Starting phenix.real_space_refine on Tue Mar 11 15:27:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j2f_35948/03_2025/8j2f_35948.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j2f_35948/03_2025/8j2f_35948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j2f_35948/03_2025/8j2f_35948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j2f_35948/03_2025/8j2f_35948.map" model { file = "/net/cci-nas-00/data/ceres_data/8j2f_35948/03_2025/8j2f_35948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j2f_35948/03_2025/8j2f_35948.cif" } resolution = 3.07 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= 0.004 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 Mg 2 5.21 5 S 34 5.16 5 C 4002 2.51 5 N 1052 2.21 5 O 1074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6164 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3060 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 1, 'C14': 1, 'HP6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 1, 'C14': 1, 'HP6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 5.55, per 1000 atoms: 0.90 Number of scatterers: 6164 At special positions: 0 Unit cell: (76.2034, 91.2766, 103.838, 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 34 16.00 Mg 2 11.99 O 1074 8.00 N 1052 7.00 C 4002 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: 1.70 Conformation dependent library (CDL) restraints added in 935.6 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 4 sheets defined 45.1% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 25 through 41 Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.504A pdb=" N PHE A 113 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 115 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 167 Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.515A pdb=" N ASN A 214 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 348 Processing helix chain 'A' and resid 353 through 401 Proline residue: A 360 - end of helix removed outlier: 3.641A pdb=" N ALA A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 41 Processing helix chain 'B' and resid 52 through 63 Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.505A pdb=" N PHE B 113 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 115 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 167 Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.515A pdb=" N ASN B 214 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 348 Processing helix chain 'B' and resid 353 through 401 Proline residue: B 360 - end of helix removed outlier: 3.641A pdb=" N ALA B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 73 removed outlier: 4.279A pdb=" N LEU A 82 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LEU A 44 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG A 10 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU A 46 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE A 12 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLU A 48 " --> pdb=" O PHE A 12 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU A 14 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 50 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N CYS A 16 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N MET A 276 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE A 255 " --> pdb=" O MET A 276 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR A 278 " --> pdb=" O LYS A 253 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP A 206 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N THR A 257 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS A 208 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 97 removed outlier: 3.606A pdb=" N GLU A 92 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA A 117 " --> pdb=" O HIS A 136 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS A 136 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 135 " --> pdb=" O CYS A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.280A pdb=" N LEU B 82 " --> pdb=" O PHE B 73 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LEU B 44 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG B 10 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU B 46 " --> pdb=" O ARG B 10 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE B 12 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLU B 48 " --> pdb=" O PHE B 12 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 14 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL B 50 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N CYS B 16 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N MET B 276 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE B 255 " --> pdb=" O MET B 276 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR B 278 " --> pdb=" O LYS B 253 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP B 206 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N THR B 257 