Starting phenix.real_space_refine on Fri Sep 11 06:16:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oz3_13119/09_2026/7oz3_13119.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oz3_13119/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7oz3_13119/09_2026/7oz3_13119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oz3_13119/09_2026/7oz3_13119.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oz3_13119/09_2026/7oz3_13119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oz3_13119/09_2026/7oz3_13119.map" } 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-2.2.1-6174/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: 1.76, per 1000 atoms: 0.21 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: 0.72 Conformation dependent library (CDL) restraints added in 292.0 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: 1.05 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: 1.33 Time building geometry restraints manager: 0.96 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.400 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.820 ------------------------------------------------------------------------------- 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= 0.722 Angle : 1.274 13.460 11955 Z= 0.907 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 1.27406 / 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 : 0.219 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: 0.7808 (m-30) REVERT: A 207 PHE cc_start: 0.8466 (m-80) cc_final: 0.7294 (m-10) REVERT: B 110 GLN cc_start: 0.8990 (mt0) cc_final: 0.8498 (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: 0.7518 (m170) REVERT: D 26 ASN cc_start: 0.9393 (t0) cc_final: 0.8861 (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: 0.0885 time to fit residues: 21.7391 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 : 0.279 ------------------------------------------------------------------------------- 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: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.1980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 GLN A 190 HIS 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.065313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.052758 restraints weight = 36062.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.054404 restraints weight = 19819.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.055551 restraints weight = 12988.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.056380 restraints weight = 9475.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.056913 restraints weight = 7531.891| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 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 = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8547 Z= 0.150 Angle : 0.762 7.083 11955 Z= 0.416 Chirality : 0.055 0.327 1371 Planarity : 0.004 0.043 1203 Dihedral : 25.511 92.138 1969 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: 1.01 (0.30), residues: 796 helix: 2.15 (0.24), residues: 431 sheet: -1.03 (0.58), residues: 68 loop : -1.18 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 38 TYR 0.018 0.002 TYR D 200 PHE 0.020 0.002 PHE A 192 TRP 0.017 0.003 TRP C 159 HIS 0.021 0.002 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 8547) covalent geometry : angle 0.76229 / 0.42 (11955) hydrogen bonds : bond 0.04495 / 3.12 ( 486) hydrogen bonds : angle 4.49414 / 3.16 ( 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 129 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 THR cc_start: 0.8823 (p) cc_final: 0.7988 (p) REVERT: A 203 MET cc_start: 0.9182 (tpt) cc_final: 0.8771 (tpp) REVERT: A 207 PHE cc_start: 0.8628 (m-80) cc_final: 0.7751 (m-10) REVERT: B 110 GLN cc_start: 0.8991 (mt0) cc_final: 0.8479 (mp10) REVERT: B 121 ASP cc_start: 0.9120 (t70) cc_final: 0.8555 (t70) REVERT: B 133 TYR cc_start: 0.8162 (p90) cc_final: 0.7915 (p90) REVERT: C 57 ASN cc_start: 0.8941 (m110) cc_final: 0.8634 (m110) REVERT: C 112 MET cc_start: 0.8162 (tpp) cc_final: 0.7958 (tpp) REVERT: C 190 HIS cc_start: 0.7899 (m-70) cc_final: 0.7372 (m170) REVERT: C 192 PHE cc_start: 0.8976 (m-80) cc_final: 0.8715 (m-80) REVERT: D 26 ASN cc_start: 0.9473 (t0) cc_final: 0.9196 (t0) REVERT: D 28 ASP cc_start: 0.8342 (m-30) cc_final: 0.7984 (m-30) REVERT: D 142 VAL cc_start: 0.8919 (m) cc_final: 0.8602 (p) REVERT: D 157 ASN cc_start: 0.8535 (t0) cc_final: 0.7725 (t0) outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.0715 time to fit residues: 13.3200 Evaluate side-chains 75 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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: 0.2980 chunk 15 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 HIS C 26 ASN D 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.052177 restraints weight = 35479.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.053800 restraints weight = 19674.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.054886 restraints weight = 12918.