Starting phenix.real_space_refine on Fri Jul 25 23:55:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oz3_13119/07_2025/7oz3_13119.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oz3_13119/07_2025/7oz3_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_2025/7oz3_13119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oz3_13119/07_2025/7oz3_13119.map" model { file = "/net/cci-nas-00/data/ceres_data/7oz3_13119/07_2025/7oz3_13119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oz3_13119/07_2025/7oz3_13119.cif" } resolution = 4.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.27, per 1000 atoms: 0.64 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: 2.12 Conformation dependent library (CDL) restraints added in 712.4 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: 3.18 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: 2.60 Time building geometry restraints manager: 2.49 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 - 2.27: 10904 2.27 - 4.54: 896 4.54 - 6.82: 145 6.82 - 9.09: 9 9.09 - 11.36: 1 Bond angle restraints: 11955 Sorted by residual: angle pdb=" O3' DA F 22 " pdb=" C3' DA F 22 " pdb=" C2' DA F 22 " ideal model delta sigma weight residual 111.50 122.86 -11.36 1.50e+00 4.44e-01 5.74e+01 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 ... (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: 1006 0.082 - 0.165: 288 0.165 - 0.247: 63 0.247 - 0.329: 9 0.329 - 0.411: 5 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: 1.240 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.750 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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= 0.671 Angle : 1.273 11.360 11955 Z= 0.870 Chirality : 0.079 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.025 0.005 TRP B 159 HIS 0.004 0.001 HIS C 148 PHE 0.019 0.002 PHE A 122 TYR 0.025 0.002 TYR A 206 ARG 0.008 0.001 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.14259 ( 486) hydrogen bonds : angle 5.61186 ( 1310) covalent geometry : bond 0.01086 ( 8547) covalent geometry : angle 1.27289 (11955) *********************** 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 : 0.871 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: 0.7813 (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: 0.8332 (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: 0.9392 (t0) cc_final: 0.8859 (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: 0.3516 time to fit residues: 87.3529 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 : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 68 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 D 92 HIS D 171 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.065196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.052496 restraints weight = 35720.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.054092 restraints weight = 20088.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.055199 restraints weight = 13353.884| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.75 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 = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8547 Z= 0.167 Angle : 0.626 6.802 11955 Z= 0.370 Chirality : 0.041 0.297 1371 Planarity : 0.004 0.048 1203 Dihedral : 24.823 98.536 1969 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.15 % Allowed : 4.97 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.30), residues: 796 helix: 2.11 (0.24), residues: 432 sheet: -1.12 (0.56), residues: 68 loop : -1.16 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 159 HIS 0.016 0.001 HIS A 171 PHE 0.018 0.002 PHE C 207 TYR 0.017 0.002 TYR D 200 ARG 0.007 0.001 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 486) hydrogen bonds : angle 4.39510 ( 1310) covalent geometry : bond 0.00368 ( 8547) covalent geometry : angle 0.62556 (11955) *********************** 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 124 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.744 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: 0.9242 (tpt) cc_final: 0.8968 (tpp) REVERT: A 207 PHE cc_start: 0.8614 (m-80) cc_final: 0.7834 (m-10) REVERT: B 22 GLN cc_start: 0.8881 (mt0) cc_final: 0.8576 (pt0) REVERT: B 79 GLU cc_start: 0.8480 (mp0) cc_final: 0.7924 (pm20) REVERT: B 109 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 110 GLN cc_start: 0.8951 (mt0) cc_final: 0.8472 (mp10) REVERT: B 121 ASP cc_start: 0.9138 (t70) cc_final: 0.8499 (t0) REVERT: B 133 TYR cc_start: 0.8221 (p90) cc_final: 0.7984 (p90) REVERT: C 57 ASN cc_start: 0.8941 (m110) cc_final: 0.8716 (m110) REVERT: C 112 MET cc_start: 0.8142 (tpp) cc_final: 0.7889 (tpp) REVERT: C 190 HIS cc_start: 0.7853 (m-70) cc_final: 0.7366 (m170) REVERT: C 192 PHE cc_start: 0.9004 (m-80) cc_final: 0.8724 (m-80) REVERT: D 26 ASN cc_start: 0.9463 (t0) cc_final: 0.9161 (t0) REVERT: D 28 ASP cc_start: 0.8368 (m-30) cc_final: 0.7978 (m-30) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.1809 time to fit residues: 31.6825 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 : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 171 HIS ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.063270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.050943 restraints weight = 35580.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.052533 restraints weight = 19555.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.053661 restraints weight = 12820.525| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8547 Z= 0.159 Angle : 0.573 7.181 11955 Z= 0.340 Chirality : 0.039 0.163 1371 Planarity : 0.004 0.050 1203 Dihedral : 24.574 86.970 1969 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.44 % Allowed : 4.24 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.30), residues: 796 helix: 2.24 (0.24), residues: 434 sheet: -0.85 (0.58), residues: 68 loop : -0.98 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 159 HIS 0.011 0.001 HIS A 171 PHE 0.019 0.002 PHE A 122 TYR 0.023 0.002 TYR C 206 ARG 0.008 0.001 ARG C 23 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 486) hydrogen bonds : angle 4.22011 ( 1310) covalent geometry : bond 0.00355 ( 8547) covalent geometry : angle 0.57298 (11955) *********************** 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 109 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8586 (m-80) cc_final: 0.7708 (m-10) REVERT: B 79 GLU cc_start: 0.8465 (mp0) cc_final: 0.7886 (pm20) REVERT: B 121 ASP cc_start: 0.9263 (t70) cc_final: 0.8541 (t70) REVERT: B 133 TYR cc_start: 0.8322 (p90) cc_final: 0.7909 (p90) REVERT: B 171 HIS cc_start: 0.7026 (OUTLIER) cc_final: 0.6731 (t-90) REVERT: B 189 ASP cc_start: 0.7346 (m-30) cc_final: 0.6876 (m-30) REVERT: C 57 ASN cc_start: 0.8879 (m110) cc_final: 0.8561 (m110) REVERT: C 64 ILE cc_start: 0.8664 (mp) cc_final: 0.8448 (mp) REVERT: C 190 HIS cc_start: 0.7775 (m-70) cc_final: 0.7473 (m170) REVERT: D 26 ASN cc_start: 0.9401 (t0) cc_final: 0.9090 (t0) REVERT: D 28 ASP cc_start: 0.8354 (m-30) cc_final: 0.7820 (m-30) outliers start: 3 outliers final: 0 residues processed: 108 average time/residue: 0.2027 time to fit residues: 30.4295 Evaluate side-chains 77 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 61 optimal weight: 0.6980 chunk 57 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 ASN D 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.062820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.050247 restraints weight = 35716.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.051778 restraints weight = 20052.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.052886 restraints weight = 13346.112| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8547 Z= 0.140 Angle : 0.546 7.250 11955 Z= 0.323 Chirality : 0.038 0.176 1371 Planarity : 0.003 0.037 1203 Dihedral : 24.345 77.250 1969 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.30), residues: 796 helix: 2.25 (0.24), residues: 435 sheet: -0.60 (0.62), residues: 67 loop : -0.89 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 159 HIS 0.012 0.001 HIS B 171 PHE 0.019 0.001 PHE A 122 TYR 0.014 0.001 TYR B 88 ARG 0.003 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 486) hydrogen bonds : angle 4.14061 ( 1310) covalent geometry : bond 0.00306 ( 8547) covalent geometry : angle 0.54637 (11955) *********************** 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 109 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.9115 (tpt) cc_final: 0.8827 (tpt) REVERT: A 207 PHE cc_start: 0.8440 (m-80) cc_final: 0.8089 (m-10) REVERT: B 79 GLU cc_start: 0.8483 (mp0) cc_final: 0.7924 (pm20) REVERT: B 133 TYR cc_start: 0.8145 (p90) cc_final: 0.7840 (p90) REVERT: C 57 ASN cc_start: 0.8890 (m110) cc_final: 0.8585 (m110) REVERT: D 26 ASN cc_start: 0.9425 (t0) cc_final: 0.9069 (t0) REVERT: D 28 ASP cc_start: 0.8302 (m-30) cc_final: 0.7746 (m-30) REVERT: D 63 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7447 (tm-30) REVERT: D 80 LYS cc_start: 0.9378 (mmtp) cc_final: 0.9002 (mttt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2317 time to fit residues: 34.5997 Evaluate side-chains 78 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 108 GLN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.060142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.047685 restraints weight = 36388.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.049225 restraints weight = 20454.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.050307 restraints weight = 13631.435| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8547 Z= 0.174 Angle : 0.561 5.857 11955 Z= 0.332 Chirality : 0.039 0.148 1371 Planarity : 0.003 0.036 1203 Dihedral : 24.032 67.932 1969 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.15 % Allowed : 4.53 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.30), residues: 796 helix: 2.22 (0.24), residues: 435 sheet: -0.25 (0.64), residues: 67 loop : -0.92 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 159 HIS 0.010 0.001 HIS B 171 PHE 0.021 0.002 PHE A 122 TYR 0.016 0.002 TYR C 206 ARG 0.009 0.001 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 486) hydrogen bonds : angle 4.17506 ( 1310) covalent geometry : bond 0.00388 ( 8547) covalent geometry : angle 0.56065 (11955) *********************** 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 92 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 GLU cc_start: 0.8493 (mp0) cc_final: 0.8110 (pm20) REVERT: B 133 TYR cc_start: 0.8157 (p90) cc_final: 0.7857 (p90) REVERT: B 189 ASP cc_start: 0.7208 (m-30) cc_final: 0.6663 (m-30) REVERT: C 57 ASN cc_start: 0.8896 (m110) cc_final: 0.8551 (m110) REVERT: C 193 PHE cc_start: 0.8864 (p90) cc_final: 0.8069 (p90) REVERT: D 26 ASN cc_start: 0.9313 (t0) cc_final: 0.8939 (t0) REVERT: D 28 ASP cc_start: 0.8387 (m-30) cc_final: 0.7736 (m-30) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.1718 time to fit residues: 22.5280 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 : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 70 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 108 GLN ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.057620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.045216 restraints weight = 37212.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.046685 restraints weight = 21567.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.047728 restraints weight = 14642.292| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8547 Z= 0.196 Angle : 0.596 8.669 11955 Z= 0.346 Chirality : 0.041 0.241 1371 Planarity : 0.003 0.034 1203 Dihedral : 23.374 63.379 1969 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.30), residues: 796 helix: 2.16 (0.24), residues: 434 sheet: 0.02 (0.69), residues: 67 loop : -0.99 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 159 HIS 0.008 0.001 HIS A 171 PHE 0.023 0.002 PHE A 122 TYR 0.017 0.002 TYR A 13 ARG 0.006 0.001 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 486) hydrogen bonds : angle 4.25514 ( 1310) covalent geometry : bond 0.00439 ( 8547) covalent geometry : angle 0.59589 (11955) *********************** 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 91 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.9036 (tpp) cc_final: 0.8466 (tpt) REVERT: B 79 GLU cc_start: 0.8537 (mp0) cc_final: 0.8145 (pm20) REVERT: B 124 LEU cc_start: 0.8738 (mm) cc_final: 0.8286 (tp) REVERT: B 189 ASP cc_start: 0.7258 (m-30) cc_final: 0.6762 (m-30) REVERT: C 57 ASN cc_start: 0.8872 (m110) cc_final: 0.8523 (m110) REVERT: D 26 ASN cc_start: 0.9321 (t0) cc_final: 0.8896 (t0) REVERT: D 28 ASP cc_start: 0.8455 (m-30) cc_final: 0.7693 (m-30) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2017 time to fit residues: 25.7802 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 : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN C 26 ASN C 208 ASN D 160 HIS D 171 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.058688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.046620 restraints weight = 36361.