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS B 208 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 97 removed outlier: 3.606A pdb=" N GLU B 92 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA B 117 " --> pdb=" O HIS B 136 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS B 136 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 135 " --> pdb=" O CYS B 176 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1937 1.34 - 1.45: 1006 1.45 - 1.57: 3341 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 6334 Sorted by residual: bond pdb=" C TYR B 103 " pdb=" N PRO B 104 " ideal model delta sigma weight residual 1.336 1.370 -0.035 1.23e-02 6.61e+03 8.00e+00 bond pdb=" C TYR A 103 " pdb=" N PRO A 104 " ideal model delta sigma weight residual 1.336 1.370 -0.035 1.23e-02 6.61e+03 7.87e+00 bond pdb=" C ASP A 262 " pdb=" N PRO A 263 " ideal model delta sigma weight residual 1.337 1.363 -0.026 9.80e-03 1.04e+04 7.11e+00 bond pdb=" C ASP B 262 " pdb=" N PRO B 263 " ideal model delta sigma weight residual 1.337 1.362 -0.025 9.80e-03 1.04e+04 6.77e+00 bond pdb=" C THR B 267 " pdb=" N PRO B 268 " ideal model delta sigma weight residual 1.332 1.361 -0.030 1.33e-02 5.65e+03 4.94e+00 ... (remaining 6329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 7907 2.09 - 4.18: 541 4.18 - 6.28: 100 6.28 - 8.37: 20 8.37 - 10.46: 14 Bond angle restraints: 8582 Sorted by residual: angle pdb=" N THR A 259 " pdb=" CA THR A 259 " pdb=" C THR A 259 " ideal model delta sigma weight residual 111.74 120.68 -8.94 1.35e+00 5.49e-01 4.39e+01 angle pdb=" N THR B 259 " pdb=" CA THR B 259 " pdb=" C THR B 259 " ideal model delta sigma weight residual 111.74 120.66 -8.92 1.35e+00 5.49e-01 4.37e+01 angle pdb=" C TYR B 67 " pdb=" N PRO B 68 " pdb=" CA PRO B 68 " ideal model delta sigma weight residual 119.56 113.66 5.90 1.01e+00 9.80e-01 3.41e+01 angle pdb=" C TYR A 67 " pdb=" N PRO A 68 " pdb=" CA PRO A 68 " ideal model delta sigma weight residual 119.56 113.68 5.88 1.01e+00 9.80e-01 3.39e+01 angle pdb=" N ILE B 147 " pdb=" CA ILE B 147 " pdb=" C ILE B 147 " ideal model delta sigma weight residual 112.80 106.35 6.45 1.15e+00 7.56e-01 3.15e+01 ... (remaining 8577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.77: 3277 12.77 - 25.55: 277 25.55 - 38.32: 76 38.32 - 51.10: 18 51.10 - 63.87: 6 Dihedral angle restraints: 3654 sinusoidal: 1444 harmonic: 2210 Sorted by residual: dihedral pdb=" C THR A 258 " pdb=" N THR A 258 " pdb=" CA THR A 258 " pdb=" CB THR A 258 " ideal model delta harmonic sigma weight residual -122.00 -135.74 13.74 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" C THR B 258 " pdb=" N THR B 258 " pdb=" CA THR B 258 " pdb=" CB THR B 258 " ideal model delta harmonic sigma weight residual -122.00 -135.73 13.73 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" N THR A 258 " pdb=" C THR A 258 " pdb=" CA THR A 258 " pdb=" CB THR A 258 " ideal model delta harmonic sigma weight residual 123.40 134.28 -10.88 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 3651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 722 0.096 - 0.193: 154 0.193 - 0.289: 32 0.289 - 0.386: 10 0.386 - 0.482: 2 Chirality restraints: 920 Sorted by residual: chirality pdb=" CA THR A 258 " pdb=" N THR A 258 " pdb=" C THR A 258 " pdb=" CB THR A 258 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CA THR B 258 " pdb=" N THR B 258 " pdb=" C THR B 258 " pdb=" CB THR B 258 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" CA HIS B 375 " pdb=" N HIS B 375 " pdb=" C HIS B 375 " pdb=" CB HIS B 375 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 917 not shown) Planarity restraints: 1082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 359 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 360 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 359 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 360 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 360 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 360 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 229 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO B 230 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 230 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 230 " -0.023 5.00e-02 4.00e+02 ... (remaining 1079 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 2742 2.96 - 3.44: 5946 3.44 - 3.93: 10715 3.93 - 4.41: 12188 4.41 - 4.90: 19869 Nonbonded interactions: 51460 Sorted by model distance: nonbonded pdb=" OE2 GLU A 49 " pdb="MG MG A 501 " model vdw 2.473 2.170 nonbonded pdb=" OE2 GLU B 49 " pdb="MG MG B 502 " model vdw 2.473 2.170 nonbonded pdb=" N ILE B 147 " pdb=" N TYR B 148 " model vdw 2.517 2.560 nonbonded pdb=" N ILE A 147 " pdb=" N TYR A 148 " model vdw 2.517 2.560 nonbonded pdb=" O THR B 258 " pdb=" OG1 THR B 258 " model vdw 2.568 3.040 ... (remaining 51455 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 401) selection = (chain 