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.055708 restraints weight = 9528.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.056305 restraints weight = 7556.178| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8547 Z= 0.142 Angle : 0.651 6.844 11955 Z= 0.371 Chirality : 0.047 0.186 1371 Planarity : 0.004 0.049 1203 Dihedral : 25.090 79.956 1969 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.29 % Allowed : 4.09 % 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: 1.13 (0.30), residues: 796 helix: 2.22 (0.24), residues: 433 sheet: -1.26 (0.57), residues: 70 loop : -1.01 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 202 TYR 0.024 0.002 TYR C 206 PHE 0.018 0.002 PHE A 122 TRP 0.013 0.002 TRP C 159 HIS 0.010 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 8547) covalent geometry : angle 0.65147 / 0.37 (11955) hydrogen bonds : bond 0.04062 / 2.79 ( 486) hydrogen bonds : angle 4.32666 / 3.08 ( 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 107 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8500 (m-80) cc_final: 0.8191 (m-10) REVERT: B 79 GLU cc_start: 0.8449 (mp0) cc_final: 0.7817 (pm20) REVERT: B 121 ASP cc_start: 0.9160 (t70) cc_final: 0.8436 (t0) REVERT: B 133 TYR cc_start: 0.8361 (p90) cc_final: 0.7896 (p90) REVERT: B 189 ASP cc_start: 0.7437 (m-30) cc_final: 0.7174 (m-30) REVERT: C 57 ASN cc_start: 0.8852 (m110) cc_final: 0.8553 (m110) REVERT: C 190 HIS cc_start: 0.7786 (m-70) cc_final: 0.7340 (m170) REVERT: D 26 ASN cc_start: 0.9402 (t0) cc_final: 0.9112 (t0) REVERT: D 28 ASP cc_start: 0.8373 (m-30) cc_final: 0.7899 (m-30) outliers start: 2 outliers final: 1 residues processed: 107 average time/residue: 0.0748 time to fit residues: 11.5178 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 : 0.259 ------------------------------------------------------------------------------- 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: 3.9990 chunk 30 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.063686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.051403 restraints weight = 36615.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.052989 restraints weight = 20424.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.054070 restraints weight = 13450.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.054863 restraints weight = 9921.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.055465 restraints weight = 7870.188| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 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: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8547 Z= 0.139 Angle : 0.616 6.736 11955 Z= 0.353 Chirality : 0.045 0.152 1371 Planarity : 0.003 0.034 1203 Dihedral : 24.980 70.857 1969 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % 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: 1.10 (0.30), residues: 796 helix: 2.14 (0.24), residues: 434 sheet: -1.13 (0.58), residues: 70 loop : -0.97 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 23 TYR 0.013 0.001 TYR D 200 PHE 0.018 0.002 PHE A 122 TRP 0.012 0.002 TRP C 159 HIS 0.012 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 ( 8547) covalent geometry : angle 0.61557 / 0.35 (11955) hydrogen bonds : bond 0.03871 / 2.66 ( 486) hydrogen bonds : angle 4.30845 / 3.06 ( 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 106 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.9149 (tpt) cc_final: 0.8876 (tpp) REVERT: B 38 ARG cc_start: 0.8832 (mtp180) cc_final: 0.8577 (mtp180) REVERT: B 79 GLU cc_start: 0.8402 (mp0) cc_final: 0.7806 (pm20) REVERT: B 121 ASP cc_start: 0.9207 (t70) cc_final: 0.8439 (t70) REVERT: B 133 TYR cc_start: 0.8199 (p90) cc_final: 0.7840 (p90) REVERT: C 57 ASN cc_start: 0.8843 (m110) cc_final: 0.8543 (m110) REVERT: C 190 HIS cc_start: 0.7733 (m-70) cc_final: 0.7453 (m170) REVERT: D 26 ASN cc_start: 0.9369 (t0) cc_final: 0.9070 (t0) REVERT: D 28 ASP cc_start: 0.8305 (m-30) cc_final: 0.7807 (m-30) REVERT: D 158 VAL cc_start: 0.9123 (t) cc_final: 0.8882 (t) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0771 time to fit residues: 11.5496 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 : 0.262 ------------------------------------------------------------------------------- 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: 0.6980 chunk 62 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 53 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 110 GLN C 26 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.063244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.050695 restraints weight = 35884.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.052287 restraints weight = 19915.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.053353 restraints weight = 13132.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.054151 restraints weight = 9725.