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.048108 restraints weight = 21041.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.049088 restraints weight = 14169.249| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8547 Z= 0.139 Angle : 0.534 7.049 11955 Z= 0.315 Chirality : 0.039 0.150 1371 Planarity : 0.003 0.036 1203 Dihedral : 23.209 60.383 1969 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.15 % Allowed : 2.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.31), residues: 796 helix: 2.29 (0.24), residues: 434 sheet: -0.01 (0.67), residues: 67 loop : -1.00 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 159 HIS 0.006 0.001 HIS A 171 PHE 0.018 0.001 PHE A 122 TYR 0.020 0.001 TYR C 206 ARG 0.004 0.001 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 486) hydrogen bonds : angle 4.05940 ( 1310) covalent geometry : bond 0.00301 ( 8547) covalent geometry : angle 0.53357 (11955) *********************** 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 94 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 GLU cc_start: 0.8445 (mp0) cc_final: 0.8067 (pm20) REVERT: B 124 LEU cc_start: 0.8741 (mm) cc_final: 0.8288 (tp) REVERT: C 57 ASN cc_start: 0.8861 (m110) cc_final: 0.8518 (m110) REVERT: D 26 ASN cc_start: 0.9306 (t0) cc_final: 0.8859 (t0) REVERT: D 28 ASP cc_start: 0.8438 (m-30) cc_final: 0.7634 (m-30) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1954 time to fit residues: 25.8863 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 : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.0870 chunk 78 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 160 HIS C 26 ASN D 160 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.058882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.046548 restraints weight = 37490.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.048089 restraints weight = 21215.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.049130 restraints weight = 14222.797| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8547 Z= 0.135 Angle : 0.540 7.459 11955 Z= 0.314 Chirality : 0.039 0.146 1371 Planarity : 0.003 0.036 1203 Dihedral : 23.043 59.750 1969 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.31), residues: 796 helix: 2.34 (0.24), residues: 434 sheet: -0.09 (0.67), residues: 68 loop : -1.03 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 159 HIS 0.006 0.001 HIS A 171 PHE 0.020 0.001 PHE A 122 TYR 0.012 0.001 TYR B 88 ARG 0.004 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 486) hydrogen bonds : angle 4.03540 ( 1310) covalent geometry : bond 0.00292 ( 8547) covalent geometry : angle 0.53974 (11955) *********************** 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 97 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 GLU cc_start: 0.8485 (mp0) cc_final: 0.8116 (pm20) REVERT: B 124 LEU cc_start: 0.8708 (mm) cc_final: 0.8302 (tp) REVERT: B 133 TYR cc_start: 0.8236 (p90) cc_final: 0.7978 (p90) REVERT: B 189 ASP cc_start: 0.7063 (m-30) cc_final: 0.6511 (m-30) REVERT: C 57 ASN cc_start: 0.8820 (m110) cc_final: 0.8479 (m110) REVERT: D 26 ASN cc_start: 0.9303 (t0) cc_final: 0.8873 (t0) REVERT: D 28 ASP cc_start: 0.8501 (m-30) cc_final: 0.7668 (m-30) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2163 time to fit residues: 29.6442 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 : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.0050 chunk 83 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN C 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.059301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.047107 restraints weight = 36713.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.048650 restraints weight = 20421.