'B' and resid 3 through 401) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.010 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.170 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.005 0.035 6334 Z= 0.357 Angle : 1.212 10.460 8582 Z= 0.791 Chirality : 0.089 0.482 920 Planarity : 0.005 0.048 1082 Dihedral : 10.867 63.871 2242 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.63 % Allowed : 3.76 % Favored : 95.61 % Cbeta Deviations : 0.28 % 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: 3.43 (0.30), residues: 760 helix: 4.63 (0.25), residues: 318 sheet: 2.15 (0.36), residues: 174 loop : -0.81 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 310 HIS 0.007 0.001 HIS A 109 PHE 0.015 0.002 PHE B 371 TYR 0.013 0.002 TYR B 105 ARG 0.004 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 383 TYR cc_start: 0.7201 (t80) cc_final: 0.6796 (t80) REVERT: B 92 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8169 (mt-10) REVERT: B 106 MET cc_start: 0.8874 (mmm) cc_final: 0.8563 (mmt) REVERT: B 223 VAL cc_start: 0.8039 (t) cc_final: 0.7754 (t) REVERT: B 238 ASP cc_start: 0.7996 (m-30) cc_final: 0.7501 (m-30) REVERT: B 253 LYS cc_start: 0.7515 (tptt) cc_final: 0.7122 (tttm) REVERT: B 337 LEU cc_start: 0.8083 (tp) cc_final: 0.7878 (mm) outliers start: 4 outliers final: 0 residues processed: 146 average time/residue: 0.2614 time to fit residues: 46.6260 Evaluate side-chains 83 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 108 HIS A 136 HIS A 182 HIS A 272 HIS A 319 GLN A 400 GLN B 72 HIS B 108 HIS B 136 HIS B 182 HIS B 272 HIS B 319 GLN B 400 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.126363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.084187 restraints weight = 6973.372| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.13 r_work: 0.2668 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 6334 Z= 0.381 Angle : 0.633 8.404 8582 Z= 0.336 Chirality : 0.046 0.187 920 Planarity : 0.005 0.036 1082 Dihedral : 5.996 46.449 862 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.88 % Allowed : 8.31 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.31), residues: 760 helix: 3.96 (0.27), residues: 320 sheet: 1.65 (0.35), residues: 174 loop : -0.93 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 17 HIS 0.008 0.001 HIS B 198 PHE 0.022 0.002 PHE B 371 TYR 0.011 0.002 TYR A 105 ARG 0.006 0.001 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7215 (ttpp) REVERT: A 253 LYS cc_start: 0.7804 (tptt) cc_final: 0.7309 (tttm) REVERT: A 383 TYR cc_start: 0.8327 (t80) cc_final: 0.7884 (t80) REVERT: B 145 LYS cc_start: 0.7273 (tttt) cc_final: 0.7027 (tttm) REVERT: B 184 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: B 253 LYS cc_start: 0.7772 (tptt) cc_final: 0.7244 (tttm) REVERT: B 383 TYR cc_start: 0.8289 (t80) cc_final: 0.7870 (t80) outliers start: 12 outliers final: 5 residues processed: 94 average time/residue: 0.2628 time to fit residues: 30.5429 Evaluate side-chains 83 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 184 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 59 optimal weight: 0.0570 chunk 69 optimal weight: 4.9990 chunk 24 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.138323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.096519 restraints weight = 6846.627| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.09 r_work: 0.2837 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6334 Z= 0.134 Angle : 0.452 4.777 8582 Z= 0.245 Chirality : 0.039 0.145 920 Planarity : 0.003 0.031 1082 Dihedral : 5.279 53.096 862 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.78 % Allowed : 9.56 % Favored : 89.66 % 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: 3.17 (0.31), residues: 760 helix: 4.45 (0.27), residues: 318 sheet: 1.54 (0.35), residues: 174 loop : -0.61 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 310 HIS 0.004 0.001 HIS A 375 PHE 0.011 0.001 PHE A 371 TYR 0.006 0.001 TYR A 105 ARG 0.003 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7069 (tptp) REVERT: A 383 TYR cc_start: 0.8245 (t80) cc_final: 0.7881 (t80) REVERT: B 30 MET cc_start: 0.8184 (mmt) cc_final: 0.7919 (mmp) REVERT: B 145 LYS cc_start: 0.7324 (tttt) cc_final: 0.7063 (tttm) REVERT: B 184 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: B 383 TYR cc_start: 0.8192 (t80) cc_final: 0.7885 (t80) outliers start: 5 outliers final: 1 residues processed: 87 average time/residue: 0.2345 time to fit residues: 25.9531 Evaluate side-chains 78 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain B residue 184 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 4 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 0.0570 chunk 71 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.091851 restraints weight = 6964.303| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.13 r_work: 0.2757 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6334 Z= 