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.054740 restraints weight = 7763.634| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 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 = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8547 Z= 0.131 Angle : 0.585 6.414 11955 Z= 0.336 Chirality : 0.043 0.167 1371 Planarity : 0.003 0.037 1203 Dihedral : 24.786 65.108 1969 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: 1.25 (0.30), residues: 796 helix: 2.24 (0.24), residues: 434 sheet: -0.72 (0.61), residues: 67 loop : -0.98 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 202 TYR 0.018 0.002 TYR C 206 PHE 0.020 0.002 PHE A 122 TRP 0.011 0.002 TRP C 159 HIS 0.007 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 8547) covalent geometry : angle 0.58548 / 0.34 (11955) hydrogen bonds : bond 0.03723 / 2.55 ( 486) hydrogen bonds : angle 4.15211 / 2.94 ( 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 106 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.9169 (mmm) cc_final: 0.8819 (mmm) REVERT: A 207 PHE cc_start: 0.8416 (m-10) cc_final: 0.8208 (m-10) REVERT: B 38 ARG cc_start: 0.8883 (mtp180) cc_final: 0.8658 (mtp180) REVERT: B 79 GLU cc_start: 0.8410 (mp0) cc_final: 0.7822 (pm20) REVERT: B 133 TYR cc_start: 0.8184 (p90) cc_final: 0.7844 (p90) REVERT: B 189 ASP cc_start: 0.7172 (m-30) cc_final: 0.6592 (m-30) REVERT: C 57 ASN cc_start: 0.8856 (m110) cc_final: 0.8552 (m110) REVERT: C 64 ILE cc_start: 0.8599 (mp) cc_final: 0.8394 (mp) REVERT: C 190 HIS cc_start: 0.7653 (m-70) cc_final: 0.7436 (m170) REVERT: D 26 ASN cc_start: 0.9400 (t0) cc_final: 0.9051 (t0) REVERT: D 28 ASP cc_start: 0.8257 (m-30) cc_final: 0.7677 (m-30) REVERT: D 112 MET cc_start: 0.8690 (tpp) cc_final: 0.8406 (tpp) REVERT: D 158 VAL cc_start: 0.9106 (t) cc_final: 0.8882 (t) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0835 time to fit residues: 12.5140 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 : 0.168 ------------------------------------------------------------------------------- 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: 0.0770 chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 = 0.3203 r_free = 0.3203 target = 0.062755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.050472 restraints weight = 35904.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.051937 restraints weight = 20838.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.052983 restraints weight = 14095.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.053663 restraints weight = 10567.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.054214 restraints weight = 8594.845| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8547 Z= 0.124 Angle : 0.568 6.815 11955 Z= 0.328 Chirality : 0.042 0.152 1371 Planarity : 0.003 0.039 1203 Dihedral : 24.650 62.226 1969 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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 (0.30), residues: 796 helix: 2.33 (0.24), residues: 434 sheet: -0.59 (0.62), residues: 67 loop : -0.89 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.015 0.001 TYR B 88 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 0.00236 / 0.12 ( 8547) covalent geometry : angle 0.56825 / 0.33 (11955) hydrogen bonds : bond 0.03649 / 2.50 ( 486) hydrogen bonds : angle 4.13995 / 2.95 ( 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 108 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ARG cc_start: 0.8967 (mtp180) cc_final: 0.8731 (mtp180) REVERT: B 79 GLU cc_start: 0.8384 (mp0) cc_final: 0.7797 (pm20) REVERT: B 110 GLN cc_start: 0.8974 (mt0) cc_final: 0.8447 (mp10) REVERT: B 124 LEU cc_start: 0.8709 (mm) cc_final: 0.8252 (tp) REVERT: B 133 TYR cc_start: 0.8173 (p90) cc_final: 0.7852 (p90) REVERT: B 189 ASP cc_start: 0.7188 (m-30) cc_final: 0.6660 (m-30) REVERT: C 57 ASN cc_start: 0.8876 (m110) cc_final: 0.8561 (m110) REVERT: C 190 HIS cc_start: 0.7525 (m-70) cc_final: 0.7311 (m170) REVERT: D 26 ASN cc_start: 0.9317 (t0) cc_final: 0.8993 (t0) REVERT: D 28 ASP cc_start: 0.8284 (m-30) cc_final: 0.7674 (m-30) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0806 time to fit residues: 12.3183 Evaluate side-chains 79 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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: 0.9990 chunk 60 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3179 r_free = 0.3179 target = 0.061674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.049256 restraints weight = 36584.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.050843 restraints weight = 20276.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.051951 restraints weight = 13422.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.052731 restraints weight = 9902.