLU cc_start: 0.8374 (mp0) cc_final: 0.7803 (pm20) REVERT: B 121 ASP cc_start: 0.9226 (t70) cc_final: 0.8328 (t70) REVERT: B 133 TYR cc_start: 0.8177 (p90) cc_final: 0.7829 (p90) REVERT: C 57 ASN cc_start: 0.8850 (m110) cc_final: 0.8547 (m110) REVERT: C 190 HIS cc_start: 0.7631 (m-70) cc_final: 0.7411 (m170) REVERT: D 26 ASN cc_start: 0.9328 (t0) cc_final: 0.9029 (t0) REVERT: D 28 ASP cc_start: 0.8243 (m-30) cc_final: 0.7659 (m-30) REVERT: D 158 VAL cc_start: 0.9166 (t) cc_final: 0.8944 (t) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.0686 time to fit residues: 10.2649 Evaluate side-chains 76 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 60 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.062181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.049611 restraints weight = 36236.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.051181 restraints weight = 20356.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.052273 restraints weight = 13568.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.053043 restraints weight = 10080.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.053616 restraints weight = 8102.454| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8547 Z= 0.128 Angle : 0.559 6.425 11955 Z= 0.325 Chirality : 0.042 0.169 1371 Planarity : 0.003 0.045 1203 Dihedral : 24.662 63.915 1969 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.30), residues: 796 helix: 2.38 (0.24), residues: 434 sheet: -0.58 (0.63), residues: 67 loop : -0.92 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 127 TYR 0.016 0.001 TYR B 88 PHE 0.020 0.002 PHE A 122 TRP 0.012 0.002 TRP C 159 HIS 0.009 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 ( 8547) covalent geometry : angle 0.55937 / 0.32 (11955) hydrogen bonds : bond 0.03663 / 2.51 ( 486) hydrogen bonds : angle 4.10813 / 2.90 ( 1310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.9082 (mmm) cc_final: 0.8738 (tmm) REVERT: A 203 MET cc_start: 0.9020 (tpt) cc_final: 0.8684 (tpt) REVERT: A 207 PHE cc_start: 0.8399 (m-80) cc_final: 0.8190 (m-10) REVERT: B 79 GLU cc_start: 0.8396 (mp0) cc_final: 0.7804 (pm20) REVERT: B 110 GLN cc_start: 0.8942 (mt0) cc_final: 0.8474 (mp10) REVERT: B 124 LEU cc_start: 0.8664 (mm) cc_final: 0.8227 (tp) REVERT: B 133 TYR cc_start: 0.8175 (p90) cc_final: 0.7851 (p90) REVERT: B 189 ASP cc_start: 0.7181 (m-30) cc_final: 0.6640 (m-30) REVERT: C 57 ASN cc_start: 0.8878 (m110) cc_final: 0.8563 (m110) REVERT: C 64 ILE cc_start: 0.8649 (mp) cc_final: 0.8438 (mp) REVERT: C 193 PHE cc_start: 0.8853 (p90) cc_final: 0.8147 (p90) REVERT: D 23 ARG cc_start: 0.8504 (mpt180) cc_final: 0.8291 (tpp80) REVERT: D 26 ASN cc_start: 0.9336 (t0) cc_final: 0.8987 (t0) REVERT: D 28 ASP cc_start: 0.8290 (m-30) cc_final: 0.7646 (m-30) REVERT: D 158 VAL cc_start: 0.9118 (t) cc_final: 0.8885 (t) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0665 time to fit residues: 9.7649 Evaluate side-chains 81 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 0.2980 chunk 60 optimal weight: 0.0270 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 14 optimal weight: 0.0770 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.062341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.049960 restraints weight = 36392.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.051536 restraints weight = 20271.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.052590 restraints weight = 13368.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.053397 restraints weight = 9902.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.053921 restraints weight = 7910.918| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 8547 Z= 0.118 Angle : 0.548 7.456 11955 Z= 0.321 Chirality : 0.041 0.177 1371 Planarity : 0.003 0.039 1203 Dihedral : 24.524 62.900 1969 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.31), residues: 796 helix: 2.42 (0.24), residues: 434 sheet: -0.51 (0.64), residues: 67 loop : -0.88 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 127 TYR 0.020 0.002 TYR C 206 PHE 0.020 0.001 PHE A 122 TRP 0.011 0.002 TRP C 159 HIS 0.010 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.12 ( 8547) covalent geometry : angle 0.54792 / 0.32 (11955) hydrogen bonds : bond 