0.154 Angle : 0.452 5.033 8582 Z= 0.240 Chirality : 0.039 0.137 920 Planarity : 0.003 0.031 1082 Dihedral : 5.214 57.271 862 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.72 % Allowed : 10.50 % Favored : 87.77 % 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: 3.07 (0.31), residues: 760 helix: 4.39 (0.27), residues: 318 sheet: 1.44 (0.35), residues: 174 loop : -0.64 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.003 0.001 HIS B 375 PHE 0.013 0.001 PHE A 371 TYR 0.007 0.001 TYR A 105 ARG 0.002 0.000 ARG B 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7097 (tptp) REVERT: A 383 TYR cc_start: 0.8231 (t80) cc_final: 0.7940 (t80) REVERT: B 30 MET cc_start: 0.8177 (mmt) cc_final: 0.7959 (mmp) REVERT: B 145 LYS cc_start: 0.7404 (tttt) cc_final: 0.7191 (tttm) REVERT: B 184 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: B 212 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7097 (tm-30) REVERT: B 383 TYR cc_start: 0.8203 (t80) cc_final: 0.7908 (t80) outliers start: 11 outliers final: 5 residues processed: 87 average time/residue: 0.2278 time to fit residues: 25.0760 Evaluate side-chains 83 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 184 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 50 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.085554 restraints weight = 6942.337| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.12 r_work: 0.2654 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 6334 Z= 0.390 Angle : 0.572 8.408 8582 Z= 0.298 Chirality : 0.043 0.140 920 Planarity : 0.004 0.040 1082 Dihedral : 5.747 48.355 862 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.88 % Allowed : 11.13 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.31), residues: 760 helix: 3.91 (0.27), residues: 318 sheet: 1.32 (0.36), residues: 174 loop : -0.74 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 17 HIS 0.006 0.001 HIS B 72 PHE 0.016 0.002 PHE A 371 TYR 0.008 0.001 TYR B 98 ARG 0.003 0.001 ARG B 384 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7107 (tptp) REVERT: A 383 TYR cc_start: 0.8368 (t80) cc_final: 0.8079 (t80) REVERT: B 212 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7100 (tm-30) REVERT: B 383 TYR cc_start: 0.8334 (t80) cc_final: 0.8001 (t80) outliers start: 12 outliers final: 6 residues processed: 84 average time/residue: 0.2439 time to fit residues: 25.7958 Evaluate side-chains 80 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 147 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.085504 restraints weight = 6880.481| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.16 r_work: 0.2660 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 6334 Z= 0.225 Angle : 0.501 9.507 8582 Z= 0.260 Chirality : 0.040 0.137 920 Planarity : 0.003 0.038 1082 Dihedral : 5.466 50.097 862 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.57 % Allowed : 11.76 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.31), residues: 760 helix: 4.04 (0.27), residues: 318 sheet: 1.21 (0.36), residues: 174 loop : -0.66 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 310 HIS 0.004 0.001 HIS B 72 PHE 0.013 0.001 PHE A 371 TYR 0.005 0.001 TYR A 105 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7207 (tptp) REVERT: A 383 TYR cc_start: 0.8314 (t80) cc_final: 0.8013 (t80) REVERT: B 30 MET cc_start: 0.8111 (mmt) cc_final: 0.7857 (mmp) REVERT: B 383 TYR cc_start: 0.8271 (t80) cc_final: 0.7943 (t80) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 0.2605 time to fit residues: 26.2180 Evaluate side-chains 78 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain B residue 147 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 52 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.126432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.083443 restraints weight = 6917.219| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.17 r_work: 0.2649 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 6334 Z= 0.278 Angle : 0.524 8.099 8582 Z= 0.270 Chirality : 0.041 0.138 920 Planarity : 0.004 0.041 1082 Dihedral : 5.558 49.758 862 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.35 % Allowed : 11.44 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.31), residues: 760 helix: 3.86 (0.28), residues: 322 sheet: 1.08 (0.36), residues: 174 loop : -0.78 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.004 0.001 HIS B 72 PHE 0.015 0.001 PHE B 371 TYR 0.006 0.001 TYR A 105 ARG 0.003 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7247 (tptp) REVERT: A 307 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7609 (ttmt) REVERT: A 383 TYR cc_start: 0.8309 (t80) cc_final: 0.8017 (t80) REVERT: B 30 MET cc_start: 0.8083 (mmt) cc_final: 0.7846 (mmp) REVERT: B 383 TYR cc_start: 0.8276 (t80) cc_final: 0.7950 (t80) outliers start: 15 outliers final: 9 residues processed: 81 average time/residue: 0.2367 time to fit residues: 24.3515 Evaluate