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.053244 restraints weight = 7904.874| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 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 = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8547 Z= 0.133 Angle : 0.561 7.311 11955 Z= 0.324 Chirality : 0.042 0.172 1371 Planarity : 0.003 0.040 1203 Dihedral : 24.504 60.201 1969 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.36 (0.24), residues: 434 sheet: -0.45 (0.64), residues: 67 loop : -0.92 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 127 TYR 0.018 0.002 TYR C 206 PHE 0.020 0.002 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 0.00276 / 0.13 ( 8547) covalent geometry : angle 0.56104 / 0.32 (11955) hydrogen bonds : bond 0.03659 / 2.51 ( 486) hydrogen bonds : angle 4.08450 / 2.90 ( 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 99 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 HIS cc_start: 0.8676 (m-70) cc_final: 0.7963 (m90) REVERT: A 203 MET cc_start: 0.8856 (tpt) cc_final: 0.8637 (tpt) REVERT: B 79 GLU cc_start: 0.8416 (mp0) cc_final: 0.7822 (pm20) REVERT: B 124 LEU cc_start: 0.8726 (mm) cc_final: 0.8263 (tp) REVERT: B 133 TYR cc_start: 0.8148 (p90) cc_final: 0.7836 (p90) REVERT: B 189 ASP cc_start: 0.7320 (m-30) cc_final: 0.6789 (m-30) REVERT: C 57 ASN cc_start: 0.8875 (m110) cc_final: 0.8571 (m110) REVERT: D 26 ASN cc_start: 0.9354 (t0) cc_final: 0.8970 (t0) REVERT: D 28 ASP cc_start: 0.8309 (m-30) cc_final: 0.7684 (m-30) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0815 time to fit residues: 11.4418 Evaluate side-chains 77 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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: 9.9990 chunk 23 optimal weight: 0.1980 chunk 79 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 0.0870 chunk 81 optimal weight: 10.0000 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 = 0.3175 r_free = 0.3175 target = 0.061530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.049233 restraints weight = 36559.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.050738 restraints weight = 21200.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.051792 restraints weight = 14332.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.052490 restraints weight = 10756.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.053027 restraints weight = 8761.930| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8547 Z= 0.119 Angle : 0.556 6.637 11955 Z= 0.320 Chirality : 0.040 0.151 1371 Planarity : 0.003 0.039 1203 Dihedral : 24.370 59.942 1969 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.32 (0.24), residues: 435 sheet: -0.36 (0.65), residues: 67 loop : -0.88 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 127 TYR 0.014 0.001 TYR B 88 PHE 0.020 0.001 PHE A 122 TRP 0.011 0.002 TRP C 159 HIS 0.009 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 ( 8547) covalent geometry : angle 0.55597 / 0.32 (11955) hydrogen bonds : bond 0.03544 / 2.42 ( 486) hydrogen bonds : angle 4.07076 / 2.89 ( 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 102 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 HIS cc_start: 0.8646 (m-70) cc_final: 0.8201 (m170) REVERT: B 79 GLU cc_start: 0.8425 (mp0) cc_final: 0.7950 (pm20) REVERT: B 121 ASP cc_start: 0.9067 (t70) cc_final: 0.8333 (t0) REVERT: B 124 LEU cc_start: 0.8645 (mm) cc_final: 0.8248 (tp) REVERT: B 133 TYR cc_start: 0.8109 (p90) cc_final: 0.7832 (p90) REVERT: B 189 ASP cc_start: 0.7219 (m-30) cc_final: 0.6735 (m-30) REVERT: C 57 ASN cc_start: 0.8833 (m110) cc_final: 0.8491 (m110) REVERT: C 112 MET cc_start: 0.8359 (tpp) cc_final: 0.7866 (tpp) REVERT: D 26 ASN cc_start: 0.9316 (t0) cc_final: 0.8964 (t0) REVERT: D 28 ASP cc_start: 0.8338 (m-30) cc_final: 0.7662 (m-30) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0782 time to fit residues: 11.3763 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 : 0.203 ------------------------------------------------------------------------------- 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: 2.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3107 r_free = 0.3107 target = 0.058548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.046105 restraints weight = 37075.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.047664 restraints weight = 20762.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.048707 restraints weight = 13797.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.049496 restraints weight = 10301.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.050000 restraints weight = 8265.422| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 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 = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8547 Z= 0.186 Angle : 0.643 9.735 11955 Z= 0.360 Chirality : 0.043 0.176 1371 Planarity : 0.004 0.041 1203 Dihedral : 24.170 59.892 1969 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.30), residues: 796 helix: 2.06 (0.24), residues: 440 sheet: -0.28 (0.67), residues: 68 loop : -0.90 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 127 TYR 0.027 0.002 TYR B 200 PHE 0.026 0.002 PHE A 122 TRP 0.013 0.002 TRP C 159 HIS 0.010 0.002 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 ( 8547) covalent geometry : angle 0.64303 / 0.36 (11955) hydrogen bonds : bond 