0.03541 / 2.40 ( 486) hydrogen bonds : angle 4.10372 / 2.92 ( 1310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.9042 (mmm) cc_final: 0.8682 (tmm) REVERT: A 203 MET cc_start: 0.9006 (tpt) cc_final: 0.8636 (tpt) REVERT: A 207 PHE cc_start: 0.8370 (m-80) cc_final: 0.8150 (m-10) REVERT: B 79 GLU cc_start: 0.8374 (mp0) cc_final: 0.7799 (pm20) REVERT: B 105 ILE cc_start: 0.8869 (mt) cc_final: 0.8636 (mt) REVERT: B 110 GLN cc_start: 0.8922 (mt0) cc_final: 0.8458 (mp10) REVERT: B 133 TYR cc_start: 0.8120 (p90) cc_final: 0.7840 (p90) REVERT: B 189 ASP cc_start: 0.7057 (m-30) cc_final: 0.6608 (m-30) REVERT: C 57 ASN cc_start: 0.8849 (m110) cc_final: 0.8537 (m110) REVERT: D 23 ARG cc_start: 0.8519 (mpt180) cc_final: 0.8300 (tpp80) REVERT: D 26 ASN cc_start: 0.9305 (t0) cc_final: 0.8987 (t0) REVERT: D 28 ASP cc_start: 0.8305 (m-30) cc_final: 0.7667 (m-30) REVERT: D 158 VAL cc_start: 0.9122 (t) cc_final: 0.8889 (t) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.0679 time to fit residues: 10.0020 Evaluate side-chains 82 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 82 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 26 ASN D 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.059419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.046849 restraints weight = 37005.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.048420 restraints weight = 20760.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.049495 restraints weight = 13783.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.050248 restraints weight = 10256.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.050816 restraints weight = 8232.359| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8547 Z= 0.166 Angle : 0.598 7.111 11955 Z= 0.343 Chirality : 0.042 0.156 1371 Planarity : 0.004 0.040 1203 Dihedral : 24.362 61.310 1969 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.31), residues: 796 helix: 2.31 (0.24), residues: 434 sheet: -0.21 (0.67), residues: 67 loop : -0.88 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 127 TYR 0.016 0.002 TYR B 88 PHE 0.024 0.002 PHE A 122 TRP 0.013 0.002 TRP C 159 HIS 0.009 0.002 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 ( 8547) covalent geometry : angle 0.59836 / 0.34 (11955) hydrogen bonds : bond 0.04180 / 2.88 ( 486) hydrogen bonds : angle 4.29159 / 3.05 ( 1310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8987 (tpt) cc_final: 0.8750 (tpt) REVERT: A 207 PHE cc_start: 0.8423 (m-80) cc_final: 0.8195 (m-10) REVERT: B 38 ARG cc_start: 0.9020 (mtp180) cc_final: 0.8716 (mtm-85) REVERT: B 79 GLU cc_start: 0.8441 (mp0) cc_final: 0.7968 (pm20) REVERT: B 124 LEU cc_start: 0.8778 (mm) cc_final: 0.8350 (tp) REVERT: B 133 TYR cc_start: 0.8181 (p90) cc_final: 0.7890 (p90) REVERT: B 189 ASP cc_start: 0.7198 (m-30) cc_final: 0.6659 (m-30) REVERT: C 57 ASN cc_start: 0.8867 (m110) cc_final: 0.8526 (m110) REVERT: D 26 ASN cc_start: 0.9322 (t0) cc_final: 0.8949 (t0) REVERT: D 28 ASP cc_start: 0.8385 (m-30) cc_final: 0.7735 (m-30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0678 time to fit residues: 8.9089 Evaluate side-chains 74 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN C 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.059189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.046668 restraints weight = 36982.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.048179 restraints weight = 21122.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.049252 restraints weight = 14201.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.049981 restraints weight = 10600.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050462 restraints weight = 8572.144| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8547 Z= 0.157 Angle : 0.568 8.175 11955 Z= 0.331 Chirality : 0.041 0.150 1371 Planarity : 0.003 0.039 1203 Dihedral : 24.163 61.075 1969 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.31), residues: 796 helix: 2.29 (0.24), residues: 434 sheet: -0.21 (0.67), residues: 67 loop : -0.93 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 127 TYR 0.018 0.002 TYR B 200 PHE 0.023 0.002 PHE A 122 TRP 0.011 0.002 TRP C 159 HIS 0.008 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 ( 8547) covalent