side-chains 77 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 147 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.126405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.083838 restraints weight = 6980.106| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.15 r_work: 0.2641 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 6334 Z= 0.313 Angle : 0.535 7.776 8582 Z= 0.277 Chirality : 0.041 0.139 920 Planarity : 0.004 0.043 1082 Dihedral : 5.615 48.417 862 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.19 % Allowed : 11.44 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.31), residues: 760 helix: 3.93 (0.27), residues: 318 sheet: 1.02 (0.37), residues: 174 loop : -0.80 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 17 HIS 0.005 0.001 HIS B 72 PHE 0.016 0.002 PHE B 371 TYR 0.006 0.001 TYR B 383 ARG 0.002 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7260 (tptp) REVERT: A 307 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7605 (ttmt) REVERT: A 383 TYR cc_start: 0.8374 (t80) cc_final: 0.8091 (t80) REVERT: B 30 MET cc_start: 0.8128 (mmt) cc_final: 0.7900 (mmp) REVERT: B 383 TYR cc_start: 0.8323 (t80) cc_final: 0.7998 (t80) outliers start: 14 outliers final: 9 residues processed: 82 average time/residue: 0.2414 time to fit residues: 25.1752 Evaluate side-chains 79 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 147 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 48 optimal weight: 0.4980 chunk 64 optimal weight: 0.4980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.084322 restraints weight = 7011.402| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.16 r_work: 0.2642 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 6334 Z= 0.269 Angle : 0.509 7.552 8582 Z= 0.264 Chirality : 0.040 0.137 920 Planarity : 0.004 0.041 1082 Dihedral : 5.490 47.931 862 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.19 % Allowed : 11.60 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.32), residues: 760 helix: 4.02 (0.27), residues: 318 sheet: 0.93 (0.37), residues: 174 loop : -0.84 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.004 0.001 HIS A 375 PHE 0.015 0.001 PHE B 371 TYR 0.006 0.001 TYR B 383 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7312 (tptp) REVERT: A 307 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7631 (ttmt) REVERT: A 383 TYR cc_start: 0.8368 (t80) cc_final: 0.8091 (t80) REVERT: B 30 MET cc_start: 0.8098 (mmt) cc_final: 0.7878 (mmp) REVERT: B 383 TYR cc_start: 0.8306 (t80) cc_final: 0.7987 (t80) outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.2462 time to fit residues: 24.4969 Evaluate side-chains 80 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 306 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 43 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN B 264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.130364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.087714 restraints weight = 6966.667| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.15 r_work: 0.2719 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6334 Z= 0.144 Angle : 0.447 7.528 8582 Z= 0.233 Chirality : 0.038 0.133 920 Planarity : 0.003 0.035 1082 Dihedral : 5.145 54.709 862 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.57 % Allowed : 12.38 % Favored : 86.05 % 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: 2.74 (0.32), residues: 760 helix: 4.26 (0.27), residues: 318 sheet: 0.95 (0.36), residues: 174 loop : -0.78 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 310 HIS 0.004 0.001 HIS A 375 PHE 0.010 0.001 PHE A 371 TYR 0.004 0.001 TYR A 383 ARG 0.002 0.000 ARG A 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7384 (tptp) REVERT: A 383 TYR cc_start: 0.8242 (t80) cc_final: 0.7962 (t80) REVERT: B 383 TYR cc_start: 0.8231 (t80) cc_final: 0.7929 (t80) outliers start: 10 outliers final: 5 residues processed: 80 average time/residue: 0.2322 time to fit residues: 23.6544 Evaluate side-chains 76 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 146 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.084767 restraints weight = 7066.368| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.17 r_work: 0.2684 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 6334 Z= 0.274 Angle : 0.516 8.638 8582 Z= 0.265 Chirality : 0.041 0.135 920 Planarity : 0.003 0.039 1082 Dihedral : 5.428 48.108 862 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.41 % Allowed : 12.70 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.32), residues: 760 helix: 4.04 (0.28), residues: 318 sheet: 0.94 (0.36), residues: 174 loop : -0.80 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 310 HIS 0.005 0.001 HIS B 375 PHE 0.010 0.001 PHE A 371 TYR 0.005 0.001 TYR A 105 ARG 0.002 0.000 ARG A 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3743.22 seconds wall clock time: 64 minutes 46.23 seconds (3886.23 seconds total)