0.04497 / 3.06 ( 486) hydrogen bonds : angle 4.37909 / 3.12 ( 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 90 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 203 MET cc_start: 0.8950 (tpt) cc_final: 0.7878 (tpt) REVERT: A 207 PHE cc_start: 0.8296 (m-10) cc_final: 0.7990 (m-10) REVERT: B 79 GLU cc_start: 0.8455 (mp0) cc_final: 0.7985 (pm20) REVERT: B 133 TYR cc_start: 0.8226 (p90) cc_final: 0.7920 (p90) REVERT: B 189 ASP cc_start: 0.7210 (m-30) cc_final: 0.6668 (m-30) REVERT: C 57 ASN cc_start: 0.8870 (m110) cc_final: 0.8531 (m110) REVERT: D 26 ASN cc_start: 0.9325 (t0) cc_final: 0.8941 (t0) REVERT: D 28 ASP cc_start: 0.8421 (m-30) cc_final: 0.7750 (m-30) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0811 time to fit residues: 10.3107 Evaluate side-chains 69 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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: 1.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 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 = 0.3124 r_free = 0.3124 target = 0.059266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.046771 restraints weight = 36614.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.048326 restraints weight = 20436.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.049434 restraints weight = 13631.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.050200 restraints weight = 10124.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.050761 restraints weight = 8123.414| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 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 = 0.2890 r_free = 0.2890 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: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8547 Z= 0.131 Angle : 0.581 9.202 11955 Z= 0.335 Chirality : 0.041 0.150 1371 Planarity : 0.003 0.039 1203 Dihedral : 23.945 59.945 1969 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.77 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: 1.30 (0.31), residues: 796 helix: 2.13 (0.24), residues: 440 sheet: -0.29 (0.67), residues: 67 loop : -0.87 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 127 TYR 0.013 0.001 TYR B 88 PHE 0.023 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 0.00262 / 0.13 ( 8547) covalent geometry : angle 0.58057 / 0.34 (11955) hydrogen bonds : bond 0.03882 / 2.63 ( 486) hydrogen bonds : angle 4.25186 / 3.03 ( 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 96 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 GLN cc_start: 0.9010 (mt0) cc_final: 0.8620 (mt0) REVERT: B 79 GLU cc_start: 0.8418 (mp0) cc_final: 0.7976 (pm20) REVERT: B 124 LEU cc_start: 0.8695 (mm) cc_final: 0.8243 (tp) REVERT: B 133 TYR cc_start: 0.8206 (p90) cc_final: 0.7910 (p90) REVERT: B 189 ASP cc_start: 0.7077 (m-30) cc_final: 0.6581 (m-30) REVERT: C 57 ASN cc_start: 0.8857 (m110) cc_final: 0.8506 (m110) REVERT: C 112 MET cc_start: 0.8377 (tpp) cc_final: 0.7923 (tpp) REVERT: D 26 ASN cc_start: 0.9298 (t0) cc_final: 0.8908 (t0) REVERT: D 28 ASP cc_start: 0.8414 (m-30) cc_final: 0.7654 (m-30) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0765 time to fit residues: 10.3430 Evaluate side-chains 77 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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: 0.3980 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 73 optimal weight: 0.0770 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS C 26 ASN D 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.059353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.046946 restraints weight = 36408.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.048482 restraints weight = 20461.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.049590 restraints weight = 13648.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050340 restraints weight = 10157.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.050878 restraints weight = 8176.537| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 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 = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4368 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= 0.134 Angle : 0.594 8.937 11955 Z= 0.340 Chirality : 0.041 0.150 1371 Planarity : 0.003 0.039 1203 Dihedral : 23.882 59.850 1969 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.77 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: 1.29 (0.30), residues: 796 helix: 2.15 (0.24), residues: 440 sheet: -0.33 (0.66), residues: 67 loop : -0.91 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 127 TYR 0.018 0.001 TYR C 206 PHE 0.022 0.002 PHE A 122 TRP 0.046 0.004 TRP A 159 HIS 0.009 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 8547) covalent geometry : angle 0.59354 / 0.34 (11955) hydrogen bonds : bond 0.03848 / 2.62 ( 486) hydrogen bonds : angle 4.29125 / 3.08 ( 1310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1193.12 seconds wall clock time: 21 minutes 25.55 seconds (1285.55 seconds total)