geometry : angle 0.56849 / 0.33 (11955) hydrogen bonds : bond 0.04010 / 2.73 ( 486) hydrogen bonds : angle 4.24860 / 3.01 ( 1310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8418 (m-80) cc_final: 0.8189 (m-10) REVERT: B 79 GLU cc_start: 0.8337 (mp0) cc_final: 0.7936 (pm20) REVERT: B 124 LEU cc_start: 0.8776 (mm) cc_final: 0.8354 (tp) REVERT: B 133 TYR cc_start: 0.8241 (p90) cc_final: 0.7943 (p90) REVERT: B 189 ASP cc_start: 0.7092 (m-30) cc_final: 0.6588 (m-30) REVERT: C 57 ASN cc_start: 0.8850 (m110) cc_final: 0.8514 (m110) REVERT: D 26 ASN cc_start: 0.9289 (t0) cc_final: 0.8929 (t0) REVERT: D 28 ASP cc_start: 0.8426 (m-30) cc_final: 0.7751 (m-30) REVERT: D 158 VAL cc_start: 0.9297 (t) cc_final: 0.9077 (t) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0791 time to fit residues: 9.9030 Evaluate side-chains 71 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 0.0070 chunk 5 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 26 ASN D 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.047349 restraints weight = 36263.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.048889 restraints weight = 20360.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.049943 restraints weight = 13532.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.050716 restraints weight = 10072.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.051199 restraints weight = 8095.837| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8547 Z= 0.127 Angle : 0.558 8.588 11955 Z= 0.325 Chirality : 0.041 0.149 1371 Planarity : 0.003 0.038 1203 Dihedral : 23.980 59.942 1969 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.31), residues: 796 helix: 2.33 (0.24), residues: 434 sheet: -0.23 (0.67), residues: 66 loop : -0.88 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 127 TYR 0.014 0.001 TYR B 88 PHE 0.022 0.002 PHE A 122 TRP 0.011 0.002 TRP C 159 HIS 0.007 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 8547) covalent geometry : angle 0.55818 / 0.32 (11955) hydrogen bonds : bond 0.03846 / 2.59 ( 486) hydrogen bonds : angle 4.14586 / 2.93 ( 1310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8798 (tpt) cc_final: 0.8153 (tpt) REVERT: B 79 GLU cc_start: 0.8331 (mp0) cc_final: 0.7922 (pm20) REVERT: B 124 LEU cc_start: 0.8713 (mm) cc_final: 0.8299 (tp) REVERT: B 133 TYR cc_start: 0.8253 (p90) cc_final: 0.7968 (p90) REVERT: B 189 ASP cc_start: 0.7022 (m-30) cc_final: 0.6526 (m-30) REVERT: C 57 ASN cc_start: 0.8842 (m110) cc_final: 0.8494 (m110) REVERT: C 112 MET cc_start: 0.8242 (tpp) cc_final: 0.7819 (tpp) REVERT: D 26 ASN cc_start: 0.9289 (t0) cc_final: 0.8927 (t0) REVERT: D 28 ASP cc_start: 0.8423 (m-30) cc_final: 0.7713 (m-30) REVERT: D 158 VAL cc_start: 0.9279 (t) cc_final: 0.9064 (t) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0694 time to fit residues: 9.0601 Evaluate side-chains 75 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 0.0270 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS C 26 ASN C 148 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.047323 restraints weight = 36412.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.048831 restraints weight = 20862.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.049875 restraints weight = 14042.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.050591 restraints weight = 10545.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.051148 restraints weight = 8543.127| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8547 Z= 0.126 Angle : 0.559 8.723 11955 Z= 0.323 Chirality : 0.040 0.147 1371 Planarity : 0.003 0.038 1203 Dihedral : 23.912 59.766 1969 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.31), residues: 796 helix: 2.30 (0.24), residues: 440 sheet: -0.29 (0.66), residues: 67 loop : -0.93 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.013 0.001 TYR B 88 PHE 0.021 0.002 PHE A 122 TRP 0.050 0.004 TRP A 159 HIS 0.006 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 8547) covalent geometry : angle 0.55882 / 0.32 (11955) hydrogen bonds : bond 0.03766 / 2.56 ( 486) hydrogen bonds : angle 4.11279 / 2.91 ( 1310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1116.23 seconds wall clock time: 20 minutes 7.39 seconds (1207.39 seconds total)