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.049664 restraints weight = 13536.826| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8547 Z= 0.136 Angle : 0.549 9.254 11955 Z= 0.318 Chirality : 0.039 0.147 1371 Planarity : 0.003 0.037 1203 Dihedral : 22.949 59.542 1969 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.31), residues: 796 helix: 2.26 (0.24), residues: 434 sheet: 0.03 (0.67), residues: 67 loop : -1.03 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 159 HIS 0.006 0.001 HIS A 171 PHE 0.019 0.001 PHE A 122 TYR 0.020 0.001 TYR C 206 ARG 0.007 0.001 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 486) hydrogen bonds : angle 4.10632 ( 1310) covalent geometry : bond 0.00298 ( 8547) covalent geometry : angle 0.54928 (11955) *********************** 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 93 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8837 (tpt) cc_final: 0.8632 (tpt) REVERT: B 79 GLU cc_start: 0.8470 (mp0) cc_final: 0.8114 (pm20) REVERT: B 124 LEU cc_start: 0.8758 (mm) cc_final: 0.8331 (tp) REVERT: B 133 TYR cc_start: 0.8220 (p90) cc_final: 0.7947 (p90) REVERT: B 189 ASP cc_start: 0.7002 (m-30) cc_final: 0.6662 (m-30) REVERT: C 57 ASN cc_start: 0.8813 (m110) cc_final: 0.8470 (m110) REVERT: D 26 ASN cc_start: 0.9319 (t0) cc_final: 0.8844 (t0) REVERT: D 28 ASP cc_start: 0.8465 (m-30) cc_final: 0.7655 (m-30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1949 time to fit residues: 25.1794 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 : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.056906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.044510 restraints weight = 38129.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.045958 restraints weight = 22365.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.046919 restraints weight = 15256.033| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8547 Z= 0.196 Angle : 0.600 8.212 11955 Z= 0.345 Chirality : 0.041 0.152 1371 Planarity : 0.003 0.037 1203 Dihedral : 22.723 59.988 1969 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.31), residues: 796 helix: 2.08 (0.24), residues: 440 sheet: 0.05 (0.69), residues: 67 loop : -1.03 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 159 HIS 0.007 0.001 HIS A 171 PHE 0.025 0.002 PHE A 122 TYR 0.016 0.002 TYR A 13 ARG 0.005 0.001 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 486) hydrogen bonds : angle 4.33932 ( 1310) covalent geometry : bond 0.00438 ( 8547) covalent geometry : angle 0.59990 (11955) ********************** 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 84 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 GLU cc_start: 0.8482 (mp0) cc_final: 0.8118 (pm20) REVERT: B 124 LEU cc_start: 0.8831 (mm) cc_final: 0.8419 (tp) REVERT: B 189 ASP cc_start: 0.6870 (m-30) cc_final: 0.6021 (m-30) REVERT: C 57 ASN cc_start: 0.8820 (m110) cc_final: 0.8489 (m110) REVERT: C 112 MET cc_start: 0.8266 (tpp) cc_final: 0.7828 (tpp) REVERT: D 26 ASN cc_start: 0.9258 (t0) cc_final: 0.8861 (t0) REVERT: D 28 ASP cc_start: 0.8581 (m-30) cc_final: 0.7759 (m-30) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1980 time to fit residues: 23.4425 Evaluate side-chains 64 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 36 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN C 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.057248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.044656 restraints weight = 38403.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.046222 restraints weight = 21440.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.047310 restraints weight = 14280.513| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8547 Z= 0.171 Angle : 0.584 8.366 11955 Z= 0.336 Chirality : 0.041 0.173 1371 Planarity : 0.003 0.038 1203 Dihedral : 22.708 59.806 1969 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.31), residues: 796 helix: 2.07 (0.24), residues: 446 sheet: -0.23 (0.67), residues: 69 loop : -1.05 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 159 HIS 0.006 0.001 HIS A 171 PHE 0.023 0.002 PHE C 175 TYR 0.017 0.002 TYR C 206 ARG 0.004 0.001 ARG D 53 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 486) hydrogen bonds : angle 4.29793 ( 1310) covalent geometry : bond 0.00383 ( 8547) covalent geometry : angle 0.58444 (11955) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2582.07 seconds wall clock time: 46 minutes 48.36 seconds (2808.36 seconds total)